Electron Microscopy Data Bank

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EMD-33065

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The SARS-CoV-2 receptor binding domain bound with the Fab fragment of a human neutralizing antibody Ab765

Release date: March 22, 2023
Resolution: 3.3 Å
EM Method: Single-particle
Fitted PDBs: 7x93
Q-score: 0.486

Takeshita M, Fukuyama H, Kamada K, Matsumoto T, Makino-Okamura C, Lin Q, Sakuma M, Kawahara E, Yamazaki I, Uchikubo-Kamo T, Tomabechi Y, Hanada K, Hisano T, Moriyama S, Takahashi Y, Ito M, Imai M, Maemura T, Furusawa Y, Yamayoshi S, Kawaoka Y, Shirouzu M, Ishii M, Saya H, Kondo Y, Kaneko Y, Suzuki K, Fukunaga K, Takeuchi T

iScience (2023) 26 pp. 106955-106955 [ DOI: doi:10.1016/j.isci.2023.106955 Pubmed: 37288342 ]

Sample:

Ab765 heavy chain (28 kDa, Protein from Homo sapiens)
The sars-cov-2 spike protein bound with the fab fragment of a human neutralizing antibody ab354 (560 kDa, Complex from Homo sapiens)
Ab765 light chain (25 kDa, Protein from Homo sapiens)
Spike glycoprotein (141 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)

[Show more]

EMD-33066

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The SARS-CoV-2 receptor binding domain bound with the Fab fragment of a human neutralizing antibody Ab712

Release date: March 22, 2023
Resolution: 4.0 Å
EM Method: Single-particle
Fitted PDBs: 7x94
Q-score: 0.359

iScience (2023) 26 pp. 106955-106955 [ DOI: doi:10.1016/j.isci.2023.106955 Pubmed: 37288342 ]

Sample:

Ab712 heavy chain (29 kDa, Protein from Homo sapiens)
Spike glycoprotein (141 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
The sars-cov-2 spike protein bound with the fab fragment of a human neutralizing antibody ab712 (560 kDa, Complex from Homo sapiens)
Ab712 light chain (25 kDa, Protein from Homo sapiens)

[Show more]

EMD-33067

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The SARS-CoV-2 receptor binding domain bound with the Fab fragment of a human neutralizing antibody Ab709

Release date: March 22, 2023
Resolution: 3.9 Å
EM Method: Single-particle
Fitted PDBs: 7x95
Q-score: 0.386

iScience (2023) 26 pp. 106955-106955 [ DOI: doi:10.1016/j.isci.2023.106955 Pubmed: 37288342 ]

Sample:

Ab709 heavy chain (28 kDa, Protein from Homo sapiens)
Ab709 light chain (25 kDa, Protein from Homo sapiens)
Spike glycoprotein (141 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
The sars-cov-2 spike protein bound with the fab fragment of a human neutralizing antibody ab709 (560 kDa, Complex from Homo sapiens)

[Show more]

EMD-33068

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The SARS-CoV-2 receptor binding domain bound with the Fab fragment of a human neutralizing antibody Ab847

Release date: March 22, 2023
Resolution: 3.4 Å
EM Method: Single-particle
Fitted PDBs: 7x96
Q-score: 0.46

iScience (2023) 26 pp. 106955-106955 [ DOI: doi:10.1016/j.isci.2023.106955 Pubmed: 37288342 ]

Sample:

Ab847 light chain (26 kDa, Protein from Homo sapiens)
Ab847 heavy chain (28 kDa, Protein from Homo sapiens)
Spike glycoprotein (141 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
The sars-cov-2 spike protein bound with the fab fragment of a human neutralizing antibody ab847 (560 kDa, Complex from Homo sapiens)

[Show more]

EMD-10223

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Cryo-EM Structure of T. kodakarensis 70S ribosome

Release date: July 29, 2020
Resolution: 2.95 Å
EM Method: Single-particle
Fitted PDBs: 6skf
Q-score: 0.597

