Electron Microscopy Data Bank

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Cryo-EM structure of the T=4 lake sinai virus 2 virus-like capsid at pH 7.5

Release date: Feb. 8, 2023
Resolution: 3.24 Å
EM Method: Single-particle
Fitted PDBs: 7xgz
Q-score: 0.314

Chen NC, Wang CH, Yoshimura M, Yeh YQ, Guan HH, Chuankhayan P, Lin CC, Lin PJ, Huang YC, Wakatsuki S, Ho MC, Chen CJ

Nat Commun (2023) 14 pp. 545- [ DOI: doi:10.1038/s41467-023-36235-3 ]

Sample:

Lake sinai virus 2 (Virus from Lake Sinai virus 2)
Capsid protein alpha (57 kDa, Protein from Lake Sinai virus 2)

EMD-33368

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Cryo-EM structure of the T=3 lake sinai virus 2 virus-like capsid at pH 7.5

Release date: Feb. 8, 2023
Resolution: 3.33 Å
EM Method: Single-particle
Fitted PDBs: 7xpa
Q-score: 0.338

Chen NC, Wang CH, Yoshimura M, Yeh YQ, Guan HH, Chuankhayan P, Lin CC, Lin PJ, Huang YC, Wakatsuki S, Ho MC, Chen CJ

Nat Commun (2023) 14 pp. 545-545 [ DOI: doi:10.1038/s41467-023-36235-3 Pubmed: 36726015 ]

Sample:

Lake sinai virus 2 (Virus from Lake Sinai virus 2)
Capsid protein alpha (57 kDa, Protein from Lake Sinai virus 2)

EMD-33369

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Cryo-EM structure of the T=4 lake sinai virus 2 virus-like capsid at pH 6.5

Release date: Feb. 8, 2023
Resolution: 3.91 Å
EM Method: Single-particle
Fitted PDBs: 7xpb
Q-score: 0.288

Chen NC, Wang CH, Yoshimura M, Yeh YQ, Guan HH, Chuankhayan P, Lin CC, Lin PJ, Huang YC, Wakatsuki S, Ho MC, Chen CJ

Nat Commun (2023) 14 pp. 545-545 [ DOI: doi:10.1038/s41467-023-36235-3 Pubmed: 36726015 ]

Sample:

Lake sinai virus 2 (Virus from Lake Sinai virus 2)
Capsid protein alpha (57 kDa, Protein from Lake Sinai virus 2)

EMD-33370

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Cryo-EM structure of the T=3 lake sinai virus 2 virus-like capsid at pH 6.5

Release date: Feb. 8, 2023
Resolution: 3.74 Å
EM Method: Single-particle
Fitted PDBs: 7xpd
Q-score: 0.271

Chen NC, Wang CH, Yoshimura M, Yeh YQ, Guan HH, Chuankhayan P, Lin CC, Lin PJ, Huang YC, Wakatsuki S, Ho MC, Chen CJ

Nat Commun (2023) 14 pp. 545-545 [ DOI: doi:10.1038/s41467-023-36235-3 Pubmed: 36726015 ]

Sample:

Lake sinai virus 2 (Virus from Lake Sinai virus 2)
Capsid protein alpha (57 kDa, Protein from Lake Sinai virus 2)

EMD-33371

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Cryo-EM structure of the T=4 lake sinai virus 2 virus-like capsid at pH 8.5

Release date: Feb. 8, 2023
Resolution: 3.32 Å
EM Method: Single-particle
Fitted PDBs: 7xpe
Q-score: 0.325

Chen NC, Wang CH, Yoshimura M, Yeh YQ, Guan HH, Chuankhayan P, Lin CC, Lin PJ, Huang YC, Wakatsuki S, Ho MC, Chen CJ

Nat Commun (2023) 14 pp. 545-545 [ DOI: doi:10.1038/s41467-023-36235-3 Pubmed: 36726015 ]

Sample:

Lake sinai virus 2 (Virus from Lake Sinai virus 2)
Capsid protein alpha (57 kDa, Protein from Lake Sinai virus 2)

EMD-33372

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Cryo-EM structure of the T=3 lake sinai virus 2 virus-like capsid at pH 8.5

Release date: Feb. 8, 2023
Resolution: 3.13 Å
EM Method: Single-particle
Fitted PDBs: 7xpf
Q-score: 0.351

Chen NC, Wang CH, Yoshimura M, Yeh YQ, Guan HH, Chuankhayan P, Lin CC, Lin PJ, Huang YC, Wakatsuki S, Ho MC, Chen CJ

