Resolution: 2.9 Å
EM Method: Single-particle
Fitted PDBs: 8sq9
Q-score: 0.528
Small GI, Fedorova O, Olinares PDB, Chandanani J, Banerjee A, Choi YJ, Molina H, Chait BT, Darst SA, Campbell EA
Mol Cell (2023) 83 pp. 3921-3930.e7 [ Pubmed: 37890482 DOI: doi:10.1016/j.molcel.2023.10.001 ]
- Zinc ion (65 Da, Ligand)
- Magnesium ion (24 Da, Ligand)
- Non-structural protein 9 (12 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Rna-directed rna polymerase (106 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Sars-cov-2 replication-transcription complex bound to nsp9 and umpcpp, as a pre-catalytic nmpylation intermediate (Complex from Severe acute respiratory syndrome coronavirus 2)
- Template rna (17 kDa, RNA from Severe acute respiratory syndrome coronavirus)
- Non-structural protein 7 (9 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Primer rna (11 kDa, RNA from Severe acute respiratory syndrome coronavirus)
- Non-structural protein 8 (21 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Water (18 Da, Ligand)
- 5'-o-[(s)-hydroxy{[(s)-hydroxy(phosphonooxy)phosphoryl]methyl}phosphoryl]uridine (482 Da, Ligand)
SARS Cov2 Spike RBD in complex with Fab47
Resolution: 2.64 Å
EM Method: Single-particle
Fitted PDBs: 8a95
Q-score: 0.269
Pushparaj P, Nicoletto A, Sheward DJ, Das H, Castro Dopico X, Perez Vidakovics L, Hanke L, Chernyshev M, Narang S, Kim S, Fischbach J, Ekstrom S, McInerney G, Hallberg BM, Murrell B, Corcoran M, Karlsson Hedestam GB
Immunity (2023) 56 pp. 193-206.e7 [ DOI: doi:10.1016/j.immuni.2022.12.005 Pubmed: 36574772 ]
- Fab47 (heavy chain variable domain) (13 kDa, Protein from Homo sapiens)
- Sars-cov2 trimeric spike in 1-up conformation in complex with three fab47 (142 kDa, Protein from Severe acute respiratory syndrome coronavirus)
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
- Fab47 (light chain variable domain) (11 kDa, Protein from Homo sapiens)
- Sars-cov-2 spike in complex with fab47 (629 MDa, Complex from Homo sapiens)
Structure of the Ancestral Scaffold Antigen-5 of Coronavirus Spike protein
Resolution: 2.59 Å
EM Method: Single-particle
Fitted PDBs: 8aja
Q-score: 0.604
Hueting D, Schriever K, Sun R, Vlachiotis S, Zuo F, Du L, Persson H, Hofstrom C, Ohlin M, Wallden K, Buggert M, Hammarstrom L, Marcotte H, Pan-Hammarstrom Q, Andrell J, Syren PO
Nat Commun (2023) 14 pp. 6527-6527 [ DOI: doi:10.1038/s41467-023-42200-x Pubmed: 37845250 ]
Structure of the Ancestral Scaffold Antigen-6 of Coronavirus Spike protein
Resolution: 2.77 Å
EM Method: Single-particle
Fitted PDBs: 8ajl
Q-score: 0.555
Hueting D, Schriever K, Sun R, Vlachiotis S, Zuo F, Du L, Persson H, Hofstrom C, Ohlin M, Wallden K, Buggert M, Hammarstrom L, Marcotte H, Pan-Hammarstrom Q, Andrell J, Syren PO
Nat Commun (2023) 14 pp. 6527-6527 [ DOI: doi:10.1038/s41467-023-42200-x Pubmed: 37845250 ]
Cryo-EM structure of SARS-CoV-2 postfusion spike in membrane
Resolution: 2.9 Å
EM Method: Single-particle
Fitted PDBs: 8fdw
Q-score: 0.327
Shi W, Cai Y, Zhu H, Peng H, Voyer J, Rits-Volloch S, Cao H, Mayer ML, Song K, Xu C, Lu J, Zhang J, Chen B
Nature (2023) 619 pp. 403-409 [ DOI: doi:10.1038/s41586-023-06273-4 Pubmed: 37285872 ]
- Spike protein s2 (68 kDa, Protein from Severe acute respiratory syndrome coronavirus)
- Sras-cov-2 postfusion spike protein in nanodisc (210 kDa, Complex from Severe acute respiratory syndrome coronavirus 2)
- Alpha-d-mannopyranose (180 Da, Ligand)