Sas-Chen A, Thomas JM, Matzov D, Taoka M, Nance KD, Nir R, Bryson KM, Shachar R, Liman GLS, Burkhart BW, Gamage ST, Nobe Y, Briney CA, Levy MJ, Fuchs RT, Robb GB, Hartmann J, Sharma S, Lin Q, Florens L, Washburn MP, Isobe T, Santangelo TJ, Shalev-Benami M, Meier JL, Schwartz S

Nature (2020) 583 pp. 638-643 [ DOI: doi:10.1038/s41586-020-2418-2 Pubmed: 32555463 ]

Sample:

50s ribosomal protein l37ae (9 kDa, Protein from Thermococcus kodakarensis)
50s ribosomal protein l44e (11 kDa, Protein from Thermococcus kodakarensis)
30s ribosomal protein s9 (15 kDa, Protein from Thermococcus kodakarensis)
50s ribosomal protein l18 (22 kDa, Protein from Thermococcus kodakarensis)
50s ribosomal protein l10e (21 kDa, Protein from Thermococcus kodakarensis)
50s ribosomal protein l15e (22 kDa, Protein from Thermococcus kodakarensis)
50s ribosomal protein l39e (6 kDa, Protein from Thermococcus kodakarensis)
30s ribosomal protein s27e (7 kDa, Protein from Thermococcus kodakarensis)
30s ribosomal protein s3ae (23 kDa, Protein from Thermococcus kodakarensis)
50s ribosomal protein l21e (11 kDa, Protein from Thermococcus kodakarensis)
30s ribosomal protein s24e (11 kDa, Protein from Thermococcus kodakarensis)
Zinc ion (65 Da, Ligand)
50s ribosomal protein l30 (17 kDa, Protein from Thermococcus kodakarensis)
50s ribosomal protein l19e (17 kDa, Protein from Thermococcus kodakarensis)
50s ribosomal protein l37e (7 kDa, Protein from Thermococcus kodakarensis)
30s ribosomal protein s19e (17 kDa, Protein from Thermococcus kodakarensis)
50s ribosomal protein l15 (16 kDa, Protein from Thermococcus kodakarensis)
30s ribosomal protein s6e (13 kDa, Protein from Thermococcus kodakarensis)
23s rrna (990 kDa, RNA from Thermococcus kodakarensis)
30s ribosomal protein s10 (11 kDa, Protein from Thermococcus kodakarensis)
30s ribosomal protein s8e (14 kDa, Protein from Thermococcus kodakarensis)
Predicted zinc-ribbon rna-binding protein involved in translation (7 kDa, Protein from Thermococcus kodakarensis)
50s ribosomal protein l22 (17 kDa, Protein from Thermococcus kodakarensis)
Water (18 Da, Ligand)
5s rrna (40 kDa, RNA from Thermococcus kodakarensis)
50s ribosomal protein l24 (14 kDa, Protein from Thermococcus kodakarensis)
50s ribosomal protein l7ae (13 kDa, Protein from Thermococcus kodakarensis)
30s ribosomal protein s8 (14 kDa, Protein from Thermococcus kodakarensis)
30s ribosomal protein s4e (27 kDa, Protein from Thermococcus kodakarensis)
50s ribosomal protein l29 (7 kDa, Protein from Thermococcus kodakarensis)
30s ribosomal protein s17 (13 kDa, Protein from Thermococcus kodakarensis)
50s ribosomal protein l4 (28 kDa, Protein from Thermococcus kodakarensis)
50s ribosomal protein l6 (20 kDa, Protein from Thermococcus kodakarensis)
30s ribosomal protein s17e (8 kDa, Protein from Thermococcus kodakarensis)
50s ribosomal protein l18ae (9 kDa, Protein from Thermococcus kodakarensis)
50s ribosomal protein l31e (10 kDa, Protein from Thermococcus kodakarensis)
70s ribosome from thermococcus kodakarensis (Complex from Thermococcus kodakarensis)
50s ribosomal protein l34e (10 kDa, Protein from Thermococcus kodakarensis)
30s ribosomal protein s3 (23 kDa, Protein from Thermococcus kodakarensis)
50s ribosomal protein l24e (8 kDa, Protein from Thermococcus kodakarensis)
50s ribosomal protein l3 (39 kDa, Protein from Thermococcus kodakarensis)
30s ribosomal protein s13 (17 kDa, Protein from Thermococcus kodakarensis)
30s ribosomal protein s15 (17 kDa, Protein from Thermococcus kodakarensis)
50s ribosomal protein l2 (26 kDa, Protein from Thermococcus kodakarensis)
30s ribosomal protein s4 (21 kDa, Protein from Thermococcus kodakarensis)
50s ribosomal protein l5 (21 kDa, Protein from Thermococcus kodakarensis)
50s ribosomal protein l14 (15 kDa, Protein from Thermococcus kodakarensis)
50s ribosomal protein l18e (13 kDa, Protein from Thermococcus kodakarensis)
30s ribosomal protein s14 type z (6 kDa, Protein from Thermococcus kodakarensis)
30s ribosomal protein s28e (7 kDa, Protein from Thermococcus kodakarensis)
50s ribosomal protein l30e (10 kDa, Protein from Thermococcus kodakarensis)
50s ribosomal protein l13 (16 kDa, Protein from Thermococcus kodakarensis)
50s ribosomal protein l40e (5 kDa, Protein from Thermococcus kodakarensis)
50s ribosomal protein l14e (8 kDa, Protein from Thermococcus kodakarensis)
Lsu ribosomal protein l41e (5 kDa, Protein from Thermococcus kodakarensis)
30s ribosomal protein s19 (15 kDa, Protein from Thermococcus kodakarensis)
30s ribosomal protein s11 (15 kDa, Protein from Thermococcus kodakarensis)
30s ribosomal protein s12 (16 kDa, Protein from Thermococcus kodakarensis)
30s ribosomal protein s5 (26 kDa, Protein from Thermococcus kodakarensis)
50s ribosomal protein l32e (14 kDa, Protein from Thermococcus kodakarensis)
16s rrna (488 kDa, RNA from Thermococcus kodakarensis)
50s ribosomal protein l23 (9 kDa, Protein from Thermococcus kodakarensis)
30s ribosomal protein s7 (24 kDa, Protein from Thermococcus kodakarensis)
30s ribosomal protein s2 (23 kDa, Protein from Thermococcus kodakarensis)

