Electron Microscopy Data Bank

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initial_angle_assignment_type:"MAXIMUM LIKELIHOOD" AND xref_links:"pdb" AND assembly_molecular_weight:{2000000 TO 5000000] AND author_orcid:"0000-0002-4877-7914"

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EMD-28254

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Composite 70S ribosome structure for "Atomistic simulations of the E. coli ribosome provide selection criteria for translationally active substrates

Release date: May 31, 2023
Resolution: 2.1 Å
EM Method: Single-particle
Fitted PDBs: 8emm
Q-score: 0.678

Watson ZL, Knudson IJ, Ward FR, Miller SJ, Cate JHD, Schepartz A, Abramyan AM

Nat Chem (2023) 15 pp. 913-921 [ DOI: doi:10.1038/s41557-023-01226-w Pubmed: 37308707 ]

Sample:

30s ribosomal protein s10 (11 kDa, Protein from Escherichia coli)
50s ribosomal protein l20 (13 kDa, Protein from Escherichia coli)
50s ribosomal protein l23 (11 kDa, Protein from Escherichia coli)
30s ribosomal protein s2 (26 kDa, Protein from Escherichia coli)
50s ribosomal protein l22 (12 kDa, Protein from Escherichia coli)
30s ribosomal protein s17 (9 kDa, Protein from Escherichia coli)
Methionine (149 Da, Ligand)
30s ribosomal protein s7 (20 kDa, Protein from Escherichia coli)
30s ribosomal protein s11 (13 kDa, Protein from Escherichia coli)
30s ribosomal protein s5 (17 kDa, Protein from Escherichia coli)
30s ribosomal protein s21 (8 kDa, Protein from Escherichia coli)
30s ribosomal protein s20 (9 kDa, Protein from Escherichia coli)
50s ribosomal protein l36 (4 kDa, Protein from Escherichia coli)
30s ribosomal protein s6 (15 kDa, Protein from Escherichia coli)
50s ribosomal protein l13 (16 kDa, Protein from Escherichia coli)
30s ribosomal protein s12 (13 kDa, Protein from Escherichia coli)
50s ribosomal protein l14 (13 kDa, Protein from Escherichia coli)
50s ribosomal protein l27 (9 kDa, Protein from Escherichia coli)
30s ribosomal protein s19 (10 kDa, Protein from Escherichia coli)
Ribosomal protein l21 (11 kDa, Protein from Escherichia coli)
50s ribosomal protein l4 (22 kDa, Protein from Escherichia coli)
Spermine (202 Da, Ligand)
50s ribosomal protein l17 (14 kDa, Protein from Escherichia coli)
50s ribosomal protein l5 (20 kDa, Protein from Escherichia coli)
Potassium ion (39 Da, Ligand)
50s ribosomal protein l28 (9 kDa, Protein from Escherichia coli)
Met-nh-trna (24 kDa, RNA from Escherichia coli)
50s ribosomal protein l9 (15 kDa, Protein from Escherichia coli)
50s ribosomal protein l18 (12 kDa, Protein from Escherichia coli)
Zinc ion (65 Da, Ligand)
30s ribosomal protein s18 (9 kDa, Protein from Escherichia coli)
50s ribosomal protein l24 (11 kDa, Protein from Escherichia coli)
Spermidine (145 Da, Ligand)
50s ribosomal protein l34 (5 kDa, Protein from Escherichia coli)
50s ribosomal protein l19 (13 kDa, Protein from Escherichia coli)
16s rrna (499 kDa, RNA from Escherichia coli)
50s ribosomal protein l35 (7 kDa, Protein from Escherichia coli)
30s ribosomal protein s9 (14 kDa, Protein from Escherichia coli)
30s ribosomal protein s4 (23 kDa, Protein from Escherichia coli)
50s ribosomal protein l33 (6 kDa, Protein from Escherichia coli)
Water (18 Da, Ligand)
30s ribosomal protein s14 (11 kDa, Protein from Escherichia coli)
Magnesium ion (24 Da, Ligand)
50s ribosomal protein l6 (18 kDa, Protein from Escherichia coli)
50s ribosomal protein l32 (6 kDa, Protein from Escherichia coli)
50s ribosomal protein l31 (7 kDa, Protein from Escherichia coli)
50s ribosomal protein l15 (15 kDa, Protein from Escherichia coli)
30s ribosomal protein s15 (10 kDa, Protein from Escherichia coli)
30s ribosomal protein s13 (13 kDa, Protein from Escherichia coli)
50s ribosomal protein l2 (29 kDa, Protein from Escherichia coli)
50s ribosomal protein l30 (6 kDa, Protein from Escherichia coli)
50s ribosomal protein l25 (10 kDa, Protein from Escherichia coli)
50s ribosomal protein l3 (22 kDa, Protein from Escherichia coli)
Mrna (9 kDa, RNA from Escherichia coli)
23s rrna (941 kDa, RNA from Escherichia coli)
70s ribosome complex with mrna, a- and p-site met-nh-trnas (Complex from Escherichia coli)
30s ribosomal protein s3 (26 kDa, Protein from Escherichia coli)
5s rrna (38 kDa, RNA from Escherichia coli)
50s ribosomal protein l29 (7 kDa, Protein from Escherichia coli)
30s ribosomal protein s8 (14 kDa, Protein from Escherichia coli)
50s ribosomal protein l16 (15 kDa, Protein from Escherichia coli)
Paromomycin (615 Da, Ligand)
30s ribosomal protein s16 (9 kDa, Protein from Escherichia coli)

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EMD-29757

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mRNA decoding in human is kinetically and structurally distinct from bacteria (IC state)

Release date: April 19, 2023
Resolution: 2.29 Å
EM Method: Single-particle
Fitted PDBs: 8g5y
Q-score: 0.605

Holm M, Natchiar SK, Rundlet EJ, Myasnikov AG, Watson ZL, Altman RB, Wang HY, Taunton J, Blanchard SC

Nature (2023) 617 pp. 200-207 [ Pubmed: 37020024 DOI: doi:10.1038/s41586-023-05908-w ]

Sample:

Eif5a1 (16 kDa, Protein from Homo sapiens)
60s ribosomal protein l10 (24 kDa, Protein from Homo sapiens)
60s ribosomal protein l18a (20 kDa, Protein from Homo sapiens)
60s ribosomal protein l7 (29 kDa, Protein from Homo sapiens)
40s ribosomal protein s16 (16 kDa, Protein from Homo sapiens)
60s ribosomal protein l38 (8 kDa, Protein from Homo sapiens)
60s ribosomal protein l24 (17 kDa, Protein from Homo sapiens)
60s ribosomal protein l31 (14 kDa, Protein from Homo sapiens)
60s ribosomal protein l14 (23 kDa, Protein from Homo sapiens)
60s ribosomal protein l35 (14 kDa, Protein from Homo sapiens)
40s ribosomal protein s24 (15 kDa, Protein from Homo sapiens)
18s rrna (603 kDa, RNA from Homo sapiens)
60s ribosomal protein l9 (21 kDa, Protein from Homo sapiens)
P-site trna (24 kDa, RNA from Homo sapiens)
40s ribosomal protein s19 (16 kDa, Protein from Homo sapiens)
60s ribosomal protein l26 (17 kDa, Protein from Homo sapiens)
40s ribosomal protein s13 (17 kDa, Protein from Homo sapiens)
Water (18 Da, Ligand)
Receptor of activated protein c kinase 1 (35 kDa, Protein from Homo sapiens)
Us12 (15 kDa, Protein from Homo sapiens)
60s ribosomal protein l4 (47 kDa, Protein from Homo sapiens)
40s ribosomal protein s2 (31 kDa, Protein from Homo sapiens)
60s ribosomal protein l3 (46 kDa, Protein from Homo sapiens)
40s ribosomal protein s3a (30 kDa, Protein from Homo sapiens)
Mrna (19 kDa, RNA from Homo sapiens)
Methionine (149 Da, Ligand)
60s ribosomal protein l10a (24 kDa, Protein from Homo sapiens)
40s ribosomal protein s6 (28 kDa, Protein from Homo sapiens)
5s rrna (38 kDa, RNA from Homo sapiens)
4-{(2r,5s,6e)-2-hydroxy-5-methyl-7-[(2r,3s,4e,6z,10e)-3-methyl-12-oxooxacyclododeca-4,6,10-trien-2-yl]-4-oxooct-6-en-1-yl}piperidine-2,6-dione (457 Da, Ligand)
60s ribosomal protein l23a (17 kDa, Protein from Homo sapiens)
Fau ubiquitin-like and ribosomal protein s30 (14 kDa, Protein from Homo sapiens)
40s ribosomal protein s14 (16 kDa, Protein from Homo sapiens)
40s ribosomal protein s26 (13 kDa, Protein from Homo sapiens)
Potassium ion (39 Da, Ligand)
40s ribosomal protein s12 (14 kDa, Protein from Homo sapiens)
1,4-diaminobutane (88 Da, Ligand)
60s ribosomal protein l37 (11 kDa, Protein from Homo sapiens)
40s ribosomal protein s11 (18 kDa, Protein from Homo sapiens)
60s ribosomal protein l23 (14 kDa, Protein from Homo sapiens)
60s ribosomal protein l13a (23 kDa, Protein from Homo sapiens)
60s ribosomal protein l27 (15 kDa, Protein from Homo sapiens)
40s ribosomal protein s4, x isoform (29 kDa, Protein from Homo sapiens)
40s ribosomal protein sa (32 kDa, Protein from Homo sapiens)
60s ribosomal protein l32 (15 kDa, Protein from Homo sapiens)
60s ribosomal protein l18 (21 kDa, Protein from Homo sapiens)
40s ribosomal protein s21 (9 kDa, Protein from Homo sapiens)
60s ribosomal protein l27a (16 kDa, Protein from Homo sapiens)
40s ribosomal protein s18 (17 kDa, Protein from Homo sapiens)
60s ribosomal protein l41 (3 kDa, Protein from Homo sapiens)
Ul2 (28 kDa, Protein from Homo sapiens)
40s ribosomal protein s15 (17 kDa, Protein from Homo sapiens)
60s ribosomal protein l30 (12 kDa, Protein from Homo sapiens)
60s ribosomal protein l39 (6 kDa, Protein from Homo sapiens)
60s ribosomal protein l13 (24 kDa, Protein from Homo sapiens)
40s ribosomal protein s29 (6 kDa, Protein from Homo sapiens)
40s ribosomal protein s9 (22 kDa, Protein from Homo sapiens)
40s ribosomal protein s5 (22 kDa, Protein from Homo sapiens)
Anisomycin (265 Da, Ligand)
Magnesium ion (24 Da, Ligand)
60s ribosomal protein l5 (34 kDa, Protein from Homo sapiens)
Human ribosome (Complex from Homo sapiens)
60s ribosomal protein l36a (12 kDa, Protein from Homo sapiens)
60s ribosomal protein l11 (20 kDa, Protein from Homo sapiens)
5.8s rrna (50 kDa, RNA from Homo sapiens)
40s ribosomal protein s8 (24 kDa, Protein from Homo sapiens)
40s ribosomal protein s17 (15 kDa, Protein from Homo sapiens)
60s ribosomal protein l29 (17 kDa, Protein from Homo sapiens)
40s ribosomal protein s27 (9 kDa, Protein from Homo sapiens)
60s ribosomal protein l7a (30 kDa, Protein from Homo sapiens)
40s ribosomal protein s15a (14 kDa, Protein from Homo sapiens)
60s ribosomal protein l36 (12 kDa, Protein from Homo sapiens)
60s ribosomal protein l15 (24 kDa, Protein from Homo sapiens)
40s ribosomal protein s7 (22 kDa, Protein from Homo sapiens)
60s ribosomal protein l6 (32 kDa, Protein from Homo sapiens)
60s ribosomal protein l37a (10 kDa, Protein from Homo sapiens)
40s ribosomal protein s28 (7 kDa, Protein from Homo sapiens)
40s ribosomal protein s3 (26 kDa, Protein from Homo sapiens)
40s ribosomal protein s20 (13 kDa, Protein from Homo sapiens)
40s ribosomal protein s25 (13 kDa, Protein from Homo sapiens)
60s ribosomal protein l21 (18 kDa, Protein from Homo sapiens)
60s ribosomal protein l19 (23 kDa, Protein from Homo sapiens)
28s rrna (1 MDa, RNA from Homo sapiens)
Zinc ion (65 Da, Ligand)
60s ribosomal protein l34 (13 kDa, Protein from Homo sapiens)
Spermidine (145 Da, Ligand)
El40 (14 kDa, Protein from Homo sapiens)
40s ribosomal protein s10 (18 kDa, Protein from Homo sapiens)
60s ribosomal protein l35a (12 kDa, Protein from Homo sapiens)
60s ribosomal protein l22 (14 kDa, Protein from Homo sapiens)
60s ribosomal protein l28 (15 kDa, Protein from Homo sapiens)
Ubiquitin-40s ribosomal protein s27a (18 kDa, Protein from Homo sapiens)
60s ribosomal protein l17 (21 kDa, Protein from Homo sapiens)

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EMD-29758

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mRNA decoding in human is kinetically and structurally distinct from bacteria (GA state)

Release date: April 19, 2023
Resolution: 2.64 Å
EM Method: Single-particle
Fitted PDBs: 8g5z
Q-score: 0.57

Holm M, Natchiar SK, Rundlet EJ, Myasnikov AG, Watson ZL, Altman RB, Wang HY, Taunton J, Blanchard SC

Nature (2023) 617 pp. 200-207 [ Pubmed: 37020024 DOI: doi:10.1038/s41586-023-05908-w ]

Sample:

60s ribosomal protein l34 (12 kDa, Protein from Homo sapiens)
Plitidepsin (1 kDa, Ligand)
60s ribosomal protein l38 (8 kDa, Protein from Homo sapiens)
60s ribosomal protein l18a (20 kDa, Protein from Homo sapiens)
40s ribosomal protein s13 (17 kDa, Protein from Homo sapiens)
Ribosomal protein l36a (12 kDa, Protein from Homo sapiens)
60s ribosomal protein l32 (15 kDa, Protein from Homo sapiens)
Us19 (15 kDa, Protein from Homo sapiens)
60s acidic ribosomal protein p0 (21 kDa, Protein from Homo sapiens)
Us9 (15 kDa, Protein from Homo sapiens)
60s ribosomal protein l7 (26 kDa, Protein from Homo sapiens)
Es12 (13 kDa, Protein from Homo sapiens)
40s ribosomal protein s7 (21 kDa, Protein from Homo sapiens)
60s ribosomal protein l17 (17 kDa, Protein from Homo sapiens)
Water (18 Da, Ligand)
40s ribosomal protein s8 (24 kDa, Protein from Homo sapiens)
60s ribosomal protein l36 (11 kDa, Protein from Homo sapiens)
Es10 (11 kDa, Protein from Homo sapiens)
40s ribosomal protein s3 (25 kDa, Protein from Homo sapiens)
Us12 (15 kDa, Protein from Homo sapiens)
60s ribosomal protein l11 (19 kDa, Protein from Homo sapiens)
60s ribosomal protein l22 (11 kDa, Protein from Homo sapiens)
Methionine (149 Da, Ligand)
40s ribosomal protein s3a (25 kDa, Protein from Homo sapiens)
60s ribosomal protein l27a (16 kDa, Protein from Homo sapiens)
5s rrna (38 kDa, RNA from Homo sapiens)
40s ribosomal protein s26 (11 kDa, Protein from Homo sapiens)
60s ribosomal protein l5 (34 kDa, Protein from Homo sapiens)
4-{(2r,5s,6e)-2-hydroxy-5-methyl-7-[(2r,3s,4e,6z,10e)-3-methyl-12-oxooxacyclododeca-4,6,10-trien-2-yl]-4-oxooct-6-en-1-yl}piperidine-2,6-dione (457 Da, Ligand)
60s ribosomal protein l28 (14 kDa, Protein from Homo sapiens)
P-site trna fmet (24 kDa, RNA from Escherichia coli)
40s ribosomal protein s9 (21 kDa, Protein from Homo sapiens)
Potassium ion (39 Da, Ligand)
El40 (6 kDa, Protein from Homo sapiens)
1,4-diaminobutane (88 Da, Ligand)
60s ribosomal protein l37 (10 kDa, Protein from Homo sapiens)
40s ribosomal protein s15a (14 kDa, Protein from Homo sapiens)
60s ribosomal protein l21 (18 kDa, Protein from Homo sapiens)
El24 (13 kDa, Protein from Homo sapiens)
60s ribosomal protein l23 (14 kDa, Protein from Homo sapiens)
Es4 (29 kDa, Protein from Homo sapiens)
Es31 (8 kDa, Protein from Homo sapiens)
Ul2 (27 kDa, Protein from Homo sapiens)
60s ribosomal protein l12 (16 kDa, Protein from Homo sapiens)
18s rrna (549 kDa, RNA from Homo sapiens)
60s ribosomal protein l39 (6 kDa, Protein from Homo sapiens)
40s ribosomal protein s21 (9 kDa, Protein from Homo sapiens)
60s ribosomal protein l37a (10 kDa, Protein from Homo sapiens)
Elongation factor 1-alpha 1 (48 kDa, Protein from Homo sapiens)
60s ribosomal protein l41 (3 kDa, Protein from Homo sapiens)
Mrna (3 kDa, RNA from Homo sapiens)
5'-guanosine-diphosphate-monothiophosphate (539 Da, Ligand)
60s ribosomal protein l3 (46 kDa, Protein from Homo sapiens)
60s ribosomal protein l19 (22 kDa, Protein from Homo sapiens)
40s ribosomal protein s6 (27 kDa, Protein from Homo sapiens)
40s ribosomal protein s2 (24 kDa, Protein from Homo sapiens)
Es27 (9 kDa, Protein from Homo sapiens)
60s ribosomal protein l9 (21 kDa, Protein from Homo sapiens)
60s ribosomal protein l4 (41 kDa, Protein from Homo sapiens)
El6 (25 kDa, Protein from Homo sapiens)
Anisomycin (265 Da, Ligand)
Receptor of activated protein c kinase 1 (34 kDa, Protein from Homo sapiens)
40s ribosomal protein s19 (15 kDa, Protein from Homo sapiens)
Magnesium ion (24 Da, Ligand)
Human ribosome 80s with p-site trna, a-site trna eef1a and eif5a1 (5 MDa, Complex)
60s ribosomal protein l13a (23 kDa, Protein from Homo sapiens)
A-site trna phe (24 kDa, RNA from Escherichia coli)
28s rrna (1 MDa, RNA from Homo sapiens)
5.8s rrna (50 kDa, RNA from Homo sapiens)
40s ribosomal protein sa (24 kDa, Protein from Homo sapiens)
60s ribosomal protein l26 (15 kDa, Protein from Homo sapiens)
60s ribosomal protein l35a (12 kDa, Protein from Homo sapiens)
60s ribosomal protein l31 (12 kDa, Protein from Homo sapiens)
40s ribosomal protein s29 (6 kDa, Protein from Homo sapiens)
60s ribosomal protein l14 (15 kDa, Protein from Homo sapiens)
60s ribosomal protein l15 (24 kDa, Protein from Homo sapiens)
Ul23 (13 kDa, Protein from Homo sapiens)
Us17 (16 kDa, Protein from Homo sapiens)
Phenylalanine (165 Da, Ligand)
40s ribosomal protein s30 (6 kDa, Protein from Homo sapiens)
40s ribosomal protein s28 (7 kDa, Protein from Homo sapiens)
40s ribosomal protein s5 (21 kDa, Protein from Homo sapiens)
40s ribosomal protein s17 (15 kDa, Protein from Homo sapiens)
Zinc ion (65 Da, Ligand)
60s ribosomal protein l13 (23 kDa, Protein from Homo sapiens)
Spermidine (145 Da, Ligand)
Us13 (17 kDa, Protein from Homo sapiens)
El29 (12 kDa, Protein from Homo sapiens)
60s ribosomal protein l10 (23 kDa, Protein from Homo sapiens)
40s ribosomal protein s24 (15 kDa, Protein from Homo sapiens)
Es25 (9 kDa, Protein from Homo sapiens)
60s ribosomal protein l27 (15 kDa, Protein from Homo sapiens)
Eif5a1 (15 kDa, Protein from Homo sapiens)
60s ribosomal protein l35 (14 kDa, Protein from Homo sapiens)
60s ribosomal protein l18 (21 kDa, Protein from Homo sapiens)
Us11 (14 kDa, Protein from Homo sapiens)
60s ribosomal protein l7a (27 kDa, Protein from Homo sapiens)
Us10 (11 kDa, Protein from Homo sapiens)
Ul1 (24 kDa, Protein from Homo sapiens)
60s ribosomal protein l30 (10 kDa, Protein from Homo sapiens)

[Show more]

EMD-29759

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mRNA decoding in human is kinetically and structurally distinct from bacteria (CR state)

Release date: April 19, 2023
Resolution: 2.54 Å
EM Method: Single-particle
Fitted PDBs: 8g60
Q-score: 0.576

Holm M, Natchiar SK, Rundlet EJ, Myasnikov AG, Watson ZL, Altman RB, Wang HY, Taunton J, Blanchard SC

Nature (2023) 617 pp. 200-207 [ Pubmed: 37020024 DOI: doi:10.1038/s41586-023-05908-w ]

Sample:

Plitidepsin (1 kDa, Ligand)
El18 (21 kDa, Protein from Homo sapiens)
El34 (13 kDa, Protein from Homo sapiens)
Us3 (26 kDa, Protein from Homo sapiens)
Us4 (22 kDa, Protein from Homo sapiens)
El32 (15 kDa, Protein from Homo sapiens)
Es8 (24 kDa, Protein from Homo sapiens)
El39 (6 kDa, Protein from Homo sapiens)
Es4 (29 kDa, Protein from Homo sapiens)
Us13 (17 kDa, Protein from Homo sapiens)
Es19 (16 kDa, Protein from Homo sapiens)
18s rrna (603 kDa, RNA from Homo sapiens)
P-site trna (24 kDa, RNA from Homo sapiens)
Us17 (18 kDa, Protein from Homo sapiens)
El30 (12 kDa, Protein from Homo sapiens)
Ul22 (21 kDa, Protein from Homo sapiens)
Ul16 (24 kDa, Protein from Homo sapiens)
Water (18 Da, Ligand)
Us8 (14 kDa, Protein from Homo sapiens)
El8 (30 kDa, Protein from Homo sapiens)
Es12 (14 kDa, Protein from Homo sapiens)
Us12 (15 kDa, Protein from Homo sapiens)
El14 (23 kDa, Protein from Homo sapiens)
Ul29 (14 kDa, Protein from Homo sapiens)
Es17 (15 kDa, Protein from Homo sapiens)
El29 (17 kDa, Protein from Homo sapiens)
Us7 (22 kDa, Protein from Homo sapiens)
Mrna (19 kDa, RNA from Homo sapiens)
Methionine (149 Da, Ligand)
El37 (11 kDa, Protein from Homo sapiens)
5s rrna (38 kDa, RNA from Homo sapiens)
Es6 (28 kDa, Protein from Homo sapiens)
4-{(2r,5s,6e)-2-hydroxy-5-methyl-7-[(2r,3s,4e,6z,10e)-3-methyl-12-oxooxacyclododeca-4,6,10-trien-2-yl]-4-oxooct-6-en-1-yl}piperidine-2,6-dione (457 Da, Ligand)
Ul4 (47 kDa, Protein from Homo sapiens)
El15 (24 kDa, Protein from Homo sapiens)
Potassium ion (39 Da, Ligand)
Ul13 (23 kDa, Protein from Homo sapiens)
Es25 (13 kDa, Protein from Homo sapiens)
Es1 (30 kDa, Protein from Homo sapiens)
Ul30 (29 kDa, Protein from Homo sapiens)
1,4-diaminobutane (88 Da, Ligand)
El27 (15 kDa, Protein from Homo sapiens)
Ul15 (16 kDa, Protein from Homo sapiens)
El21 (18 kDa, Protein from Homo sapiens)
Us2 (32 kDa, Protein from Homo sapiens)
Es7 (22 kDa, Protein from Homo sapiens)
El41 (3 kDa, Protein from Homo sapiens)
Es21 (9 kDa, Protein from Homo sapiens)
Es30 (14 kDa, Protein from Homo sapiens)
Ul23 (17 kDa, Protein from Homo sapiens)
El43 (10 kDa, Protein from Homo sapiens)
El22 (14 kDa, Protein from Homo sapiens)
Ul10 (34 kDa, Protein from Homo sapiens)
Us11 (16 kDa, Protein from Homo sapiens)
Ul2 (28 kDa, Protein from Homo sapiens)
5'-guanosine-diphosphate-monothiophosphate (539 Da, Ligand)
Us5 (31 kDa, Protein from Homo sapiens)
El13 (31 kDa, Protein from Homo sapiens)
Us19 (17 kDa, Protein from Homo sapiens)
El33 (12 kDa, Protein from Homo sapiens)
Eef1a (50 kDa, Protein from Homo sapiens)
El6 (32 kDa, Protein from Homo sapiens)
El36 (12 kDa, Protein from Homo sapiens)
Anisomycin (265 Da, Ligand)
Rack1 (35 kDa, Protein from Homo sapiens)
Ul14 (14 kDa, Protein from Homo sapiens)
Us15 (17 kDa, Protein from Homo sapiens)
El28 (15 kDa, Protein from Homo sapiens)
Magnesium ion (24 Da, Ligand)
El20 (20 kDa, Protein from Homo sapiens)
Es27 (9 kDa, Protein from Homo sapiens)
Human ribosome (Complex from Homo sapiens)
Ul24 (17 kDa, Protein from Homo sapiens)
5.8s rrna (50 kDa, RNA from Homo sapiens)
Es24 (15 kDa, Protein from Homo sapiens)
Us9 (16 kDa, Protein from Homo sapiens)
El19 (23 kDa, Protein from Homo sapiens)
El31 (14 kDa, Protein from Homo sapiens)
El42 (12 kDa, Protein from Homo sapiens)
Ul18 (34 kDa, Protein from Homo sapiens)
Es10 (18 kDa, Protein from Homo sapiens)
Ul3 (46 kDa, Protein from Homo sapiens)
Es31 (18 kDa, Protein from Homo sapiens)
El24 (17 kDa, Protein from Homo sapiens)
Es26 (13 kDa, Protein from Homo sapiens)
Us10 (13 kDa, Protein from Homo sapiens)
Phenylalanine (165 Da, Ligand)
28s rrna (1 MDa, RNA from Homo sapiens)
Zinc ion (65 Da, Ligand)
Spermidine (145 Da, Ligand)
El40 (14 kDa, Protein from Homo sapiens)
Us14 (6 kDa, Protein from Homo sapiens)
Ul1 (24 kDa, Protein from Homo sapiens)
Ul6 (21 kDa, Protein from Homo sapiens)
Es28 (7 kDa, Protein from Homo sapiens)
Ul11 (17 kDa, Protein from Homo sapiens)
Ul5 (20 kDa, Protein from Homo sapiens)
A-site trna (24 kDa, RNA from Homo sapiens)
El38 (8 kDa, Protein from Homo sapiens)

[Show more]

EMD-29760

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mRNA decoding in human is kinetically and structurally distinct from bacteria (AC state)

Release date: April 19, 2023
Resolution: 2.94 Å
EM Method: Single-particle
Fitted PDBs: 8g61
Q-score: 0.51

Holm M, Natchiar SK, Rundlet EJ, Myasnikov AG, Watson ZL, Altman RB, Wang HY, Taunton J, Blanchard SC

Nature (2023) 617 pp. 200-207 [ Pubmed: 37020024 DOI: doi:10.1038/s41586-023-05908-w ]

Sample:

Eif5a1 (16 kDa, Protein from Homo sapiens)
60s ribosomal protein l10 (24 kDa, Protein from Homo sapiens)
60s ribosomal protein l18a (20 kDa, Protein from Homo sapiens)
60s ribosomal protein l7 (29 kDa, Protein from Homo sapiens)
40s ribosomal protein s16 (16 kDa, Protein from Homo sapiens)
60s ribosomal protein l38 (8 kDa, Protein from Homo sapiens)
60s ribosomal protein l24 (17 kDa, Protein from Homo sapiens)
60s ribosomal protein l31 (14 kDa, Protein from Homo sapiens)
60s ribosomal protein l14 (23 kDa, Protein from Homo sapiens)
60s ribosomal protein l35 (14 kDa, Protein from Homo sapiens)
40s ribosomal protein s24 (15 kDa, Protein from Homo sapiens)
18s rrna (603 kDa, RNA from Homo sapiens)
60s ribosomal protein l9 (21 kDa, Protein from Homo sapiens)
40s ribosomal protein s19 (16 kDa, Protein from Homo sapiens)
60s ribosomal protein l26 (17 kDa, Protein from Homo sapiens)
40s ribosomal protein s13 (17 kDa, Protein from Homo sapiens)
Receptor of activated protein c kinase 1 (35 kDa, Protein from Homo sapiens)
Us12 (15 kDa, Protein from Homo sapiens)
60s ribosomal protein l4 (47 kDa, Protein from Homo sapiens)
40s ribosomal protein s2 (31 kDa, Protein from Homo sapiens)
60s ribosomal protein l3 (46 kDa, Protein from Homo sapiens)
A-site trna (24 kDa, RNA from Escherichia coli)
40s ribosomal protein s3a (30 kDa, Protein from Homo sapiens)
Mrna (19 kDa, RNA from Homo sapiens)
Methionine (149 Da, Ligand)
60s ribosomal protein l10a (24 kDa, Protein from Homo sapiens)
40s ribosomal protein s6 (28 kDa, Protein from Homo sapiens)
5s rrna (38 kDa, RNA from Homo sapiens)
4-{(2r,5s,6e)-2-hydroxy-5-methyl-7-[(2r,3s,4e,6z,10e)-3-methyl-12-oxooxacyclododeca-4,6,10-trien-2-yl]-4-oxooct-6-en-1-yl}piperidine-2,6-dione (457 Da, Ligand)
60s ribosomal protein l23a (17 kDa, Protein from Homo sapiens)
Fau ubiquitin-like and ribosomal protein s30 (14 kDa, Protein from Homo sapiens)
40s ribosomal protein s14 (16 kDa, Protein from Homo sapiens)
40s ribosomal protein s26 (13 kDa, Protein from Homo sapiens)
Potassium ion (39 Da, Ligand)
40s ribosomal protein s12 (14 kDa, Protein from Homo sapiens)
1,4-diaminobutane (88 Da, Ligand)
60s ribosomal protein l37 (11 kDa, Protein from Homo sapiens)
40s ribosomal protein s11 (18 kDa, Protein from Homo sapiens)
60s ribosomal protein l23 (14 kDa, Protein from Homo sapiens)
60s ribosomal protein l13a (23 kDa, Protein from Homo sapiens)
60s ribosomal protein l27 (15 kDa, Protein from Homo sapiens)
40s ribosomal protein s4, x isoform (29 kDa, Protein from Homo sapiens)
40s ribosomal protein sa (32 kDa, Protein from Homo sapiens)
60s ribosomal protein l32 (15 kDa, Protein from Homo sapiens)
60s ribosomal protein l18 (21 kDa, Protein from Homo sapiens)
40s ribosomal protein s21 (9 kDa, Protein from Homo sapiens)
60s ribosomal protein l27a (16 kDa, Protein from Homo sapiens)
40s ribosomal protein s18 (17 kDa, Protein from Homo sapiens)
60s ribosomal protein l41 (3 kDa, Protein from Homo sapiens)
Ul2 (28 kDa, Protein from Homo sapiens)
40s ribosomal protein s15 (17 kDa, Protein from Homo sapiens)
60s ribosomal protein l30 (12 kDa, Protein from Homo sapiens)
60s ribosomal protein l39 (6 kDa, Protein from Homo sapiens)
60s ribosomal protein l13 (24 kDa, Protein from Homo sapiens)
40s ribosomal protein s29 (6 kDa, Protein from Homo sapiens)
40s ribosomal protein s9 (22 kDa, Protein from Homo sapiens)
40s ribosomal protein s5 (22 kDa, Protein from Homo sapiens)
Anisomycin (265 Da, Ligand)
Magnesium ion (24 Da, Ligand)
60s ribosomal protein l5 (34 kDa, Protein from Homo sapiens)
Human ribosome (Complex from Homo sapiens)
60s ribosomal protein l36a (12 kDa, Protein from Homo sapiens)
60s ribosomal protein l11 (20 kDa, Protein from Homo sapiens)
5.8s rrna (50 kDa, RNA from Homo sapiens)
40s ribosomal protein s8 (24 kDa, Protein from Homo sapiens)
40s ribosomal protein s17 (15 kDa, Protein from Homo sapiens)
60s ribosomal protein l29 (17 kDa, Protein from Homo sapiens)
40s ribosomal protein s27 (9 kDa, Protein from Homo sapiens)
60s ribosomal protein l7a (30 kDa, Protein from Homo sapiens)
40s ribosomal protein s15a (14 kDa, Protein from Homo sapiens)
60s ribosomal protein l36 (12 kDa, Protein from Homo sapiens)
60s ribosomal protein l15 (24 kDa, Protein from Homo sapiens)
40s ribosomal protein s7 (22 kDa, Protein from Homo sapiens)
60s ribosomal protein l6 (32 kDa, Protein from Homo sapiens)
60s ribosomal protein l37a (10 kDa, Protein from Homo sapiens)
40s ribosomal protein s28 (7 kDa, Protein from Homo sapiens)
40s ribosomal protein s3 (26 kDa, Protein from Homo sapiens)
40s ribosomal protein s20 (13 kDa, Protein from Homo sapiens)
40s ribosomal protein s25 (13 kDa, Protein from Homo sapiens)
60s ribosomal protein l21 (18 kDa, Protein from Homo sapiens)
60s ribosomal protein l19 (23 kDa, Protein from Homo sapiens)
28s rrna (1 MDa, RNA from Homo sapiens)
Zinc ion (65 Da, Ligand)
60s ribosomal protein l34 (13 kDa, Protein from Homo sapiens)
Rna (77-mer) (24 kDa, RNA from Escherichia coli)
Spermidine (145 Da, Ligand)
El40 (14 kDa, Protein from Homo sapiens)
40s ribosomal protein s10 (18 kDa, Protein from Homo sapiens)
60s ribosomal protein l35a (12 kDa, Protein from Homo sapiens)
60s ribosomal protein l22 (14 kDa, Protein from Homo sapiens)
60s ribosomal protein l28 (15 kDa, Protein from Homo sapiens)
Ubiquitin-40s ribosomal protein s27a (18 kDa, Protein from Homo sapiens)
60s ribosomal protein l17 (21 kDa, Protein from Homo sapiens)

[Show more]

EMD-29771

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mRNA decoding in human is kinetically and structurally distinct from bacteria (GA state 2)

Release date: April 19, 2023
Resolution: 2.8 Å
EM Method: Single-particle
Fitted PDBs: 8g6j
Q-score: 0.548

Holm M, Natchiar SK, Rundlet EJ, Myasnikov AG, Watson ZL, Altman RB, Wang HY, Taunton J, Blanchard SC

Nature (2023) 617 pp. 200-207 [ Pubmed: 37020024 DOI: doi:10.1038/s41586-023-05908-w ]

Sample:

60s ribosomal protein l10 (24 kDa, Protein from Homo sapiens)
60s ribosomal protein l18a (20 kDa, Protein from Homo sapiens)
60s ribosomal protein l7 (29 kDa, Protein from Homo sapiens)
40s ribosomal protein s16 (16 kDa, Protein from Homo sapiens)
60s ribosomal protein l38 (8 kDa, Protein from Homo sapiens)
60s ribosomal protein l24 (17 kDa, Protein from Homo sapiens)
60s ribosomal protein l31 (14 kDa, Protein from Homo sapiens)
60s ribosomal protein l14 (23 kDa, Protein from Homo sapiens)
60s ribosomal protein l35 (14 kDa, Protein from Homo sapiens)
40s ribosomal protein s24 (15 kDa, Protein from Homo sapiens)
18s rrna (603 kDa, RNA from Homo sapiens)
60s ribosomal protein l9 (21 kDa, Protein from Homo sapiens)
P-site trna (24 kDa, RNA from Homo sapiens)
40s ribosomal protein s19 (16 kDa, Protein from Homo sapiens)
60s ribosomal protein l26 (17 kDa, Protein from Homo sapiens)
40s ribosomal protein s13 (17 kDa, Protein from Homo sapiens)
Water (18 Da, Ligand)
Receptor of activated protein c kinase 1 (35 kDa, Protein from Homo sapiens)
Us12 (15 kDa, Protein from Homo sapiens)
60s ribosomal protein l4 (47 kDa, Protein from Homo sapiens)
40s ribosomal protein s2 (31 kDa, Protein from Homo sapiens)
60s ribosomal protein l3 (46 kDa, Protein from Homo sapiens)
40s ribosomal protein s3a (30 kDa, Protein from Homo sapiens)
Mrna (19 kDa, RNA from Homo sapiens)
Methionine (149 Da, Ligand)
60s ribosomal protein l10a (24 kDa, Protein from Homo sapiens)
40s ribosomal protein s6 (28 kDa, Protein from Homo sapiens)
5s rrna (38 kDa, RNA from Homo sapiens)
60s ribosomal protein l23a (17 kDa, Protein from Homo sapiens)
Fau ubiquitin-like and ribosomal protein s30 (14 kDa, Protein from Homo sapiens)
40s ribosomal protein s14 (16 kDa, Protein from Homo sapiens)
40s ribosomal protein s26 (13 kDa, Protein from Homo sapiens)
Potassium ion (39 Da, Ligand)
40s ribosomal protein s12 (14 kDa, Protein from Homo sapiens)
1,4-diaminobutane (88 Da, Ligand)
60s ribosomal protein l37 (11 kDa, Protein from Homo sapiens)
60s ribosomal protein l12 (17 kDa, Protein from Homo sapiens)
40s ribosomal protein s11 (18 kDa, Protein from Homo sapiens)
60s ribosomal protein l23 (14 kDa, Protein from Homo sapiens)
60s ribosomal protein l13a (23 kDa, Protein from Homo sapiens)
60s ribosomal protein l27 (15 kDa, Protein from Homo sapiens)
40s ribosomal protein s4, x isoform (29 kDa, Protein from Homo sapiens)
40s ribosomal protein sa (32 kDa, Protein from Homo sapiens)
60s ribosomal protein l32 (15 kDa, Protein from Homo sapiens)
60s ribosomal protein l18 (21 kDa, Protein from Homo sapiens)
40s ribosomal protein s21 (9 kDa, Protein from Homo sapiens)
60s ribosomal protein l27a (16 kDa, Protein from Homo sapiens)
40s ribosomal protein s18 (17 kDa, Protein from Homo sapiens)
60s ribosomal protein l41 (3 kDa, Protein from Homo sapiens)
Ul2 (28 kDa, Protein from Homo sapiens)
5'-guanosine-diphosphate-monothiophosphate (539 Da, Ligand)
El13 (31 kDa, Protein from Homo sapiens)
40s ribosomal protein s15 (17 kDa, Protein from Homo sapiens)
60s ribosomal protein l30 (12 kDa, Protein from Homo sapiens)
60s ribosomal protein l39 (6 kDa, Protein from Homo sapiens)
40s ribosomal protein s29 (6 kDa, Protein from Homo sapiens)
40s ribosomal protein s9 (22 kDa, Protein from Homo sapiens)
40s ribosomal protein s5 (22 kDa, Protein from Homo sapiens)
Magnesium ion (24 Da, Ligand)
60s ribosomal protein l5 (34 kDa, Protein from Homo sapiens)
Human ribosome (Complex from Homo sapiens)
60s ribosomal protein l36a (12 kDa, Protein from Homo sapiens)
60s ribosomal protein l11 (20 kDa, Protein from Homo sapiens)
4-{(2r)-2-[(1s,3s,5s)-3,5-dimethyl-2-oxocyclohexyl]-2-hydroxyethyl}piperidine-2,6-dione (281 Da, Ligand)
5.8s rrna (50 kDa, RNA from Homo sapiens)
40s ribosomal protein s8 (24 kDa, Protein from Homo sapiens)
40s ribosomal protein s17 (15 kDa, Protein from Homo sapiens)
60s ribosomal protein l29 (17 kDa, Protein from Homo sapiens)
(3r,6r,9s,12s,15s,18s,20r,24ar)-6-[(2s)-butan-2-yl]-3,12-bis[(1r)-1-hydroxy-2-methylpropyl]-8,9,11,17,18-pentamethyl-15-[(2s)-2-methylbutyl]hexadecahydropyrido[1,2-a][1,4,7,10,13,16,19]heptaazacyclohenicosine-1,4,7,10,13,16,19(21h)-heptone (794 Da, Ligand)
40s ribosomal protein s27 (9 kDa, Protein from Homo sapiens)
60s ribosomal protein l7a (30 kDa, Protein from Homo sapiens)
40s ribosomal protein s15a (14 kDa, Protein from Homo sapiens)
60s ribosomal protein l36 (12 kDa, Protein from Homo sapiens)
60s ribosomal protein l15 (24 kDa, Protein from Homo sapiens)
40s ribosomal protein s7 (22 kDa, Protein from Homo sapiens)
60s ribosomal protein l6 (32 kDa, Protein from Homo sapiens)
Elongation factor 1-alpha 1 (50 kDa, Protein from Homo sapiens)
60s ribosomal protein l37a (10 kDa, Protein from Homo sapiens)
40s ribosomal protein s28 (7 kDa, Protein from Homo sapiens)
(3beta)-o~3~-[(2r)-2,6-dihydroxy-2-(2-methoxy-2-oxoethyl)-6-methylheptanoyl]cephalotaxine (545 Da, Ligand)
40s ribosomal protein s3 (26 kDa, Protein from Homo sapiens)
40s ribosomal protein s20 (13 kDa, Protein from Homo sapiens)
40s ribosomal protein s25 (13 kDa, Protein from Homo sapiens)
Phenylalanine (165 Da, Ligand)
60s ribosomal protein l21 (18 kDa, Protein from Homo sapiens)
60s ribosomal protein l19 (23 kDa, Protein from Homo sapiens)
28s rrna (1 MDa, RNA from Homo sapiens)
Zinc ion (65 Da, Ligand)
60s ribosomal protein l34 (13 kDa, Protein from Homo sapiens)
Spermidine (145 Da, Ligand)
El40 (14 kDa, Protein from Homo sapiens)
40s ribosomal protein s10 (18 kDa, Protein from Homo sapiens)
60s ribosomal protein l35a (12 kDa, Protein from Homo sapiens)
60s ribosomal protein l22 (14 kDa, Protein from Homo sapiens)
60s ribosomal protein l28 (15 kDa, Protein from Homo sapiens)
Ubiquitin-40s ribosomal protein s27a (18 kDa, Protein from Homo sapiens)
A-site trna (24 kDa, RNA from Homo sapiens)
60s acidic ribosomal protein p0 (34 kDa, Protein from Homo sapiens)
60s ribosomal protein l17 (21 kDa, Protein from Homo sapiens)

[Show more]

EMD-40205

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mRNA decoding in human is kinetically and structurally distinct from bacteria (Consensus LSU focused refined structure)

Release date: April 19, 2023
Resolution: 1.67 Å
EM Method: Single-particle
Fitted PDBs: 8glp
Q-score: 0.673

Holm M, Natchiar SK, Rundlet EJ, Myasnikov AG, Watson ZL, Altman RB, Wang HY, Taunton J, Blanchard SC

Nature (2023) 617 pp. 200-207 [ Pubmed: 37020024 DOI: doi:10.1038/s41586-023-05908-w ]

Sample:

