Electron Microscopy Data Bank

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sample_name:"50S ribosomal protein L31" AND author_name:"Ignatova Z"

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EMD-15558

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Structure of Escherischia coli heat shock protein Hsp15 in complex with ribosomal 50S subunits bearing peptidyl-tRNA

Release date: Nov. 16, 2022
Resolution: 3.0 Å
EM Method: Single-particle
Fitted PDBs: 8ap4
Q-score: 0.493

Safdari HA, Kasvandik S, Polte C, Ignatova Z, Tenson T, Wilson DN

Nucleic Acids Res (2022) 50 pp. 12515-12526 [ Pubmed: 36370110 DOI: doi:10.1093/nar/gkac1035 ]

Sample:

50s ribosomal protein l36 (4 kDa, Protein from Escherichia coli K-12)
50s ribosomal protein l28 (9 kDa, Protein from Escherichia coli K-12)
50s ribosomal protein l16 (15 kDa, Protein from Escherichia coli K-12)
50s ribosomal protein l14 (13 kDa, Protein from Escherichia coli K-12)
50s ribosomal protein l27 (9 kDa, Protein from Escherichia coli K-12)
50s ribosomal protein l25 (10 kDa, Protein from Escherichia coli K-12)
50s ribosomal protein l21 (11 kDa, Protein from Escherichia coli K-12)
50s ribosomal protein l15 (15 kDa, Protein from Escherichia coli K-12)
50s ribosomal protein l31 (7 kDa, Protein from Escherichia coli K-12)
5s rrna (38 kDa, RNA from Escherichia coli K-12)
50s ribosomal protein l5 (20 kDa, Protein from Escherichia coli K-12)
23s rrna (941 kDa, RNA from Escherichia coli K-12)
50s ribosomal protein l17 (14 kDa, Protein from Escherichia coli K-12)
P-trna (24 kDa, RNA from Escherichia coli K-12)
50s ribosomal protein l32 (6 kDa, Protein from Escherichia coli K-12)
50s ribosomal protein l23 (11 kDa, Protein from Escherichia coli K-12)
50s ribosomal protein l2 (29 kDa, Protein from Escherichia coli K-12)
50s ribosomal protein l18 (12 kDa, Protein from Escherichia coli K-12)
Heat shock protein 15 (15 kDa, Protein from Escherichia coli K-12)
50s ribosomal protein l3 (22 kDa, Protein from Escherichia coli K-12)
50s ribosomal protein l30 (6 kDa, Protein from Escherichia coli K-12)
50s ribosomal protein l13 (16 kDa, Protein from Escherichia coli K-12)
50s ribosomal protein l33 (6 kDa, Protein from Escherichia coli K-12)
50s ribosomal protein l22 (12 kDa, Protein from Escherichia coli K-12)
50s ribosomal protein l19 (13 kDa, Protein from Escherichia coli K-12)
Structure of escherischia coli heat shock protein hsp15 in complex with ribosomal 50s subunits bearing peptidyl-trna (Complex from Escherichia coli K-12)
50s ribosomal protein l29 (7 kDa, Protein from Escherichia coli K-12)
50s ribosomal protein l4 (22 kDa, Protein from Escherichia coli K-12)
50s ribosomal protein l9 (15 kDa, Protein from Escherichia coli K-12)
50s ribosomal protein l34 (5 kDa, Protein from Escherichia coli K-12)
50s ribosomal protein l6 (18 kDa, Protein from Escherichia coli K-12)
50s ribosomal protein l20 (13 kDa, Protein from Escherichia coli K-12)
50s ribosomal protein l35 (7 kDa, Protein from Escherichia coli K-12)
50s ribosomal protein l24 (11 kDa, Protein from Escherichia coli K-12)

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EMD-12035

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E. coli 70S containing suppressor tRNA in the A-site stabilized by a Negamycin analogue and P-site tRNA-nascent chain.

Release date: May 26, 2021
Resolution: 2.9 Å
EM Method: Single-particle
Fitted PDBs: 7b5k
Q-score: 0.564

Albers S, Beckert B, Wilson ND, Ignatova Z

Nat Commun (2021) [ ]

Sample:

Atrna synthetic stop trna (76-mer) (24 kDa, RNA from Escherichia coli K-12)
50s ribosomal protein l36 (4 kDa, Protein from Escherichia coli K-12)
50s ribosomal protein l14 (13 kDa, Protein from Escherichia coli K-12)
50s ribosomal protein l16 (15 kDa, Protein from Escherichia coli K-12)
50s ribosomal protein l25 (10 kDa, Protein from Escherichia coli K-12)
50s ribosomal protein l21 (11 kDa, Protein from Escherichia coli K-12)
50s ribosomal protein l15 (15 kDa, Protein from Escherichia coli K-12)
30s ribosomal protein s16 (9 kDa, Protein from Escherichia coli K-12)
Mrna (Complex from Escherichia coli K-12)
30s ribosomal protein s11 (12 kDa, Protein from Escherichia coli K-12)
50s ribosomal protein l23 (10 kDa, Protein from Escherichia coli K-12)
P-site isoleucine trna (77-mer) (24 kDa, RNA from Escherichia coli K-12)
30s ribosomal protein s10 (11 kDa, Protein from Escherichia coli K-12)
5s rrna (38 kDa, RNA from Escherichia coli K-12)
30s ribosomal protein s9 (14 kDa, Protein from Escherichia coli K-12)
30s ribosomal protein s15 (10 kDa, Protein from Escherichia coli K-12)
30s ribosomal protein s8 (14 kDa, Protein from Escherichia coli K-12)
30s ribosomal protein s20 (9 kDa, Protein from Escherichia coli K-12)
E-site val trna (76-mer) (24 kDa, RNA from Escherichia coli K-12)
30s ribosomal protein s6 (12 kDa, Protein from Escherichia coli K-12)
50s ribosomal protein l5 (20 kDa, Protein from Escherichia coli K-12)
50s ribosomal protein l31 (7 kDa, Protein from Escherichia coli K-12)
50s ribosomal protein l35 (7 kDa, Protein from Escherichia coli K-12)
30s ribosomal protein s21 (6 kDa, Protein from Escherichia coli K-12)
16s rrna (497 kDa, RNA from Escherichia coli K-12)
50s ribosomal protein l18 (12 kDa, Protein from Escherichia coli K-12)
50s ribosomal protein l28 (8 kDa, Protein from Escherichia coli K-12)
50s ribosomal protein l33 (5 kDa, Protein from Escherichia coli K-12)
30s ribosomal protein s18 (6 kDa, Protein from Escherichia coli K-12)
Magnesium ion (24 Da, Ligand)
50s ribosomal protein l32 (6 kDa, Protein from Escherichia coli K-12)
50s ribosomal protein l27 (8 kDa, Protein from Escherichia coli K-12)
30s ribosomal protein s3 (23 kDa, Protein from Escherichia coli K-12)
30s ribosomal protein s14 (11 kDa, Protein from Escherichia coli K-12)
30s ribosomal protein s5 (16 kDa, Protein from Escherichia coli K-12)
50s ribosomal protein l13 (16 kDa, Protein from Escherichia coli K-12)
23s rrna (939 kDa, RNA from Escherichia coli K-12)
50s ribosomal protein l17 (13 kDa, Protein from Escherichia coli K-12)
30s ribosomal protein s4 (23 kDa, Protein from Escherichia coli K-12)
30s ribosomal protein s12 (13 kDa, Protein from Escherichia coli K-12)
50s ribosomal protein l30 (6 kDa, Protein from Escherichia coli K-12)
50s ribosomal protein l22 (12 kDa, Protein from Escherichia coli K-12)
50s ribosomal protein l19 (13 kDa, Protein from Escherichia coli K-12)
30s ribosomal protein s7 (16 kDa, Protein from Escherichia coli K-12)
30s ribosomal protein s2 (24 kDa, Protein from Escherichia coli K-12)
2-[[[(3~{r},5~{r})-3-azanyl-6-(3-azanylpropylamino)-5-oxidanyl-hexanoyl]amino]-methyl-amino]ethanoic acid (305 Da, Ligand)
Ermc nacent chain (895 Da, Protein from Escherichia coli K-12)
50s ribosomal protein l4 (22 kDa, Protein from Escherichia coli K-12)
50s ribosomal protein l9 (15 kDa, Protein from Escherichia coli K-12)
50s ribosomal protein l20 (13 kDa, Protein from Escherichia coli K-12)
50s ribosomal protein l24 (11 kDa, Protein from Escherichia coli K-12)
50s ribosomal protein l2 (29 kDa, Protein from Escherichia coli K-12)
30s ribosomal protein s17 (9 kDa, Protein from Escherichia coli K-12)
30s ribosomal protein s19 (9 kDa, Protein from Escherichia coli K-12)
Erythromycin a (733 Da, Ligand)
50s ribosomal protein l34 (5 kDa, Protein from Escherichia coli K-12)
50s ribosomal protein l3 (22 kDa, Protein from Escherichia coli K-12)
50s ribosomal protein l29 (7 kDa, Protein from Escherichia coli K-12)
30s ribosomal protein s13 (12 kDa, Protein from Escherichia coli K-12)
Water (18 Da, Ligand)
70s ribosome with a,p,e-site trna (Complex)
50s ribosomal protein l6 (18 kDa, Protein from Escherichia coli K-12)
70s ribosome with a,p,e-site trna (Complex from Escherichia coli K-12)
Mrna (3 kDa, RNA from Escherichia coli K-12)

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EMD-12331

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LsaA, an antibiotic resistance ABCF, in complex with 70S ribosome from Enterococcus faecalis

Release date: May 5, 2021
Resolution: 2.9 Å
EM Method: Single-particle
Fitted PDBs: 7nhk
Q-score: 0.519

Crowe-McAuliffe C, Murina V, Turnbull KJ, Kasari M, Mohamad M, Polte C, Takada H, Vaitkevicius K, Johansson J, Ignatova Z, Atkinson GC, O'Neill AJ, Hauryliuk V, Wilson DN

Nat Commun (2021) 12 pp. 3577-3577 [ Pubmed: 34117249 DOI: doi:10.1038/s41467-021-23753-1 ]

Sample:

30s ribosomal protein s3 (24 kDa, Protein from Enterococcus faecalis)
30s ribosomal protein s19 (10 kDa, Protein from Enterococcus faecalis)
Rna (5'-r(p*gp*gp*ap*gp*gp*up*ap*up*gp*ap*cp*ap*a)-3') (5 kDa, RNA from Enterococcus faecalis)
50s ribosomal protein l21 (11 kDa, Protein from Enterococcus faecalis)
50s ribosomal protein l15 (15 kDa, Protein from Enterococcus faecalis)
50s ribosomal protein l18 (12 kDa, Protein from Enterococcus faecalis)
Adenosine-5'-triphosphate (507 Da, Ligand)
50s ribosomal protein l16 (16 kDa, Protein from Enterococcus faecalis)
Zinc ion (65 Da, Ligand)
30s ribosomal protein s16 (10 kDa, Protein from Enterococcus faecalis)
5s rrna (37 kDa, RNA from Enterococcus faecalis)
30s ribosomal protein s15 (10 kDa, Protein from Enterococcus faecalis)
30s ribosomal protein s14 type z (7 kDa, Protein from Enterococcus faecalis)
30s ribosomal protein s6 (11 kDa, Protein from Enterococcus faecalis)
Lsaa-in complex with 70s ribosome, mrna, and trna (2 MDa, Complex from Enterococcus faecalis)
30s ribosomal protein s20 (8 kDa, Protein from Enterococcus faecalis)
50s ribosomal protein l22 (12 kDa, Protein from Enterococcus faecalis)
50s ribosomal protein l1 (24 kDa, Protein from Enterococcus faecalis)
30s ribosomal protein s18 (9 kDa, Protein from Enterococcus faecalis)
1,4-diaminobutane (88 Da, Ligand)
50s ribosomal protein l34 (5 kDa, Protein from Enterococcus faecalis)
50s ribosomal protein l3 (22 kDa, Protein from Enterococcus faecalis)
50s ribosomal protein l6 (19 kDa, Protein from Enterococcus faecalis)
50s ribosomal protein l31 type b (10 kDa, Protein from Enterococcus faecalis)
50s ribosomal protein l32 (6 kDa, Protein from Enterococcus faecalis)
50s ribosomal protein l4 (22 kDa, Protein from Enterococcus faecalis)
50s ribosomal protein l19 (13 kDa, Protein from Enterococcus faecalis)
30s ribosomal protein s11 (13 kDa, Protein from Enterococcus faecalis)
Abc-f type ribosomal protection protein lsa(a) (62 kDa, Protein from Enterococcus faecalis)
50s ribosomal protein l24 (11 kDa, Protein from Enterococcus faecalis)
30s ribosomal protein s7 (17 kDa, Protein from Enterococcus faecalis)
30s ribosomal protein s9 (14 kDa, Protein from Enterococcus faecalis)
Potassium ion (39 Da, Ligand)
50s ribosomal protein l29 (7 kDa, Protein from Enterococcus faecalis)
23s rrna (944 kDa, RNA from Enterococcus faecalis)
50s ribosomal protein l20 (13 kDa, Protein from Enterococcus faecalis)
30s ribosomal protein s8 (14 kDa, Protein from Enterococcus faecalis)
Trna-fmeti (24 kDa, RNA from Enterococcus faecalis)
50s ribosomal protein l27 (10 kDa, Protein from Enterococcus faecalis)
30s ribosomal protein s2 (29 kDa, Protein from Enterococcus faecalis)
50s ribosomal protein l23 (11 kDa, Protein from Enterococcus faecalis)
30s ribosomal protein s4 (23 kDa, Protein from Enterococcus faecalis)
30s ribosomal protein s5 (17 kDa, Protein from Enterococcus faecalis)
50s ribosomal protein l30 (6 kDa, Protein from Enterococcus faecalis)
50s ribosomal protein l36 (4 kDa, Protein from Enterococcus faecalis)
50s ribosomal protein l17 (14 kDa, Protein from Enterococcus faecalis)
50s ribosomal protein l28 (7 kDa, Protein from Enterococcus faecalis)
50s ribosomal protein l33 (6 kDa, Protein from Enterococcus faecalis)
30s ribosomal protein s17 (10 kDa, Protein from Enterococcus faecalis)
50s ribosomal protein l5 (20 kDa, Protein from Enterococcus faecalis)
50s ribosomal protein l13 (16 kDa, Protein from Enterococcus faecalis)
30s ribosomal protein s12 (15 kDa, Protein from Enterococcus faecalis)
30s ribosomal protein s10 (11 kDa, Protein from Enterococcus faecalis)
30s ribosomal protein s13 (13 kDa, Protein from Enterococcus faecalis)
50s ribosomal protein l35 (7 kDa, Protein from Enterococcus faecalis)
Magnesium ion (24 Da, Ligand)
50s ribosomal protein l14 (13 kDa, Protein from Enterococcus faecalis)
16s rrna (504 kDa, RNA from Enterococcus faecalis)
50s ribosomal protein l2 (30 kDa, Protein from Enterococcus faecalis)

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EMD-12332

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VgaA-LC, an antibiotic resistance ABCF, in complex with 70S ribosome from Staphylococcus aureus

Release date: May 5, 2021
Resolution: 3.1 Å
EM Method: Single-particle
Fitted PDBs: 7nhl
Q-score: 0.476

Crowe-McAuliffe C, Murina V, Turnbull KJ, Kasari M, Mohamad M, Polte C, Takada H, Vaitkevicius K, Johansson J, Ignatova Z, Atkinson GC, O'Neill AJ, Hauryliuk V, Wilson DN

Nat Commun (2021) 12 pp. 3577-3577 [ Pubmed: 34117249 DOI: doi:10.1038/s41467-021-23753-1 ]

Sample:

50s ribosomal protein l6 (19 kDa, Protein from Staphylococcus aureus subsp. aureus NCTC 8325)
50s ribosomal protein l36 (4 kDa, Protein from Staphylococcus aureus subsp. aureus NCTC 8325)
30s ribosomal protein s5 (17 kDa, Protein from Staphylococcus aureus subsp. aureus NCTC 8325)
50s ribosomal protein l31 type b (9 kDa, Protein from Staphylococcus aureus subsp. aureus NCTC 8325)
30s ribosomal protein s15 (10 kDa, Protein from Staphylococcus aureus subsp. aureus NCTC 8325)
50s ribosomal protein l23 (10 kDa, Protein from Staphylococcus aureus subsp. aureus NCTC 8325)
50s ribosomal protein l3 (23 kDa, Protein from Staphylococcus aureus subsp. aureus NCTC 8325)
50s ribosomal protein l15 (15 kDa, Protein from Staphylococcus aureus subsp. aureus NCTC 8325)
Adenosine-5'-triphosphate (507 Da, Ligand)
Zinc ion (65 Da, Ligand)
50s ribosomal protein l17 (13 kDa, Protein from Staphylococcus aureus subsp. aureus NCTC 8325)
5s rrna (36 kDa, RNA from Staphylococcus aureus subsp. aureus NCTC 8325)
50s ribosomal protein l30 (6 kDa, Protein from Staphylococcus aureus subsp. aureus NCTC 8325)
Rna (5'-r(p*gp*gp*ap*gp*gp*up*ap*up*g)-3') (4 kDa, RNA from Staphylococcus aureus subsp. aureus NCTC 8325)
30s ribosomal protein s6 (11 kDa, Protein from Staphylococcus aureus subsp. aureus NCTC 8325)
50s ribosomal protein l19 (13 kDa, Protein from Staphylococcus aureus subsp. aureus NCTC 8325)
30s ribosomal protein s11 (13 kDa, Protein from Staphylococcus aureus subsp. aureus NCTC 8325)
P-trna fmet (24 kDa, RNA from Staphylococcus aureus subsp. aureus NCTC 8325)
Vgaa-lc (Complex from Staphylococcus haemolyticus)
30s ribosomal protein s17 (10 kDa, Protein from Staphylococcus aureus subsp. aureus NCTC 8325)
30s ribosomal protein s12 (15 kDa, Protein from Staphylococcus aureus subsp. aureus NCTC 8325)
50s ribosomal protein l20 (13 kDa, Protein from Staphylococcus aureus subsp. aureus NCTC 8325)
Magnesium ion (24 Da, Ligand)
30s ribosomal protein s10 (11 kDa, Protein from Staphylococcus aureus subsp. aureus NCTC 8325)
Potassium ion (39 Da, Ligand)
50s ribosomal protein l22 (12 kDa, Protein from Staphylococcus aureus subsp. aureus NCTC 8325)
50s ribosomal protein l4 (22 kDa, Protein from Staphylococcus aureus subsp. aureus NCTC 8325)
50s ribosomal protein l18 (13 kDa, Protein from Staphylococcus aureus subsp. aureus NCTC 8325)
50s ribosomal protein l14 (13 kDa, Protein from Staphylococcus aureus subsp. aureus NCTC 8325)
50s ribosomal protein l27 (10 kDa, Protein from Staphylococcus aureus subsp. aureus NCTC 8325)
30s ribosomal protein s3 (24 kDa, Protein from Staphylococcus aureus subsp. aureus NCTC 8325)
30s ribosomal protein s14 type z (7 kDa, Protein from Staphylococcus aureus subsp. aureus NCTC 8325)
16s rrna (501 kDa, RNA from Staphylococcus aureus subsp. aureus NCTC 8325)
50s ribosomal protein l28 (6 kDa, Protein from Staphylococcus aureus subsp. aureus NCTC 8325)
30s ribosomal protein s19 (10 kDa, Protein from Staphylococcus aureus subsp. aureus NCTC 8325)
30s ribosomal protein s9 (14 kDa, Protein from Staphylococcus aureus subsp. aureus NCTC 8325)
30s ribosomal protein s16 (10 kDa, Protein from Staphylococcus aureus subsp. aureus NCTC 8325)
30s ribosomal protein s8 (14 kDa, Protein from Staphylococcus aureus subsp. aureus NCTC 8325)
50s ribosomal protein l5 (20 kDa, Protein from Staphylococcus aureus subsp. aureus NCTC 8325)
50s ribosomal protein l32 (6 kDa, Protein from Staphylococcus aureus subsp. aureus NCTC 8325)
30s ribosomal protein s20 (9 kDa, Protein from Staphylococcus aureus subsp. aureus NCTC 8325)
Vgaa-lc in complex with 70s ribosome, mrna, and distorted p-trna from staphylococcus aureus (2 MDa, Complex)
Lincosamide-streptogramin a resistance protein (63 kDa, Protein from Staphylococcus haemolyticus)
30s ribosomal protein s18 (9 kDa, Protein from Staphylococcus aureus subsp. aureus NCTC 8325)
30s ribosomal protein s4 (23 kDa, Protein from Staphylococcus aureus subsp. aureus NCTC 8325)
50s ribosomal protein l35 (7 kDa, Protein from Staphylococcus aureus subsp. aureus NCTC 8325)
70s ribosome (Complex from Staphylococcus aureus subsp. aureus NCTC 8325)
23s rrna (946 kDa, RNA from Staphylococcus aureus subsp. aureus NCTC 8325)
50s ribosomal protein l2 (30 kDa, Protein from Staphylococcus aureus subsp. aureus NCTC 8325)
50s ribosomal protein l29 (8 kDa, Protein from Staphylococcus aureus subsp. aureus NCTC 8325)
50s ribosomal protein l34 (5 kDa, Protein from Staphylococcus aureus subsp. aureus NCTC 8325)
50s ribosomal protein l24 (11 kDa, Protein from Staphylococcus aureus subsp. aureus NCTC 8325)
50s ribosomal protein l33 2 (5 kDa, Protein from Staphylococcus aureus subsp. aureus NCTC 8325)
30s ribosomal protein s7 (17 kDa, Protein from Staphylococcus aureus subsp. aureus NCTC 8325)
50s ribosomal protein l13 (16 kDa, Protein from Staphylococcus aureus subsp. aureus NCTC 8325)
50s ribosomal protein l16 (16 kDa, Protein from Staphylococcus aureus subsp. aureus NCTC 8325)
50s ribosomal protein l25 (23 kDa, Protein from Staphylococcus aureus subsp. aureus NCTC 8325)
30s ribosomal protein s13 (13 kDa, Protein from Staphylococcus aureus subsp. aureus NCTC 8325)
50s ribosomal protein l21 (11 kDa, Protein from Staphylococcus aureus subsp. aureus NCTC 8325)
30s ribosomal protein s2 (29 kDa, Protein from Staphylococcus aureus subsp. aureus NCTC 8325)

[Show more]

EMD-12333

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70S ribosome from Staphylococcus aureus

Release date: May 5, 2021
Resolution: 3.1 Å
EM Method: Single-particle
Fitted PDBs: 7nhm
Q-score: 0.494

Crowe-McAuliffe C, Murina V, Turnbull KJ, Kasari M, Mohamad M, Polte C, Takada H, Vaitkevicius K, Johansson J, Ignatova Z, Atkinson GC, O'Neill AJ, Hauryliuk V, Wilson DN

Nat Commun (2021) 12 pp. 3577-3577 [ Pubmed: 34117249 DOI: doi:10.1038/s41467-021-23753-1 ]

Sample:

50s ribosomal protein l6 (19 kDa, Protein from Staphylococcus aureus subsp. aureus NCTC 8325)
50s ribosomal protein l36 (4 kDa, Protein from Staphylococcus aureus subsp. aureus NCTC 8325)
30s ribosomal protein s5 (17 kDa, Protein from Staphylococcus aureus subsp. aureus NCTC 8325)
50s ribosomal protein l31 type b (9 kDa, Protein from Staphylococcus aureus subsp. aureus NCTC 8325)
50s ribosomal protein l32 (6 kDa, Protein from Staphylococcus aureus subsp. aureus NCTC 8325)
30s ribosomal protein s15 (10 kDa, Protein from Staphylococcus aureus subsp. aureus NCTC 8325)
50s ribosomal protein l23 (10 kDa, Protein from Staphylococcus aureus subsp. aureus NCTC 8325)
50s ribosomal protein l3 (23 kDa, Protein from Staphylococcus aureus subsp. aureus NCTC 8325)
50s ribosomal protein l15 (15 kDa, Protein from Staphylococcus aureus subsp. aureus NCTC 8325)
Trna-fmet (24 kDa, RNA from Staphylococcus aureus subsp. aureus NCTC 8325)
Zinc ion (65 Da, Ligand)
50s ribosomal protein l17 (13 kDa, Protein from Staphylococcus aureus subsp. aureus NCTC 8325)
5s rrna (36 kDa, RNA from Staphylococcus aureus subsp. aureus NCTC 8325)
50s ribosomal protein l30 (6 kDa, Protein from Staphylococcus aureus subsp. aureus NCTC 8325)
30s ribosomal protein s6 (11 kDa, Protein from Staphylococcus aureus subsp. aureus NCTC 8325)
50s ribosomal protein l19 (13 kDa, Protein from Staphylococcus aureus subsp. aureus NCTC 8325)
30s ribosomal protein s11 (13 kDa, Protein from Staphylococcus aureus subsp. aureus NCTC 8325)
Rna (5'-r(p*gp*gp*ap*gp*gp*up*np*np*np*np*np*np*ap*up*g)-3') (4 kDa, RNA from Staphylococcus aureus subsp. aureus NCTC 8325)
30s ribosomal protein s17 (10 kDa, Protein from Staphylococcus aureus subsp. aureus NCTC 8325)
30s ribosomal protein s12 (15 kDa, Protein from Staphylococcus aureus subsp. aureus NCTC 8325)
50s ribosomal protein l20 (13 kDa, Protein from Staphylococcus aureus subsp. aureus NCTC 8325)
Potassium ion (39 Da, Ligand)
30s ribosomal protein s10 (11 kDa, Protein from Staphylococcus aureus subsp. aureus NCTC 8325)
Magnesium ion (24 Da, Ligand)
50s ribosomal protein l22 (12 kDa, Protein from Staphylococcus aureus subsp. aureus NCTC 8325)
50s ribosomal protein l4 (22 kDa, Protein from Staphylococcus aureus subsp. aureus NCTC 8325)
50s ribosomal protein l18 (13 kDa, Protein from Staphylococcus aureus subsp. aureus NCTC 8325)
50s ribosomal protein l14 (13 kDa, Protein from Staphylococcus aureus subsp. aureus NCTC 8325)
50s ribosomal protein l27 (10 kDa, Protein from Staphylococcus aureus subsp. aureus NCTC 8325)
30s ribosomal protein s3 (24 kDa, Protein from Staphylococcus aureus subsp. aureus NCTC 8325)
70s ribosome from staphylococcus aureus (2 MDa, Complex from Staphylococcus aureus subsp. aureus NCTC 8325)
30s ribosomal protein s14 type z (7 kDa, Protein from Staphylococcus aureus subsp. aureus NCTC 8325)
16s rrna (501 kDa, RNA from Staphylococcus aureus subsp. aureus NCTC 8325)
50s ribosomal protein l28 (6 kDa, Protein from Staphylococcus aureus subsp. aureus NCTC 8325)
30s ribosomal protein s19 (10 kDa, Protein from Staphylococcus aureus subsp. aureus NCTC 8325)
30s ribosomal protein s9 (14 kDa, Protein from Staphylococcus aureus subsp. aureus NCTC 8325)
30s ribosomal protein s16 (10 kDa, Protein from Staphylococcus aureus subsp. aureus NCTC 8325)
30s ribosomal protein s8 (14 kDa, Protein from Staphylococcus aureus subsp. aureus NCTC 8325)
50s ribosomal protein l5 (20 kDa, Protein from Staphylococcus aureus subsp. aureus NCTC 8325)
30s ribosomal protein s20 (9 kDa, Protein from Staphylococcus aureus subsp. aureus NCTC 8325)
30s ribosomal protein s18 (9 kDa, Protein from Staphylococcus aureus subsp. aureus NCTC 8325)
30s ribosomal protein s4 (23 kDa, Protein from Staphylococcus aureus subsp. aureus NCTC 8325)
50s ribosomal protein l35 (7 kDa, Protein from Staphylococcus aureus subsp. aureus NCTC 8325)
23s rrna (946 kDa, RNA from Staphylococcus aureus subsp. aureus NCTC 8325)
50s ribosomal protein l2 (30 kDa, Protein from Staphylococcus aureus subsp. aureus NCTC 8325)
50s ribosomal protein l29 (8 kDa, Protein from Staphylococcus aureus subsp. aureus NCTC 8325)
50s ribosomal protein l34 (5 kDa, Protein from Staphylococcus aureus subsp. aureus NCTC 8325)
50s ribosomal protein l24 (11 kDa, Protein from Staphylococcus aureus subsp. aureus NCTC 8325)
50s ribosomal protein l33 2 (5 kDa, Protein from Staphylococcus aureus subsp. aureus NCTC 8325)
30s ribosomal protein s7 (17 kDa, Protein from Staphylococcus aureus subsp. aureus NCTC 8325)
50s ribosomal protein l13 (16 kDa, Protein from Staphylococcus aureus subsp. aureus NCTC 8325)
N-formylmethionine (177 Da, Ligand)
50s ribosomal protein l16 (16 kDa, Protein from Staphylococcus aureus subsp. aureus NCTC 8325)
50s ribosomal protein l25 (23 kDa, Protein from Staphylococcus aureus subsp. aureus NCTC 8325)
30s ribosomal protein s13 (13 kDa, Protein from Staphylococcus aureus subsp. aureus NCTC 8325)
50s ribosomal protein l21 (11 kDa, Protein from Staphylococcus aureus subsp. aureus NCTC 8325)
30s ribosomal protein s2 (29 kDa, Protein from Staphylococcus aureus subsp. aureus NCTC 8325)