[Show more]

EMD-10224

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Cryo-EM Structure of T. kodakarensis 70S ribosome in TkNat10 deleted strain

Release date: July 29, 2020
Resolution: 2.65 Å
EM Method: Single-particle
Fitted PDBs: 6skg
Q-score: 0.614

Nature (2020) 583 pp. 638-643 [ DOI: doi:10.1038/s41586-020-2418-2 Pubmed: 32555463 ]

Sample:

50s ribosomal protein l37ae (9 kDa, Protein from Thermococcus kodakarensis)
50s ribosomal protein l44e (11 kDa, Protein from Thermococcus kodakarensis)
30s ribosomal protein s9 (15 kDa, Protein from Thermococcus kodakarensis)
50s ribosomal protein l18 (22 kDa, Protein from Thermococcus kodakarensis)
50s ribosomal protein l10e (21 kDa, Protein from Thermococcus kodakarensis)
50s ribosomal protein l15e (22 kDa, Protein from Thermococcus kodakarensis)
50s ribosomal protein l39e (6 kDa, Protein from Thermococcus kodakarensis)
30s ribosomal protein s27e (7 kDa, Protein from Thermococcus kodakarensis)
30s ribosomal protein s3ae (23 kDa, Protein from Thermococcus kodakarensis)
50s ribosomal protein l21e (11 kDa, Protein from Thermococcus kodakarensis)
30s ribosomal protein s24e (11 kDa, Protein from Thermococcus kodakarensis)
Zinc ion (65 Da, Ligand)
50s ribosomal protein l30 (17 kDa, Protein from Thermococcus kodakarensis)
50s ribosomal protein l19e (17 kDa, Protein from Thermococcus kodakarensis)
Predicted exosome subunit, upf0023 family (26 kDa, Protein from Thermococcus kodakarensis)
50s ribosomal protein l37e (7 kDa, Protein from Thermococcus kodakarensis)
30s ribosomal protein s19e (17 kDa, Protein from Thermococcus kodakarensis)
50s ribosomal protein l15 (16 kDa, Protein from Thermococcus kodakarensis)
30s ribosomal protein s6e (13 kDa, Protein from Thermococcus kodakarensis)
16s ribosomal rna (487 kDa, RNA from Thermococcus kodakarensis)
30s ribosomal protein s10 (11 kDa, Protein from Thermococcus kodakarensis)
30s ribosomal protein s8e (14 kDa, Protein from Thermococcus kodakarensis)
5s ribosomal rna (40 kDa, RNA from Thermococcus kodakarensis)
Predicted zinc-ribbon rna-binding protein involved in translation (7 kDa, Protein from Thermococcus kodakarensis)
50s ribosomal protein l22 (17 kDa, Protein from Thermococcus kodakarensis)
Water (18 Da, Ligand)
50s ribosomal protein l24 (14 kDa, Protein from Thermococcus kodakarensis)
50s ribosomal protein l7ae (13 kDa, Protein from Thermococcus kodakarensis)
30s ribosomal protein s8 (14 kDa, Protein from Thermococcus kodakarensis)
30s ribosomal protein s4e (27 kDa, Protein from Thermococcus kodakarensis)
50s ribosomal protein l29 (7 kDa, Protein from Thermococcus kodakarensis)
30s ribosomal protein s17 (13 kDa, Protein from Thermococcus kodakarensis)