Nat Commun (2023) 14 pp. 545-545 [ DOI: doi:10.1038/s41467-023-36235-3 Pubmed: 36726015 ]

Sample:

Lake sinai virus 2 (Virus from Lake Sinai virus 2)
Capsid protein alpha (57 kDa, Protein from Lake Sinai virus 2)

EMD-33373

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Cryo-EM structure of the T=3 lake sinai virus 1 (delta-N48) virus-like capsid at pH 6.5

Release date: Feb. 8, 2023
Resolution: 3.51 Å
EM Method: Single-particle
Fitted PDBs: 7xpg
Q-score: 0.205

Chen NC, Wang CH, Yoshimura M, Yeh YQ, Guan HH, Chuankhayan P, Lin CC, Lin PJ, Huang YC, Wakatsuki S, Ho MC, Chen CJ

Nat Commun (2023) 14 pp. 545-545 [ DOI: doi:10.1038/s41467-023-36235-3 Pubmed: 36726015 ]

Sample:

Lake sinai virus 2 (Virus from Lake Sinai virus 2)
Rna (5'-r(p*up*g)-3') (606 Da, RNA from Escherichia coli)
Capsid protein alpha (62 kDa, Protein from Lake Sinai virus 1)

EMD-12215

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pre-50S-ObgE particle state 1

Release date: May 12, 2021
Resolution: 3.7 Å
EM Method: Single-particle
Fitted PDBs: 7bl2
Q-score: 0.328

Nikolay R, Hilal T, Schmidt S, Qin B, Schwefel D, Vieira-Vieira CH, Mielke T, Burger J, Loerke J, Amikura K, Flugel T, Ueda T, Selbach M, Deuerling E, Spahn CMT

Mol Cell (2021) 81 pp. 1200-1215.e9 [ DOI: doi:10.1016/j.molcel.2021.02.006 Pubmed: 33639093 ]

Sample:

50s ribosomal protein l18 (12 kDa, Protein from Escherichia coli (strain K12))
50s ribosomal protein l9 (15 kDa, Protein from Escherichia coli (strain K12))
50s ribosomal protein l33 (6 kDa, Protein from Escherichia coli (strain K12))
50s ribosomal protein l23 (11 kDa, Protein from Escherichia coli (strain K12))
5s ribosomal rna (38 kDa, RNA from Escherichia coli (strain K12))
50s ribosomal protein l19 (13 kDa, Protein from Escherichia coli (strain K12))
50s ribosomal protein l29 (7 kDa, Protein from Escherichia coli (strain K12))
50s ribosomal protein l25 (10 kDa, Protein from Escherichia coli (strain K12))
50s ribosomal protein l30 (6 kDa, Protein from Escherichia coli (strain K12))
50s ribosomal protein l32 (6 kDa, Protein from Escherichia coli (strain K12))
50s ribosomal protein l4 (22 kDa, Protein from Escherichia coli (strain K12))
50s ribosomal protein l14 (13 kDa, Protein from Escherichia coli (strain K12))
50s ribosomal protein l5 (20 kDa, Protein from Escherichia coli (strain K12))
50s ribosomal protein l3 (22 kDa, Protein from Escherichia coli (strain K12))
50s ribosomal protein l20 (13 kDa, Protein from Escherichia coli (strain K12))
50s ribosomal protein l13 (16 kDa, Protein from Escherichia coli (strain K12))
23s ribosomal rna (946 kDa, RNA from Escherichia coli (strain K12))
Ribosomal silencing factor rsfs (11 kDa, Protein from Escherichia coli (strain K12))
50s ribosomal protein l31 (7 kDa, Protein from Escherichia coli (strain K12))
Water (18 Da, Ligand)
50s ribosomal protein l17 (14 kDa, Protein from Escherichia coli (strain K12))
Gtpase obge/cgta (43 kDa, Protein from Escherichia coli (strain K12))
50s ribosomal protein l28 (9 kDa, Protein from Escherichia coli (strain K12))
50s ribosomal protein l27 (9 kDa, Protein from Escherichia coli (strain K12))
50s ribosomal protein l22 (12 kDa, Protein from Escherichia coli (strain K12))
Magnesium ion (24 Da, Ligand)
50s ribosomal protein l24 (11 kDa, Protein from Escherichia coli (strain K12))
50s ribosomal protein l34 (5 kDa, Protein from Escherichia coli (strain K12))
50s ribosomal protein l6 (18 kDa, Protein from Escherichia coli (strain K12))
Zinc ion (65 Da, Ligand)
50s ribosomal protein l11 (14 kDa, Protein from Escherichia coli (strain K12))
50s ribosomal protein l2 (29 kDa, Protein from Escherichia coli (strain K12))
Assembly intermediate complex 1 (1 MDa, Complex from Escherichia coli (strain K12))
50s ribosomal protein l15 (15 kDa, Protein from Escherichia coli (strain K12))
50s ribosomal protein l21 (11 kDa, Protein from Escherichia coli (strain K12))