[Show more]

EMD-12334

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VgaL, an antibiotic resistance ABCF, in complex with 70S ribosome from Listeria monocytogenes

Release date: May 5, 2021
Resolution: 2.9 Å
EM Method: Single-particle
Fitted PDBs: 7nhn
Q-score: 0.534

Crowe-McAuliffe C, Murina V, Turnbull KJ, Kasari M, Mohamad M, Polte C, Takada H, Vaitkevicius K, Johansson J, Ignatova Z, Atkinson GC, O'Neill AJ, Hauryliuk V, Wilson DN

Nat Commun (2021) 12 pp. 3577-3577 [ Pubmed: 34117249 DOI: doi:10.1038/s41467-021-23753-1 ]

Sample:

50s ribosomal protein l6 (19 kDa, Protein from Listeria monocytogenes EGD-e)
50s ribosomal protein l15 (15 kDa, Protein from Listeria monocytogenes EGD-e)
30s ribosomal protein s9 (14 kDa, Protein from Listeria monocytogenes EGD-e)
50s ribosomal protein l34 (5 kDa, Protein from Listeria monocytogenes EGD-e)
30s ribosomal protein s3 (24 kDa, Protein from Listeria monocytogenes EGD-e)
50s ribosomal protein l2 (30 kDa, Protein from Listeria monocytogenes EGD-e)
30s ribosomal protein s8 (14 kDa, Protein from Listeria monocytogenes EGD-e)
Adenosine-5'-triphosphate (507 Da, Ligand)
50s ribosomal protein l20 (13 kDa, Protein from Listeria monocytogenes EGD-e)
Zinc ion (65 Da, Ligand)
Rna (5'-r(p*gp*ap*gp*gp*up*np*np*np*np*np*np*ap*up*g)-3') (3 kDa, RNA from Listeria monocytogenes EGD-e)
30s ribosomal protein s19 (10 kDa, Protein from Listeria monocytogenes EGD-e)
30s ribosomal protein s12 (15 kDa, Protein from Listeria monocytogenes EGD-e)
30s ribosomal protein s15 (10 kDa, Protein from Listeria monocytogenes EGD-e)
Lmo0919 protein (64 kDa, Protein from Listeria monocytogenes EGD-e)
50s ribosomal protein l19 (13 kDa, Protein from Listeria monocytogenes EGD-e)
Spermidine (145 Da, Ligand)
50s ribosomal protein l21 (11 kDa, Protein from Listeria monocytogenes EGD-e)
50s ribosomal protein l23 (10 kDa, Protein from Listeria monocytogenes EGD-e)
30s ribosomal protein s5 (17 kDa, Protein from Listeria monocytogenes EGD-e)
50s ribosomal protein l32-2 (6 kDa, Protein from Listeria monocytogenes EGD-e)
30s ribosomal protein s18 (9 kDa, Protein from Listeria monocytogenes EGD-e)
50s ribosomal protein l18 (13 kDa, Protein from Listeria monocytogenes EGD-e)
50s ribosomal protein l5 (20 kDa, Protein from Listeria monocytogenes EGD-e)
30s ribosomal protein s16 (10 kDa, Protein from Listeria monocytogenes EGD-e)
30s ribosomal protein s10 (11 kDa, Protein from Listeria monocytogenes EGD-e)
Trna-fmet (24 kDa, RNA from Listeria monocytogenes EGD-e)
30s ribosomal protein s17 (10 kDa, Protein from Listeria monocytogenes EGD-e)
Potassium ion (39 Da, Ligand)
50s ribosomal protein l31 type b (9 kDa, Protein from Listeria monocytogenes EGD-e)
50s ribosomal protein l36 (4 kDa, Protein from Listeria monocytogenes EGD-e)
30s ribosomal protein s13 (13 kDa, Protein from Listeria monocytogenes EGD-e)
5s rrna (36 kDa, RNA from Listeria monocytogenes EGD-E)
50s ribosomal protein l22 (12 kDa, Protein from Listeria monocytogenes EGD-e)
30s ribosomal protein s7 (17 kDa, Protein from Listeria monocytogenes EGD-e)
30s ribosomal protein s14 type z (7 kDa, Protein from Listeria monocytogenes EGD-e)
30s ribosomal protein s4 (22 kDa, Protein from Listeria monocytogenes EGD-e)
16s rrna (499 kDa, RNA from Listeria monocytogenes EGD-e)
50s ribosomal protein l29 (7 kDa, Protein from Listeria monocytogenes EGD-e)
30s ribosomal protein s20 (9 kDa, Protein from Listeria monocytogenes EGD-e)
Vgal in complex with 70s ribosome, mrna, and distorted p-trna from listeria monocytogenes (2 MDa, Complex from Listeria monocytogenes EGD-e)
50s ribosomal protein l30 (6 kDa, Protein from Listeria monocytogenes EGD-e)
50s ribosomal protein l33 1 (6 kDa, Protein from Listeria monocytogenes EGD-e)
50s ribosomal protein l4 (22 kDa, Protein from Listeria monocytogenes EGD-e)
23s rrna (949 kDa, RNA from Listeria monocytogenes EGD-e)
50s ribosomal protein l16 (16 kDa, Protein from Listeria monocytogenes EGD-e)
50s ribosomal protein l13 (16 kDa, Protein from Listeria monocytogenes EGD-e)
50s ribosomal protein l24 (11 kDa, Protein from Listeria monocytogenes EGD-e)
50s ribosomal protein l14 (13 kDa, Protein from Listeria monocytogenes EGD-e)
30s ribosomal protein s6 (11 kDa, Protein from Listeria monocytogenes EGD-e)
50s ribosomal protein l3 (22 kDa, Protein from Listeria monocytogenes EGD-e)
30s ribosomal protein s2 (28 kDa, Protein from Listeria monocytogenes EGD-e)
50s ribosomal protein l27 (10 kDa, Protein from Listeria monocytogenes EGD-e)
30s ribosomal protein s11 (13 kDa, Protein from Listeria monocytogenes EGD-e)
50s ribosomal protein l28 (7 kDa, Protein from Listeria monocytogenes EGD-e)
Magnesium ion (24 Da, Ligand)
50s ribosomal protein l17 (15 kDa, Protein from Listeria monocytogenes EGD-e)
50s ribosomal protein l35 (7 kDa, Protein from Listeria monocytogenes EGD-e)