50s ribosomal protein l4 (28 kDa, Protein from Thermococcus kodakarensis)
50s ribosomal protein l6 (20 kDa, Protein from Thermococcus kodakarensis)
30s ribosomal protein s17e (8 kDa, Protein from Thermococcus kodakarensis)
50s ribosomal protein l18ae (9 kDa, Protein from Thermococcus kodakarensis)
50s ribosomal protein l31e (10 kDa, Protein from Thermococcus kodakarensis)
70s ribosome from thermococcus kodakarensis (Complex from Thermococcus kodakarensis)
50s ribosomal protein l34e (10 kDa, Protein from Thermococcus kodakarensis)
Unknown ribosomal protein (2 kDa, Protein from Thermococcus kodakarensis)
30s ribosomal protein s3 (23 kDa, Protein from Thermococcus kodakarensis)
50s ribosomal protein l24e (8 kDa, Protein from Thermococcus kodakarensis)
50s ribosomal protein l3 (39 kDa, Protein from Thermococcus kodakarensis)
30s ribosomal protein s15 (17 kDa, Protein from Thermococcus kodakarensis)
30s ribosomal protein s13 (17 kDa, Protein from Thermococcus kodakarensis)
50s ribosomal protein l2 (26 kDa, Protein from Thermococcus kodakarensis)
30s ribosomal protein s4 (21 kDa, Protein from Thermococcus kodakarensis)
50s ribosomal protein l5 (21 kDa, Protein from Thermococcus kodakarensis)
50s ribosomal protein l14 (15 kDa, Protein from Thermococcus kodakarensis)
Ribosomal protein el35a (11 kDa, Protein from Thermococcus kodakarensis)
23s ribosomal rna (987 kDa, RNA from Thermococcus kodakarensis)
30s ribosomal protein s14 type z (6 kDa, Protein from Thermococcus kodakarensis)
30s ribosomal protein s28e (7 kDa, Protein from Thermococcus kodakarensis)
50s ribosomal protein l30e (10 kDa, Protein from Thermococcus kodakarensis)
50s ribosomal protein l13 (16 kDa, Protein from Thermococcus kodakarensis)
50s ribosomal protein l40e (5 kDa, Protein from Thermococcus kodakarensis)
50s ribosomal protein l14e (8 kDa, Protein from Thermococcus kodakarensis)
Lsu ribosomal protein l41e (5 kDa, Protein from Thermococcus kodakarensis)
30s ribosomal protein s19 (15 kDa, Protein from Thermococcus kodakarensis)
30s ribosomal protein s11 (15 kDa, Protein from Thermococcus kodakarensis)
30s ribosomal protein s12 (16 kDa, Protein from Thermococcus kodakarensis)
30s ribosomal protein s5 (26 kDa, Protein from Thermococcus kodakarensis)
50s ribosomal protein l32e (14 kDa, Protein from Thermococcus kodakarensis)
Nucleic acid-binding protein, containing c2h2 zinc-finger (5 kDa, Protein from Thermococcus kodakarensis)
50s ribosomal protein l18e (13 kDa, Protein from Thermococcus kodakarensis)
50s ribosomal protein l23 (9 kDa, Protein from Thermococcus kodakarensis)
30s ribosomal protein s7 (24 kDa, Protein from Thermococcus kodakarensis)
30s ribosomal protein s2 (23 kDa, Protein from Thermococcus kodakarensis)