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EMD-12216

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pre-50S-ObgE particle state 2

Release date: May 12, 2021
Resolution: 3.5 Å
EM Method: Single-particle
Fitted PDBs: 7bl3
Q-score: 0.362

Nikolay R, Hilal T, Schmidt S, Qin B, Schwefel D, Vieira-Vieira CH, Mielke T, Burger J, Loerke J, Amikura K, Flugel T, Ueda T, Selbach M, Deuerling E, Spahn CMT

Mol Cell (2021) 81 pp. 1200-1215.e9 [ DOI: doi:10.1016/j.molcel.2021.02.006 Pubmed: 33639093 ]

Sample:

50s ribosomal protein l18 (12 kDa, Protein from Escherichia coli (strain K12))
50s ribosomal protein l9 (15 kDa, Protein from Escherichia coli (strain K12))
Ribosomal pre-50s assembly intermediate state 2 (1 MDa, Complex from Escherichia coli (strain K12))
50s ribosomal protein l33 (6 kDa, Protein from Escherichia coli (strain K12))
50s ribosomal protein l23 (11 kDa, Protein from Escherichia coli (strain K12))
5s ribosomal rna (38 kDa, RNA from Escherichia coli (strain K12))
50s ribosomal protein l19 (13 kDa, Protein from Escherichia coli (strain K12))
50s ribosomal protein l29 (7 kDa, Protein from Escherichia coli (strain K12))
50s ribosomal protein l25 (10 kDa, Protein from Escherichia coli (strain K12))
50s ribosomal protein l30 (6 kDa, Protein from Escherichia coli (strain K12))
50s ribosomal protein l32 (6 kDa, Protein from Escherichia coli (strain K12))
50s ribosomal protein l4 (22 kDa, Protein from Escherichia coli (strain K12))
50s ribosomal protein l14 (13 kDa, Protein from Escherichia coli (strain K12))
50s ribosomal protein l5 (20 kDa, Protein from Escherichia coli (strain K12))
50s ribosomal protein l3 (22 kDa, Protein from Escherichia coli (strain K12))
50s ribosomal protein l20 (13 kDa, Protein from Escherichia coli (strain K12))
50s ribosomal protein l13 (16 kDa, Protein from Escherichia coli (strain K12))
23s ribosomal rna (946 kDa, RNA from Escherichia coli (strain K12))
Ribosomal silencing factor rsfs (11 kDa, Protein from Escherichia coli (strain K12))
50s ribosomal protein l31 (7 kDa, Protein from Escherichia coli (strain K12))
Water (18 Da, Ligand)
50s ribosomal protein l17 (14 kDa, Protein from Escherichia coli (strain K12))
Gtpase obge/cgta (43 kDa, Protein from Escherichia coli (strain K12))
50s ribosomal protein l28 (9 kDa, Protein from Escherichia coli (strain K12))
50s ribosomal protein l27 (9 kDa, Protein from Escherichia coli (strain K12))
50s ribosomal protein l22 (12 kDa, Protein from Escherichia coli (strain K12))
Magnesium ion (24 Da, Ligand)
50s ribosomal protein l24 (11 kDa, Protein from Escherichia coli (strain K12))
50s ribosomal protein l34 (5 kDa, Protein from Escherichia coli (strain K12))
50s ribosomal protein l6 (18 kDa, Protein from Escherichia coli (strain K12))
Zinc ion (65 Da, Ligand)
50s ribosomal protein l11 (14 kDa, Protein from Escherichia coli (strain K12))
50s ribosomal protein l2 (29 kDa, Protein from Escherichia coli (strain K12))
50s ribosomal protein l15 (15 kDa, Protein from Escherichia coli (strain K12))
50s ribosomal protein l21 (11 kDa, Protein from Escherichia coli (strain K12))

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EMD-12218

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pre-50S-ObgE particle

Release date: May 12, 2021
Resolution: 3.3 Å
EM Method: Single-particle
Fitted PDBs: 7bl5
Q-score: 0.363

Nikolay R, Hilal T, Schmidt S, Qin B, Schwefel D, Vieira-Vieira CH, Mielke T, Burger J, Loerke J, Amikura K, Flugel T, Ueda T, Selbach M, Deuerling E, Spahn CMT