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EMD-0137

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Structure of a hibernating 100S ribosome reveals an inactive conformation of the ribosomal protein S1 - 70S Hibernating E. coli Ribosome

Release date: Sept. 5, 2018
Resolution: 3.0 Å
EM Method: Single-particle
Fitted PDBs: 6h4n
Q-score: 0.523

Beckert B, Turk M, Czech A, Berninghausen O, Beckmann R, Ignatova Z, Plitzko JM, Wilson DN

Nat Microbiol (2018) 3 pp. 1115-1121 [ Pubmed: 30177741 DOI: doi:10.1038/s41564-018-0237-0 ]

Sample:

50s ribosomal protein l28 (8 kDa, Protein from Escherichia coli BW25113)
50s ribosomal protein l16 (15 kDa, Protein from Escherichia coli BW25113)
50s ribosomal protein l6 (18 kDa, Protein from Escherichia coli BW25113)
50s ribosomal protein l2 (29 kDa, Protein from Escherichia coli BW25113)
50s ribosomal protein l20 (13 kDa, Protein from Escherichia coli BW25113)
30s ribosomal protein s7 (18 kDa, Protein from Escherichia coli BW25113)
30s ribosomal protein s20 (9 kDa, Protein from Escherichia coli BW25113)
30s ribosomal protein s1 (61 kDa, Protein from Escherichia coli BW25113)
50s ribosomal protein l23 (10 kDa, Protein from Escherichia coli BW25113)
30s ribosomal protein s18 (7 kDa, Protein from Escherichia coli BW25113)
50s ribosomal protein l17 (13 kDa, Protein from Escherichia coli BW25113)
50s ribosomal protein l25 (10 kDa, Protein from Escherichia coli BW25113)
Trna (24 kDa, RNA from Escherichia coli BW25113)
30s ribosomal protein s21 (7 kDa, Protein from Escherichia coli BW25113)
50s ribosomal protein l29 (7 kDa, Protein from Escherichia coli BW25113)
30s ribosomal protein s6 (11 kDa, Protein from Escherichia coli BW25113)
50s ribosomal protein l27 (8 kDa, Protein from Escherichia coli BW25113)
50s ribosomal protein l5 (20 kDa, Protein from Escherichia coli BW25113)
50s ribosomal protein l13 (16 kDa, Protein from Escherichia coli BW25113)
50s ribosomal protein l34 (5 kDa, Protein from Escherichia coli BW25113)
30s ribosomal protein s17 (9 kDa, Protein from Escherichia coli BW25113)
Ribosome modulation factor (6 kDa, Protein from Escherichia coli BW25113)
50s ribosomal protein l14 (13 kDa, Protein from Escherichia coli BW25113)
30s ribosomal protein s8 (14 kDa, Protein from Escherichia coli BW25113)
30s ribosomal protein s14 (11 kDa, Protein from Escherichia coli BW25113)
50s ribosomal protein l22 (12 kDa, Protein from Escherichia coli BW25113)
50s ribosomal protein l32 (6 kDa, Protein from Escherichia coli BW25113)
30s ribosomal protein s16 (9 kDa, Protein from Escherichia coli BW25113)
50s ribosomal protein l33 (5 kDa, Protein from Escherichia coli BW25113)
16s ribosomal rna (497 kDa, RNA from Escherichia coli BW25113)
50s ribosomal protein l35 (7 kDa, Protein from Escherichia coli BW25113)
30s ribosomal protein s5 (16 kDa, Protein from Escherichia coli BW25113)
50s ribosomal protein l21 (11 kDa, Protein from Escherichia coli BW25113)
50s ribosomal protein l31 (7 kDa, Protein from Escherichia coli BW25113)
30s ribosomal protein s10 (11 kDa, Protein from Escherichia coli BW25113)
30s ribosomal protein s9 (14 kDa, Protein from Escherichia coli BW25113)
Ribosome hibernation promoting factor (10 kDa, Protein from Escherichia coli BW25113)
30s ribosomal protein s2 (24 kDa, Protein from Escherichia coli BW25113)
50s ribosomal protein l30 (6 kDa, Protein from Escherichia coli BW25113)
Structure of a hibernating 100s ribosome reveals an inactive conformation of the ribosomal protein s1 (Complex from Escherichia coli BW25113)
50s ribosomal protein l15 (14 kDa, Protein from Escherichia coli BW25113)
50s ribosomal protein l18 (12 kDa, Protein from Escherichia coli BW25113)
50s ribosomal protein l19 (13 kDa, Protein from Escherichia coli BW25113)
50s ribosomal protein l24 (11 kDa, Protein from Escherichia coli BW25113)
50s ribosomal protein l4 (22 kDa, Protein from Escherichia coli BW25113)
50s ribosomal protein l36 (4 kDa, Protein from Escherichia coli BW25113)
30s ribosomal protein s3 (23 kDa, Protein from Escherichia coli BW25113)
30s ribosomal protein s19 (9 kDa, Protein from Escherichia coli BW25113)
50s ribosomal protein l9 (15 kDa, Protein from Escherichia coli BW25113)
30s ribosomal protein s12 (13 kDa, Protein from Escherichia coli BW25113)
30s ribosomal protein s4 (23 kDa, Protein from Escherichia coli BW25113)
5s ribosomal rna (38 kDa, RNA from Escherichia coli BW25113)
Rna (5'-r(p*cp*up*cp*cp*u)-3') (1 kDa, RNA from Escherichia coli BW25113)
30s ribosomal protein s15 (10 kDa, Protein from Escherichia coli BW25113)
23s ribosomal rna (941 kDa, RNA from Escherichia coli BW25113)
50s ribosomal protein l3 (22 kDa, Protein from Escherichia coli BW25113)
30s ribosomal protein s13 (12 kDa, Protein from Escherichia coli BW25113)
30s ribosomal protein s11 (12 kDa, Protein from Escherichia coli BW25113)