[Show more]

EMD-10503

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Cryo-EM Structure of T. kodakarensis 70S ribosome

Release date: July 29, 2020
Resolution: 2.55 Å
EM Method: Single-particle
Fitted PDBs: 6th6
Q-score: 0.622

Nature (2020) 583 pp. 638-643 [ DOI: doi:10.1038/s41586-020-2418-2 Pubmed: 32555463 ]

Sample:

30s ribosomal protein s17e (8 kDa, Protein from Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1))
30s ribosomal protein s8e (14 kDa, Protein from Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1))
50s ribosomal protein l24e (8 kDa, Protein from Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1))
30s ribosomal protein s24e (11 kDa, Protein from Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1))
50s ribosomal protein l10e (21 kDa, Protein from Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1))
50s ribosomal protein l14 (15 kDa, Protein from Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1))
50s ribosomal protein l23 (9 kDa, Protein from Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1))
30s ribosomal protein s15 (17 kDa, Protein from Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1))
50s ribosomal protein l18 (22 kDa, Protein from Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1))
Zinc ion (65 Da, Ligand)
30s ribosomal protein s3 (23 kDa, Protein from Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1))
50s ribosomal protein l29 (7 kDa, Protein from Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1))
50s ribosomal protein l15 (16 kDa, Protein from Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1))
30s ribosomal protein s14 type z (6 kDa, Protein from Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1))
30s ribosomal protein s2 (23 kDa, Protein from Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1))
50s ribosomal protein l6 (20 kDa, Protein from Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1))
Lsu ribosomal protein l41e (5 kDa, Protein from Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1))
50s ribosomal protein l3 (39 kDa, Protein from Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1))
Predicted zinc-ribbon rna-binding protein involved in translation (7 kDa, Protein from Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1))
50s ribosomal protein l32e (14 kDa, Protein from Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1))
30s ribosomal protein s28e (7 kDa, Protein from Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1))
30s ribosomal protein s11 (15 kDa, Protein from Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1))
30s ribosomal protein s9 (15 kDa, Protein from Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1))
50s ribosomal protein l14e (8 kDa, Protein from Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1))
30s ribosomal protein s12 (16 kDa, Protein from Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1))
50s ribosomal protein l30e (10 kDa, Protein from Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1))
50s ribosomal protein l40e (5 kDa, Protein from Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1))
Water (18 Da, Ligand)
70s ribosome from thermococcus kodakarensis (Complex from Thermococcus kodakarensis)
30s ribosomal protein s4e (27 kDa, Protein from Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1))
30s ribosomal protein s19e (17 kDa, Protein from Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1))
50s ribosomal protein l5 (21 kDa, Protein from Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1))
50s ribosomal protein l4 (28 kDa, Protein from Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1))
30s ribosomal protein s13 (17 kDa, Protein from Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1))
30s ribosomal protein s8 (14 kDa, Protein from Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1))
30s ribosomal protein s3ae (23 kDa, Protein from Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1))
50s ribosomal protein l21e (11 kDa, Protein from Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1))
50s ribosomal protein l22 (17 kDa, Protein from Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1))
30s ribosomal protein s19 (15 kDa, Protein from Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1))
50s ribosomal protein l15e (22 kDa, Protein from Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1))
50s ribosomal protein l24 (14 kDa, Protein from Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1))
30s ribosomal protein s10 (11 kDa, Protein from Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1))
50s ribosomal protein l39e (6 kDa, Protein from Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1))
50s ribosomal protein l31e (10 kDa, Protein from Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1))
50s ribosomal protein l37e (7 kDa, Protein from Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1))
50s ribosomal protein l18e (13 kDa, Protein from Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1))
23s ribosomal rna (987 kDa, RNA from Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1))
30s ribosomal protein s5 (26 kDa, Protein from Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1))
50s ribosomal protein l7ae (13 kDa, Protein from Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1))
50s ribosomal protein l19e (17 kDa, Protein from Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1))
50s ribosomal protein l37ae (9 kDa, Protein from Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1))
30s ribosomal protein s17 (13 kDa, Protein from Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1))
50s ribosomal protein l30 (17 kDa, Protein from Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1))
50s ribosomal protein l18ae (9 kDa, Protein from Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1))
16s ribosomal rna (486 kDa, RNA from Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1))
30s ribosomal protein s6e (13 kDa, Protein from Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1))
50s ribosomal protein l2 (26 kDa, Protein from Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1))
50s ribosomal protein l13 (16 kDa, Protein from Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1))
50s ribosomal protein l34e (10 kDa, Protein from Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1))
50s ribosomal protein l44e (11 kDa, Protein from Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1))
5s ribosomal rna (40 kDa, RNA from Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1))
30s ribosomal protein s27e (7 kDa, Protein from Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1))
30s ribosomal protein s4 (21 kDa, Protein from Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1))
30s ribosomal protein s7 (24 kDa, Protein from Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1))