Mol Cell (2021) 81 pp. 1200-1215.e9 [ DOI: doi:10.1016/j.molcel.2021.02.006 Pubmed: 33639093 ]

Sample:

23s ribosomal rna (946 kDa, RNA from Escherichia coli str. K-12 substr. MG1655)
Upf0307 protein yjga (21 kDa, Protein from Escherichia coli str. K-12 substr. MG1655)
50s ribosomal protein l4 (22 kDa, Protein from Escherichia coli str. K-12 substr. MG1655)
Ribosomal large subunit pseudouridine synthase d (37 kDa, Protein from Escherichia coli str. K-12 substr. MG1655)
Guanosine-5'-diphosphate (443 Da, Ligand)
50s ribosomal protein l28 (9 kDa, Protein from Escherichia coli str. K-12 substr. MG1655)
50s ribosomal protein l22 (12 kDa, Protein from Escherichia coli str. K-12 substr. MG1655)
50s ribosomal protein l11 (14 kDa, Protein from Escherichia coli str. K-12 substr. MG1655)
50s ribosomal protein l34 (5 kDa, Protein from Escherichia coli str. K-12 substr. MG1655)
50s ribosomal protein l30 (6 kDa, Protein from Escherichia coli str. K-12 substr. MG1655)
50s ribosomal protein l5 (20 kDa, Protein from Escherichia coli str. K-12 substr. MG1655)
50s ribosomal protein l33 (6 kDa, Protein from Escherichia coli str. K-12 substr. MG1655)
50s ribosomal protein l25 (10 kDa, Protein from Escherichia coli str. K-12 substr. MG1655)
50s ribosomal protein l3 (22 kDa, Protein from Escherichia coli str. K-12 substr. MG1655)
Assembly intermediate complex 3 (1 MDa, Complex from Escherichia coli str. K-12 substr. MG1655)
50s ribosomal protein l29 (7 kDa, Protein from Escherichia coli str. K-12 substr. MG1655)
5s ribosomal rna (38 kDa, RNA from Escherichia coli str. K-12 substr. MG1655)
50s ribosomal protein l32 (6 kDa, Protein from Escherichia coli str. K-12 substr. MG1655)
Water (18 Da, Ligand)
50s ribosomal protein l17 (14 kDa, Protein from Escherichia coli str. K-12 substr. MG1655)
50s ribosomal protein l16 (15 kDa, Protein from Escherichia coli str. K-12 substr. MG1655)
Gtpase obge/cgta (43 kDa, Protein from Escherichia coli str. K-12 substr. MG1655)
Magnesium ion (24 Da, Ligand)
50s ribosomal protein l27 (9 kDa, Protein from Escherichia coli str. K-12 substr. MG1655)
50s ribosomal protein l23 (11 kDa, Protein from Escherichia coli str. K-12 substr. MG1655)
50s ribosomal protein l13 (16 kDa, Protein from Escherichia coli str. K-12 substr. MG1655)
Ribosomal silencing factor rsfs (11 kDa, Protein from Escherichia coli str. K-12 substr. MG1655)
50s ribosomal protein l15 (15 kDa, Protein from Escherichia coli str. K-12 substr. MG1655)
50s ribosomal protein l2 (29 kDa, Protein from Escherichia coli str. K-12 substr. MG1655)
Zinc ion (65 Da, Ligand)
50s ribosomal protein l6 (18 kDa, Protein from Escherichia coli str. K-12 substr. MG1655)
50s ribosomal protein l31 (7 kDa, Protein from Escherichia coli str. K-12 substr. MG1655)
50s ribosomal protein l21 (11 kDa, Protein from Escherichia coli str. K-12 substr. MG1655)
50s ribosomal protein l19 (13 kDa, Protein from Escherichia coli str. K-12 substr. MG1655)
50s ribosomal protein l24 (11 kDa, Protein from Escherichia coli str. K-12 substr. MG1655)
50s ribosomal protein l14 (13 kDa, Protein from Escherichia coli str. K-12 substr. MG1655)
50s ribosomal protein l18 (12 kDa, Protein from Escherichia coli str. K-12 substr. MG1655)
50s ribosomal protein l20 (13 kDa, Protein from Escherichia coli str. K-12 substr. MG1655)
50s ribosomal protein l9 (15 kDa, Protein from Escherichia coli str. K-12 substr. MG1655)
50s ribosomal protein l10 (17 kDa, Protein from Escherichia coli str. K-12 substr. MG1655)

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