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
SARS CoV2 Spike in the 2-up state in complex with Fab47
Resolution: 2.4 Å
EM Method: Single-particle
Fitted PDBs: 8a94
Q-score: 0.303
Pushparaj P, Nicoletto A, Sheward DJ, Das H, Castro Dopico X, Perez Vidakovics L, Hanke L, Chernyshev M, Narang S, Kim S, Fischbach J, Ekstrom S, McInerney G, Hallberg BM, Murrell B, Corcoran M, Karlsson Hedestam GB
Immunity (2023) 56 pp. 193-206.e7 [ DOI: doi:10.1016/j.immuni.2022.12.005 Pubmed: 36574772 ]
- Sars-cov2 spike in 2-up conformation in complex with fab47 (142 kDa, Protein from Severe acute respiratory syndrome coronavirus)
- Fab47 (heavy chain variable domain) (13 kDa, Protein from Homo sapiens)
- Fab47 (light chain variable domain) (11 kDa, Protein from Homo sapiens)
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
- Sars-cov-2 spike in complex with fab47 (629 MDa, Complex from Homo sapiens)
SARS Cov2 Spike RBD in complex with Fab47
Resolution: 2.7 Å
EM Method: Single-particle
Fitted PDBs: 8a96
Q-score: 0.421
Pushparaj P, Nicoletto A, Sheward DJ, Das H, Castro Dopico X, Perez Vidakovics L, Hanke L, Chernyshev M, Narang S, Kim S, Fischbach J, Ekstrom S, McInerney G, Hallberg BM, Murrell B, Corcoran M, Karlsson Hedestam GB
Immunity (2023) 56 pp. 193-206.e7 [ Pubmed: 36574772 DOI: doi:10.1016/j.immuni.2022.12.005 ]
- Fab47 light chain (variable domain) (11 kDa, Protein from Homo sapiens)
- Spike protein s1 (23 kDa, Protein from Severe acute respiratory syndrome coronavirus)
- Fab47 heavy chain (variable domain) (13 kDa, Protein from Homo sapiens)
- Sars-cov-2 spike in complex with fab47 (629 MDa, Complex from Homo sapiens)
Resolution: 2.57 Å
EM Method: Single-particle
Fitted PDBs: 8h0x
Q-score: 0.614
Zhang X, Li Z, Zhang Y, Liu Y, Wang J, Liu B, Chen Q, Wang Q, Fu L, Wang P, Zhong X, Jin L, Yan Q, Chen L, He J, Zhao J, Xiong X
Life Sci Alliance (2023) 6 [ Pubmed: 37402591 DOI: doi:10.26508/lsa.202201796 ]
- Biliverdine ix alpha (582 Da, Ligand)
- Spike glycoprotein (136 kDa, Protein from Severe acute respiratory syndrome coronavirus)
- Sars-cov-1 spike protein (410 kDa, Complex from Severe acute respiratory syndrome coronavirus)
- Linoleic acid (280 Da, Ligand)
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
Resolution: 2.85 Å
EM Method: Single-particle
Fitted PDBs: 8h0y
Q-score: 0.59
Zhang X, Li Z, Zhang Y, Liu Y, Wang J, Liu B, Chen Q, Wang Q, Fu L, Wang P, Zhong X, Jin L, Yan Q, Chen L, He J, Zhao J, Xiong X
Life Sci Alliance (2023) 6 [ Pubmed: 37402591 DOI: doi:10.26508/lsa.202201796 ]
- Biliverdine ix alpha (582 Da, Ligand)
- Spike glycoprotein (136 kDa, Protein from Severe acute respiratory syndrome coronavirus)
- Sars-cov-1 spike protein (410 kDa, Complex from Severe acute respiratory syndrome coronavirus)
- Linoleic acid (280 Da, Ligand)
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
Resolution: 2.99 Å
EM Method: Single-particle
Fitted PDBs: 8h0z
Q-score: 0.56
Zhang X, Li Z, Zhang Y, Liu Y, Wang J, Liu B, Chen Q, Wang Q, Fu L, Wang P, Zhong X, Jin L, Yan Q, Chen L, He J, Zhao J, Xiong X
Life Sci Alliance (2023) 6 [ Pubmed: 37402591 DOI: doi:10.26508/lsa.202201796 ]
- Biliverdine ix alpha (582 Da, Ligand)
- Spike glycoprotein (136 kDa, Protein from Severe acute respiratory syndrome coronavirus)
- Sars-cov-1 spike protein (410 kDa, Complex from Severe acute respiratory syndrome coronavirus)
- Linoleic acid (280 Da, Ligand)
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)