[Show more]

EMD-8937

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Cryo-EM Structure of Mycobacterium smegmatis C(minus) 50S ribosomal subunit

Release date: Oct. 3, 2018
Resolution: 3.42 Å
EM Method: Single-particle
Fitted PDBs: 6dzp
Q-score: 0.464

Li Y, Sharma MR, Koripella RK, Yang Y, Kaushal PS, Lin Q, Wade JT, Gray TA, Derbyshire KM, Agrawal RK, Ojha AK

PNAS (2018) 115 pp. 8191-8196 [ DOI: doi:10.1073/pnas.1804555115 Pubmed: 30038002 ]

Sample:

50s ribosomal protein l11 (15 kDa, Protein from Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155))
50s ribosomal protein l35 (7 kDa, Protein from Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155))
50s ribosomal protein l22 (16 kDa, Protein from Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155))
Uncharacterized protein (2 kDa, Protein from Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155))
50s ribosomal protein l2 (30 kDa, Protein from Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155))
50s ribosomal protein l9 (15 kDa, Protein from Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155))
50s ribosomal protein l16 (15 kDa, Protein from Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155))
50s ribosomal protein l25 (22 kDa, Protein from Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155))
50s ribosomal protein l36 (4 kDa, Protein from Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155))
50s ribosomal protein l30 (7 kDa, Protein from Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155))
50s ribosomal protein l15 (15 kDa, Protein from Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155))
50s ribosomal protein l13 (16 kDa, Protein from Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155))
50s ribosomal protein l18 (13 kDa, Protein from Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155))
50s ribosomal protein l21 (10 kDa, Protein from Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155))
50s ribosomal protein l28 (8 kDa, Protein from Mycobacterium smegmatis str. MC2 155)
23s rrna (1 MDa, RNA from Mycobacterium smegmatis str. MC2 155)
50s ribosomal protein l19 (12 kDa, Protein from Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155))
50s ribosomal protein l33 2 (6 kDa, Protein from Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155))
50s ribosomal protein l24 (11 kDa, Protein from Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155))
5s rrna (38 kDa, RNA from Mycobacterium smegmatis str. MC2 155)
50s ribosomal protein l17 (21 kDa, Protein from Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155))
50s ribosomal protein l20 (14 kDa, Protein from Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155))
50s ribosomal protein l4 (22 kDa, Protein from Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155))
50s ribosomal protein l6 (19 kDa, Protein from Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155))
50s ribosomal protein l14 (13 kDa, Protein from Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155))
50s ribosomal protein l34 (5 kDa, Protein from Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155))
50s ribosomal protein l23 (10 kDa, Protein from Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155))
50s ribosomal protein l27 (9 kDa, Protein from Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155))
50s ribosomal protein l29 (8 kDa, Protein from Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155))
50s ribosomal protein l5 (21 kDa, Protein from Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155))
50s ribosomal protein l31 (9 kDa, Protein from Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155))
Mycobacterium smegmatis c(minus) 70s ribosome with mpy (Complex from Mycobacterium smegmatis str. MC2 155)
50s ribosomal protein l32 (6 kDa, Protein from Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155))
50s ribosomal protein l3 (23 kDa, Protein from Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155))
50s ribosomal protein l10 (18 kDa, Protein from Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155))