60s ribosomal protein l10 (24 kDa, Protein from Homo sapiens)
60s ribosomal protein l18a (20 kDa, Protein from Homo sapiens)
60s ribosomal protein l7 (29 kDa, Protein from Homo sapiens)
40s ribosomal protein s16 (16 kDa, Protein from Homo sapiens)
60s ribosomal protein l38 (8 kDa, Protein from Homo sapiens)
60s ribosomal protein l24 (17 kDa, Protein from Homo sapiens)
60s ribosomal protein l31 (14 kDa, Protein from Homo sapiens)
60s ribosomal protein l14 (23 kDa, Protein from Homo sapiens)
60s ribosomal protein l35 (14 kDa, Protein from Homo sapiens)
40s ribosomal protein s24 (15 kDa, Protein from Homo sapiens)
18s rrna (603 kDa, RNA from Homo sapiens)
60s ribosomal protein l9 (21 kDa, Protein from Homo sapiens)
P-site trna (24 kDa, RNA from Homo sapiens)
40s ribosomal protein s19 (16 kDa, Protein from Homo sapiens)
60s ribosomal protein l26 (17 kDa, Protein from Homo sapiens)
40s ribosomal protein s13 (17 kDa, Protein from Homo sapiens)
Water (18 Da, Ligand)
Receptor of activated protein c kinase 1 (35 kDa, Protein from Homo sapiens)
60s ribosomal protein l4 (47 kDa, Protein from Homo sapiens)
40s ribosomal protein s2 (31 kDa, Protein from Homo sapiens)
60s ribosomal protein l3 (46 kDa, Protein from Homo sapiens)
40s ribosomal protein s3a (30 kDa, Protein from Homo sapiens)
Mrna (19 kDa, RNA from Homo sapiens)
Methionine (149 Da, Ligand)
40s ribosomal protein s6 (28 kDa, Protein from Homo sapiens)
40s ribosomal protein s23 (us12) (15 kDa, Protein from Homo sapiens)
5s rrna (38 kDa, RNA from Homo sapiens)
4-{(2r,5s,6e)-2-hydroxy-5-methyl-7-[(2r,3s,4e,6z,10e)-3-methyl-12-oxooxacyclododeca-4,6,10-trien-2-yl]-4-oxooct-6-en-1-yl}piperidine-2,6-dione (457 Da, Ligand)
60s ribosomal protein l23a (17 kDa, Protein from Homo sapiens)
Fau ubiquitin-like and ribosomal protein s30 (14 kDa, Protein from Homo sapiens)
40s ribosomal protein s14 (16 kDa, Protein from Homo sapiens)
40s ribosomal protein s26 (13 kDa, Protein from Homo sapiens)
60s ribosomal protein l8 (ul2) (28 kDa, Protein from Homo sapiens)
Potassium ion (39 Da, Ligand)
40s ribosomal protein s12 (14 kDa, Protein from Homo sapiens)
1,4-diaminobutane (88 Da, Ligand)
60s ribosomal protein l37 (11 kDa, Protein from Homo sapiens)
40s ribosomal protein s11 (18 kDa, Protein from Homo sapiens)
60s ribosomal protein l23 (14 kDa, Protein from Homo sapiens)
60s ribosomal protein l13a (23 kDa, Protein from Homo sapiens)
60s ribosomal protein l27 (15 kDa, Protein from Homo sapiens)
40s ribosomal protein s4, x isoform (29 kDa, Protein from Homo sapiens)
40s ribosomal protein sa (32 kDa, Protein from Homo sapiens)
60s ribosomal protein l32 (15 kDa, Protein from Homo sapiens)
60s ribosomal protein l18 (21 kDa, Protein from Homo sapiens)
40s ribosomal protein s21 (9 kDa, Protein from Homo sapiens)
60s ribosomal protein l27a (16 kDa, Protein from Homo sapiens)
40s ribosomal protein s18 (17 kDa, Protein from Homo sapiens)
60s ribosomal protein l41 (3 kDa, Protein from Homo sapiens)
40s ribosomal protein s15 (17 kDa, Protein from Homo sapiens)
60s ribosomal protein l30 (12 kDa, Protein from Homo sapiens)
60s ribosomal protein l39 (6 kDa, Protein from Homo sapiens)
60s ribosomal protein l13 (24 kDa, Protein from Homo sapiens)
40s ribosomal protein s29 (6 kDa, Protein from Homo sapiens)
40s ribosomal protein s9 (22 kDa, Protein from Homo sapiens)
40s ribosomal protein s5 (22 kDa, Protein from Homo sapiens)
Anisomycin (265 Da, Ligand)
Magnesium ion (24 Da, Ligand)
60s ribosomal protein l5 (34 kDa, Protein from Homo sapiens)
2-amino-2-hydroxymethyl-propane-1,3-diol (122 Da, Ligand)
Human ribosome (Complex from Homo sapiens)
60s ribosomal protein l36a (12 kDa, Protein from Homo sapiens)
60s ribosomal protein l11 (20 kDa, Protein from Homo sapiens)
5.8s rrna (50 kDa, RNA from Homo sapiens)
40s ribosomal protein s8 (24 kDa, Protein from Homo sapiens)
40s ribosomal protein s17 (15 kDa, Protein from Homo sapiens)
60s ribosomal protein l29 (17 kDa, Protein from Homo sapiens)
40s ribosomal protein s27 (9 kDa, Protein from Homo sapiens)
60s ribosomal protein l7a (30 kDa, Protein from Homo sapiens)
40s ribosomal protein s15a (14 kDa, Protein from Homo sapiens)
60s ribosomal protein l36 (12 kDa, Protein from Homo sapiens)
60s ribosomal protein l15 (24 kDa, Protein from Homo sapiens)
40s ribosomal protein s7 (22 kDa, Protein from Homo sapiens)
60s ribosomal protein l6 (32 kDa, Protein from Homo sapiens)
60s ribosomal protein l37a (10 kDa, Protein from Homo sapiens)
40s ribosomal protein s28 (7 kDa, Protein from Homo sapiens)
40s ribosomal protein s3 (26 kDa, Protein from Homo sapiens)
40s ribosomal protein s20 (13 kDa, Protein from Homo sapiens)
40s ribosomal protein s25 (13 kDa, Protein from Homo sapiens)
60s ribosomal protein l21 (18 kDa, Protein from Homo sapiens)
60s ribosomal protein l19 (23 kDa, Protein from Homo sapiens)
28s rrna (1 MDa, RNA from Homo sapiens)
Zinc ion (65 Da, Ligand)
60s ribosomal protein l34 (13 kDa, Protein from Homo sapiens)
Spermidine (145 Da, Ligand)
40s ribosomal protein s10 (18 kDa, Protein from Homo sapiens)
60s ribosomal protein l35a (12 kDa, Protein from Homo sapiens)
60s ribosomal protein l40 (el40) (14 kDa, Protein from Homo sapiens)
60s ribosomal protein l22 (14 kDa, Protein from Homo sapiens)
60s ribosomal protein l28 (15 kDa, Protein from Homo sapiens)
Ubiquitin-40s ribosomal protein s27a (18 kDa, Protein from Homo sapiens)
60s ribosomal protein l17 (21 kDa, Protein from Homo sapiens)

[Show more]

EMD-28165

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E. coli 70S ribosome with A-loop mutations U2554C and U2555C (Composite Map)

Release date: Feb. 1, 2023
Resolution: 2.24 Å
EM Method: Single-particle
Fitted PDBs: 8eiu
Q-score: 0.658

Nissley AJ, Penev PI, Watson ZL, Banfield JF, Cate JHD

Nucleic Acids Res (2023) 51 pp. 1880-1894 [ Pubmed: 36660825 DOI: doi:10.1093/nar/gkac1273 ]

Sample:

30s ribosomal protein s10 (11 kDa, Protein from Escherichia coli)
50s ribosomal protein l20 (13 kDa, Protein from Escherichia coli)
30s ribosomal protein s2 (26 kDa, Protein from Escherichia coli)
30s ribosomal protein s17 (9 kDa, Protein from Escherichia coli)
50s ribosomal protein l22 (12 kDa, Protein from Escherichia coli)
50s ribosomal protein l23 (11 kDa, Protein from Escherichia coli)
Methionine (149 Da, Ligand)
30s ribosomal protein s7 (20 kDa, Protein from Escherichia coli)
30s ribosomal protein s11 (13 kDa, Protein from Escherichia coli)
30s ribosomal protein s5 (17 kDa, Protein from Escherichia coli)
30s ribosomal protein s21 (8 kDa, Protein from Escherichia coli)
30s ribosomal protein s20 (9 kDa, Protein from Escherichia coli)
30s ribosomal protein s6 (15 kDa, Protein from Escherichia coli)
50s ribosomal protein l36 (4 kDa, Protein from Escherichia coli)
50s ribosomal protein l13 (16 kDa, Protein from Escherichia coli)
E. coli 70s ribosome with a-loop mutations u2554c and u2555c (850 kDa, Complex from Escherichia coli)
30s ribosomal protein s12 (13 kDa, Protein from Escherichia coli)
30s ribosomal protein s19 (10 kDa, Protein from Escherichia coli)
50s ribosomal protein l14 (13 kDa, Protein from Escherichia coli)
50s ribosomal protein l27 (9 kDa, Protein from Escherichia coli)
Ribosomal protein l21 (11 kDa, Protein from Escherichia coli)
Mrna (8 kDa, RNA from Escherichia coli)
50s ribosomal protein l4 (22 kDa, Protein from Escherichia coli)
Spermine (202 Da, Ligand)
50s ribosomal protein l17 (14 kDa, Protein from Escherichia coli)
50s ribosomal protein l5 (20 kDa, Protein from Escherichia coli)
50s subunit (Complex from Escherichia coli)
50s ribosomal protein l28 (9 kDa, Protein from Escherichia coli)
50s ribosomal protein l9 (15 kDa, Protein from Escherichia coli)
50s ribosomal protein l18 (12 kDa, Protein from Escherichia coli)
Zinc ion (65 Da, Ligand)
30s ribosomal protein s18 (9 kDa, Protein from Escherichia coli)
50s ribosomal protein l24 (11 kDa, Protein from Escherichia coli)
30s subunit (Complex from Escherichia coli)
50s ribosomal protein l34 (5 kDa, Protein from Escherichia coli)
Spermidine (145 Da, Ligand)
16s rrna (499 kDa, RNA from Escherichia coli)
50s ribosomal protein l19 (13 kDa, Protein from Escherichia coli)
50s ribosomal protein l35 (7 kDa, Protein from Escherichia coli)
30s ribosomal protein s9 (14 kDa, Protein from Escherichia coli)
23s rrna (941 kDa, RNA from Escherichia coli)
30s ribosomal protein s4 (23 kDa, Protein from Escherichia coli)
3'-amino-3'-deoxyadenosine 5'-(dihydrogen phosphate) (346 Da, Ligand)
50s ribosomal protein l33 (6 kDa, Protein from Escherichia coli)
Water (18 Da, Ligand)
30s ribosomal protein s14 (11 kDa, Protein from Escherichia coli)
Magnesium ion (24 Da, Ligand)
50s ribosomal protein l6 (18 kDa, Protein from Escherichia coli)
50s ribosomal protein l32 (6 kDa, Protein from Escherichia coli)
50s ribosomal protein l31 (7 kDa, Protein from Escherichia coli)
30s ribosomal protein s15 (10 kDa, Protein from Escherichia coli)
50s ribosomal protein l15 (15 kDa, Protein from Escherichia coli)
30s ribosomal protein s13 (13 kDa, Protein from Escherichia coli)
50s ribosomal protein l2 (29 kDa, Protein from Escherichia coli)
50s ribosomal protein l30 (6 kDa, Protein from Escherichia coli)
50s ribosomal protein l25 (10 kDa, Protein from Escherichia coli)
50s ribosomal protein l3 (22 kDa, Protein from Escherichia coli)
30s ribosomal protein s3 (26 kDa, Protein from Escherichia coli)
5s rrna (38 kDa, RNA from Escherichia coli)
30s ribosomal protein s8 (14 kDa, Protein from Escherichia coli)
50s ribosomal protein l29 (7 kDa, Protein from Escherichia coli)
50s ribosomal protein l16 (15 kDa, Protein from Escherichia coli)
Trna-fmet (24 kDa, RNA from Escherichia coli)
Paromomycin (615 Da, Ligand)
30s ribosomal protein s16 (9 kDa, Protein from Escherichia coli)

[Show more]

EMD-22586

Download Map 3D View Raw data

Structure of the Bacterial Ribosome at 2 Angstrom Resolution (composite structure)

Release date: Sept. 23, 2020
Resolution: 1.98 Å
EM Method: Single-particle
Fitted PDBs: 7k00
Q-score: 0.677

Watson ZL, Ward FR, Meheust R, Ad O, Schepartz A, Banfield JF, Cate JH

eLife (2020) 9 [ Pubmed: 32924932 DOI: doi:10.7554/eLife.60482 ]

Sample:

30s ribosomal protein s10 (11 kDa, Protein from Escherichia coli)
50s ribosomal protein l20 (13 kDa, Protein from Escherichia coli)
30s ribosomal protein s2 (26 kDa, Protein from Escherichia coli)
30s ribosomal protein s17 (9 kDa, Protein from Escherichia coli)
50s ribosomal protein l22 (12 kDa, Protein from Escherichia coli)
50s ribosomal protein l23 (11 kDa, Protein from Escherichia coli)
30s ribosomal protein s7 (20 kDa, Protein from Escherichia coli)
30s ribosomal protein s11 (13 kDa, Protein from Escherichia coli)
30s ribosomal protein s5 (17 kDa, Protein from Escherichia coli)
30s ribosomal protein s21 (8 kDa, Protein from Escherichia coli)
30s ribosomal protein s20 (9 kDa, Protein from Escherichia coli)
30s ribosomal protein s6 (15 kDa, Protein from Escherichia coli)
50s ribosomal protein l36 (4 kDa, Protein from Escherichia coli)
50s ribosomal protein l13 (16 kDa, Protein from Escherichia coli)
30s ribosomal protein s12 (13 kDa, Protein from Escherichia coli)
30s ribosomal protein s19 (10 kDa, Protein from Escherichia coli)
50s ribosomal protein l14 (13 kDa, Protein from Escherichia coli)
50s ribosomal protein l27 (9 kDa, Protein from Escherichia coli)
E-site trna (589 Da, RNA from Escherichia coli)
50s ribosomal protein l4 (22 kDa, Protein from Escherichia coli)
Spermine (202 Da, Ligand)
50s ribosomal protein l17 (14 kDa, Protein from Escherichia coli)
50s ribosomal protein l5 (20 kDa, Protein from Escherichia coli)
50s ribosomal protein l28 (9 kDa, Protein from Escherichia coli)
50s ribosomal protein l9 (15 kDa, Protein from Escherichia coli)
50s ribosomal protein l18 (12 kDa, Protein from Escherichia coli)
Zinc ion (65 Da, Ligand)
30s ribosomal protein s18 (9 kDa, Protein from Escherichia coli)
50s ribosomal protein l24 (11 kDa, Protein from Escherichia coli)
A-site trna-val (24 kDa, RNA from Escherichia coli)
50s ribosomal protein l34 (5 kDa, Protein from Escherichia coli)
50s ribosomal protein l21 (11 kDa, Protein from Escherichia coli)
Spermidine (145 Da, Ligand)
16s rrna (499 kDa, RNA from Escherichia coli)
50s ribosomal protein l19 (13 kDa, Protein from Escherichia coli)
50s ribosomal protein l35 (7 kDa, Protein from Escherichia coli)
30s ribosomal protein s9 (14 kDa, Protein from Escherichia coli)
30s ribosomal protein s4 (23 kDa, Protein from Escherichia coli)
50s ribosomal protein l33 (6 kDa, Protein from Escherichia coli)
Water (18 Da, Ligand)
30s ribosomal protein s14 (11 kDa, Protein from Escherichia coli)
Magnesium ion (24 Da, Ligand)
50s ribosomal protein l6 (18 kDa, Protein from Escherichia coli)
50s ribosomal protein l32 (6 kDa, Protein from Escherichia coli)
50s ribosomal protein l31 (7 kDa, Protein from Escherichia coli)
30s ribosomal protein s15 (10 kDa, Protein from Escherichia coli)
50s ribosomal protein l15 (15 kDa, Protein from Escherichia coli)
E. coli 70s ribosome (2 MDa, Complex from Escherichia coli)
30s ribosomal protein s13 (13 kDa, Protein from Escherichia coli)
P-site trna-fmet (24 kDa, RNA from Escherichia coli)
50s ribosomal protein l2 (29 kDa, Protein from Escherichia coli)
50s ribosomal protein l30 (6 kDa, Protein from Escherichia coli)
50s ribosomal protein l25 (10 kDa, Protein from Escherichia coli)
50s ribosomal protein l3 (22 kDa, Protein from Escherichia coli)
Mrna (9 kDa, RNA from Escherichia coli)
30s ribosomal protein s3 (26 kDa, Protein from Escherichia coli)
23s rrna (941 kDa, RNA from Escherichia coli)
5s rrna (38 kDa, RNA from Escherichia coli)
30s ribosomal protein s8 (14 kDa, Protein from Escherichia coli)
50s ribosomal protein l29 (7 kDa, Protein from Escherichia coli)
50s ribosomal protein l16 (15 kDa, Protein from Escherichia coli)
Paromomycin (615 Da, Ligand)
30s ribosomal protein s16 (9 kDa, Protein from Escherichia coli)

[Show more]

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EMDB [9]

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