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EMD-0139

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Structure of a hibernating 100S ribosome reveals an inactive conformation of the ribosomal protein S1 - Full 100S Hibernating E. coli Ribosome

Release date: Sept. 5, 2018
Resolution: 7.9 Å
EM Method: Single-particle
Fitted PDBs: 6h58
Q-score: 0.122

Beckert B, Turk M, Czech A, Berninghausen O, Beckmann R, Ignatova Z, Plitzko JM, Wilson DN

Nat Microbiol (2018) 3 pp. 1115-1121 [ Pubmed: 30177741 DOI: doi:10.1038/s41564-018-0237-0 ]

Sample:

50s ribosomal protein l28 (8 kDa, Protein from Escherichia coli BW25113)
50s ribosomal protein l16 (15 kDa, Protein from Escherichia coli BW25113)
50s ribosomal protein l6 (18 kDa, Protein from Escherichia coli BW25113)
50s ribosomal protein l2 (29 kDa, Protein from Escherichia coli BW25113)
50s ribosomal protein l20 (13 kDa, Protein from Escherichia coli BW25113)
30s ribosomal protein s7 (18 kDa, Protein from Escherichia coli BW25113)
30s ribosomal protein s20 (9 kDa, Protein from Escherichia coli BW25113)
30s ribosomal protein s1 (61 kDa, Protein from Escherichia coli BW25113)
50s ribosomal protein l23 (10 kDa, Protein from Escherichia coli BW25113)
16s ribosomal rna (498 kDa, RNA from Escherichia coli BW25113)
30s ribosomal protein s18 (7 kDa, Protein from Escherichia coli BW25113)
50s ribosomal protein l17 (13 kDa, Protein from Escherichia coli BW25113)
50s ribosomal protein l25 (10 kDa, Protein from Escherichia coli BW25113)
30s ribosomal protein s21 (7 kDa, Protein from Escherichia coli BW25113)
50s ribosomal protein l29 (7 kDa, Protein from Escherichia coli BW25113)
50s ribosomal protein l27 (8 kDa, Protein from Escherichia coli BW25113)
30s ribosomal protein s6 (11 kDa, Protein from Escherichia coli BW25113)
50s ribosomal protein l5 (20 kDa, Protein from Escherichia coli BW25113)
50s ribosomal protein l13 (16 kDa, Protein from Escherichia coli BW25113)
30s ribosomal protein s17 (9 kDa, Protein from Escherichia coli BW25113)
Ribosome modulation factor (6 kDa, Protein from Escherichia coli BW25113)
50s ribosomal protein l14 (13 kDa, Protein from Escherichia coli BW25113)
50s ribosomal protein l32 (6 kDa, Protein from Escherichia coli BW25113)
50s ribosomal protein l22 (12 kDa, Protein from Escherichia coli BW25113)
30s ribosomal protein s8 (14 kDa, Protein from Escherichia coli BW25113)
30s ribosomal protein s14 (11 kDa, Protein from Escherichia coli BW25113)
Trna mixture (24 kDa, RNA from Escherichia coli BW25113)
30s ribosomal protein s16 (9 kDa, Protein from Escherichia coli BW25113)
50s ribosomal protein l33 (5 kDa, Protein from Escherichia coli BW25113)
50s ribosomal protein l35 (7 kDa, Protein from Escherichia coli BW25113)
50s ribosomal protein l21 (11 kDa, Protein from Escherichia coli BW25113)
30s ribosomal protein s5 (16 kDa, Protein from Escherichia coli BW25113)
50s ribosomal protein l31 (7 kDa, Protein from Escherichia coli BW25113)
30s ribosomal protein s2 (25 kDa, Protein from Escherichia coli BW25113)
30s ribosomal protein s10 (11 kDa, Protein from Escherichia coli BW25113)
30s ribosomal protein s9 (14 kDa, Protein from Escherichia coli BW25113)
Ribosome hibernation promoting factor (10 kDa, Protein from Escherichia coli BW25113)
50s ribosomal protein l30 (6 kDa, Protein from Escherichia coli BW25113)
50s ribosomal protein l15 (14 kDa, Protein from Escherichia coli BW25113)
Structure of a hibernating 100s ribosome reveals an inactive conformation of the ribosomal protein s1 (Complex from Escherichia coli BW25113)
50s ribosomal protein l18 (12 kDa, Protein from Escherichia coli BW25113)
50s ribosomal protein l19 (13 kDa, Protein from Escherichia coli BW25113)
50s ribosomal protein l24 (11 kDa, Protein from Escherichia coli BW25113)
50s ribosomal protein l4 (22 kDa, Protein from Escherichia coli BW25113)
50s ribosomal protein l36 (4 kDa, Protein from Escherichia coli BW25113)
30s ribosomal protein s11 (12 kDa, Protein from Escherichia coli BW25113)
30s ribosomal protein s3 (23 kDa, Protein from Escherichia coli BW25113)
30s ribosomal protein s19 (9 kDa, Protein from Escherichia coli BW25113)
50s ribosomal protein l9 (15 kDa, Protein from Escherichia coli BW25113)
5s ribosomal rna (38 kDa, RNA from Escherichia coli BW25113)
30s ribosomal protein s4 (23 kDa, Protein from Escherichia coli BW25113)
30s ribosomal protein s12 (13 kDa, Protein from Escherichia coli BW25113)
30s ribosomal protein s15 (10 kDa, Protein from Escherichia coli BW25113)
23s ribosomal rna (941 kDa, RNA from Escherichia coli BW25113)
50s ribosomal protein l3 (22 kDa, Protein from Escherichia coli BW25113)
30s ribosomal protein s13 (12 kDa, Protein from Escherichia coli BW25113)
50s ribosomal protein l34 (5 kDa, Protein from Escherichia coli BW25113)

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