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EMD-8932

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Cryo-EM Structure of Mycobacterium smegmatis 70S C(minus) ribosome 70S-MPY complex

Release date: Sept. 26, 2018
Resolution: 3.46 Å
EM Method: Single-particle
Fitted PDBs: 6dzi
Q-score: 0.438

Li Y, Sharma MR, Koripella RK, Yang Y, Kaushal PS, Lin Q, Wade JT, Gray TA, Derbyshire KM, Agrawal RK, Ojha AK

PNAS (2018) 115 pp. 8191-8196 [ DOI: doi:10.1073/pnas.1804555115 Pubmed: 30038002 ]

Sample:

30s ribosomal protein s8 (14 kDa, Protein from Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155))
50s ribosomal protein l22 (12 kDa, Protein from Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155))
50s ribosomal protein l33 2 (6 kDa, Protein from Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155))
30s ribosomal protein s15 (10 kDa, Protein from Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155))
30s ribosomal protein s20 (9 kDa, Protein from Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155))
50s ribosomal protein l30 (6 kDa, Protein from Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155))
5s rna (118-mer) (38 kDa, RNA from Mycobacterium smegmatis str. MC2 155)
Uncharacterized protein (2 kDa, Protein from Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155))
50s ribosomal protein l11 (14 kDa, Protein from Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155))
50s ribosomal protein l9 (15 kDa, Protein from Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155))
50s ribosomal protein l20 (14 kDa, Protein from Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155))
30s ribosomal protein s10 (11 kDa, Protein from Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155))
50s ribosomal protein l23 (10 kDa, Protein from Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155))
50s ribosomal protein l36 (4 kDa, Protein from Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155))
30s ribosomal protein s2 (25 kDa, Protein from Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155))
50s ribosomal protein l4 (22 kDa, Protein from Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155))
50s ribosomal protein l5 (20 kDa, Protein from Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155))
50s ribosomal protein l16 (15 kDa, Protein from Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155))
50s ribosomal protein l34 (5 kDa, Protein from Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155))
30s ribosomal protein s16 (12 kDa, Protein from Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155))
23 s rrna (3119-mer) (1 MDa, RNA from Mycobacterium smegmatis str. MC2 155)
50s ribosomal protein l13 (16 kDa, Protein from Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155))
50s ribosomal protein l18 (13 kDa, Protein from Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155))
50s ribosomal protein l6 (19 kDa, Protein from Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155))
50s ribosomal protein l19 (12 kDa, Protein from Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155))
50s ribosomal protein l24 (11 kDa, Protein from Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155))
50s ribosomal protein l3 (22 kDa, Protein from Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155))
50s ribosomal protein l27 (8 kDa, Protein from Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155))
30s ribosomal protein s17 (10 kDa, Protein from Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155))
16s rrna (490 kDa, RNA from Mycobacterium smegmatis str. MC2 155)
50s ribosomal protein l14 (13 kDa, Protein from Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155))
Ribosome hibernation promoting factor (12 kDa, Protein from Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155))
30s ribosomal protein s5 (18 kDa, Protein from Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155))
50s ribosomal protein l29 (7 kDa, Protein from Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155))
50s ribosomal protein l32 (6 kDa, Protein from Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155))
30s ribosomal protein s13 (13 kDa, Protein from Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155))
30s ribosomal protein s4 (23 kDa, Protein from Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155))
30s ribosomal protein s7 (17 kDa, Protein from Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155))
30s ribosomal protein s6 (10 kDa, Protein from Mycobacterium smegmatis)
30s ribosomal protein s12 (13 kDa, Protein from Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155))
30s ribosomal protein s19 (9 kDa, Protein from Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155))
70s-mpy complex (Complex from Mycobacterium smegmatis str. MC2 155)
50s ribosomal protein l35 (7 kDa, Protein from Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155))
50s ribosomal protein l21 (10 kDa, Protein from Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155))
50s ribosomal protein l31 (9 kDa, Protein from Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155))
50s ribosomal protein l25 (20 kDa, Protein from Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155))
30s ribosomal protein s11 (12 kDa, Protein from Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155))
30s ribosomal protein s18 1 (9 kDa, Protein from Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155))
Conserved protein domain (4 kDa, Protein from Mycobacterium smegmatis str. MC2 155)
30s ribosomal protein s9 (14 kDa, Protein from Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155))
50s ribosomal protein l28 (8 kDa, Protein from Mycobacterium smegmatis str. MC2 155)
30s ribosomal protein s14 (11 kDa, Protein from Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155))
50s ribosomal protein l15 (15 kDa, Protein from Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155))
50s ribosomal protein l2 (30 kDa, Protein from Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155))
30s ribosomal protein s3 (23 kDa, Protein from Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155))
50s ribosomal protein l10 (13 kDa, Protein from Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155))
50s ribosomal protein l17 (13 kDa, Protein from Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155))

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EMD-8934

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Cryo-EM Structure of Mycobacterium smegmatis C(minus) 30S ribosomal subunit with MPY

Release date: Sept. 19, 2018
Resolution: 3.6 Å
EM Method: Single-particle
Fitted PDBs: 6dzk
Q-score: 0.419

Li Y, Sharma MR, Koripella RK, Yang Y, Kaushal PS, Lin Q, Wade JT, Gray TA, Derbyshire KM, Agrawal RK, Ojha AK

PNAS (2018) 115 pp. 8191-8196 [ DOI: doi:10.1073/pnas.1804555115 Pubmed: 30038002 ]

Sample:

30s ribosomal protein s8 (14 kDa, Protein from Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155))
30s ribosomal protein s4 (23 kDa, Protein from Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155))
30s ribosomal protein s15 (10 kDa, Protein from Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155))
Conserved domain protein (4 kDa, Protein from Mycobacterium smegmatis str. MC2 155)
30s ribosomal protein s9 (16 kDa, Protein from Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155))
30s ribosomal protein s5 (21 kDa, Protein from Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155))
30s ribosomal protein s19 (10 kDa, Protein from Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155))
30s ribosomal protein s17 (11 kDa, Protein from Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155))
30s ribosomal protein s12 (13 kDa, Protein from Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155))
Mycobacterium smegmatis (cminus) 70s with mpy (Complex from Mycobacterium smegmatis str. MC2 155)
30s ribosomal protein s7 (17 kDa, Protein from Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155))
30s ribosomal protein s13 (14 kDa, Protein from Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155))
16s rrna (490 kDa, RNA from Mycobacterium smegmatis str. MC2 155)
30s ribosomal protein s18 1 (9 kDa, Protein from Mycobacterium smegmatis)
30s ribosomal protein s6 (10 kDa, Protein from Mycobacterium smegmatis)
30s ribosomal protein s3 (30 kDa, Protein from Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155))
50s ribosomal protein l31 (9 kDa, Protein from Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155))
30s ribosomal protein s20 (9 kDa, Protein from Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155))
Ribosome hibernation promoting factor (26 kDa, Protein from Mycobacterium smegmatis)
30s ribosomal protein s16 (16 kDa, Protein from Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155))
30s ribosomal protein s14 (11 kDa, Protein from Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155))
30s ribosomal protein s11 (14 kDa, Protein from Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155))
30s ribosomal protein s10 (11 kDa, Protein from Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155))
30s ribosomal protein s2 (30 kDa, Protein from Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155))

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