The complex structure of Omicron BA.4 RBD with BD604, S309, and S304
Resolution: 2.36 Å
EM Method: Single-particle
Fitted PDBs: 8hws
Q-score: 0.472
He Q, Wu L, Xu Z, Wang X, Xie Y, Chai Y, Zheng A, Zhou J, Qiao S, Huang M, Shang G, Zhao X, Feng Y, Qi J, Gao GF, Wang Q
Cell Rep Med (2023) 4 pp. 100991-100991 [ Pubmed: 37019110 DOI: doi:10.1016/j.xcrm.2023.100991 ]
- S304 fab light chain (23 kDa, Protein from Homo sapiens)
- S304 fab heavy chain (24 kDa, Protein from Homo sapiens)
- S309 fab heavy chain (25 kDa, Protein from Homo sapiens)
- S309 fab light chain (23 kDa, Protein from Homo sapiens)
- Omicron ba.4/5 rbd in complex with fabs of bd-604, s304 and s309 (Complex from Homo sapiens)
- Bd-604 fab light chain (23 kDa, Protein from Homo sapiens)
- Bd-604 fab heavy chain (24 kDa, Protein from Homo sapiens)
- Spike protein s2' (22 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
SARS-CoV-2 Omicron BA.2 RBD complexed with BD-604 and S304 Fab
Resolution: 2.91 Å
EM Method: Single-particle
Fitted PDBs: 8hwt
Q-score: 0.448
He Q, Wu L, Xu Z, Wang X, Xie Y, Chai Y, Zheng A, Zhou J, Qiao S, Huang M, Shang G, Zhao X, Feng Y, Qi J, Gao GF, Wang Q
Cell Rep Med (2023) 4 pp. 100991-100991 [ Pubmed: 37019110 DOI: doi:10.1016/j.xcrm.2023.100991 ]
- Bd-604 heavy chain (24 kDa, Protein from Homo sapiens)
- Bd-604 light chain (23 kDa, Protein from Homo sapiens)
- Spike protein s2' (25 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Sars-cov-2 omicron ba.2 rbd complexed with bd-604 and s304 fab (Complex from Homo sapiens)
- S304 heavy chain (24 kDa, Protein from Homo sapiens)
- S304 light chain (23 kDa, Protein from Homo sapiens)
Cryo-EM structure of SARS-CoV-2 Omicron spike protein (S-6P-RRAR) in complex with S309 fab
Resolution: 2.5 Å
EM Method: Single-particle
Fitted PDBs: 7xco
Q-score: 0.433
Zhao Z, Zhou J, Tian M, Huang M, Liu S, Xie Y, Han P, Bai C, Han P, Zheng A, Fu L, Gao Y, Peng Q, Li Y, Chai Y, Zhang Z, Zhao X, Song H, Qi J, Wang Q, Wang P, Gao GF
Nat Commun (2022) 13 pp. 4958- [ DOI: doi:10.1038/s41467-022-32665-7 ]
- Cryo-em structure of sars-cov-2 omicron spike protein in complex with s309 fab (Complex from Severe acute respiratory syndrome coronavirus 2)
- S309 fab (Complex)
- Sars-cov-2 omicron spike protein (Complex from Homo sapiens)
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
- S309 fab heavy chain (24 kDa, Protein from Homo sapiens)
- Spike glycoprotein (138 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- S309 fab light chain (23 kDa, Protein from Homo sapiens)
Resolution: 2.85 Å
EM Method: Single-particle
Fitted PDBs: 7y9z
Q-score: 0.365
Zhao Z, Zhou J, Tian M, Huang M, Liu S, Xie Y, Han P, Bai C, Han P, Zheng A, Fu L, Gao Y, Peng Q, Li Y, Chai Y, Zhang Z, Zhao X, Song H, Qi J, Wang Q, Wang P, Gao GF
Nat Commun (2022) 13 pp. 4958-4958 [ DOI: doi:10.1038/s41467-022-32665-7 Pubmed: 36002453 ]
- Processed angiotensin-converting enzyme 2 (69 kDa, Protein from Homo sapiens)
- Spike glycoprotein (139 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Processed angiotensin-converting enzyme 2 (Complex)
- Zinc ion (65 Da, Ligand)
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
- Spike glycoprotein (Complex from Homo sapiens)
- Cryo-em structure of sars-cov-2 omicron spike protein in complex with human ace2 ectodomain (one-rbd-up state) (Complex from Severe acute respiratory syndrome coronavirus 2)
Resolution: 3.1 Å
EM Method: Single-particle
Fitted PDBs: 7ya0
Q-score: 0.327
Zhao Z, Zhou J, Tian M, Huang M, Liu S, Xie Y, Han P, Bai C, Han P, Zheng A, Fu L, Gao Y, Peng Q, Li Y, Chai Y, Zhang Z, Zhao X, Song H, Qi J, Wang Q, Wang P, Gao GF
Nat Commun (2022) 13 pp. 4958-4958 [ DOI: doi:10.1038/s41467-022-32665-7 Pubmed: 36002453 ]
- Processed angiotensin-converting enzyme 2 (69 kDa, Protein from Homo sapiens)
- Spike glycoprotein (Complex from Homo sapiens)
- Spike glycoprotein (138 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Processed angiotensin-converting enzyme 2 (Complex)
- Zinc ion (65 Da, Ligand)
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
- Cryo-em structure of hace2-bound sars-cov-2 omicron spike protein with l371s, p373s and f375s mutations (local refinement) (Complex from Severe acute respiratory syndrome coronavirus 2)
Resolution: 3.4 Å
EM Method: Single-particle
Fitted PDBs: 7xch
Q-score: 0.31
Zhao Z, Zhou J, Tian M, Huang M, Liu S, Xie Y, Han P, Bai C, Han P, Zheng A, Fu L, Gao Y, Peng Q, Li Y, Chai Y, Zhang Z, Zhao X, Song H, Qi J, Wang Q, Wang P, Gao GF
Nat Commun (2022) 13 pp. 4958- [ DOI: doi:10.1038/s41467-022-32665-7 ]
- Processed angiotensin-converting enzyme 2 (69 kDa, Protein from Homo sapiens)
- Cryo-em structure of sars-cov-2 omicron spike protein in complex with human ace2 ectodomain (two-rbd-up state) (Complex from Severe acute respiratory syndrome coronavirus 2)
- Spike glycoprotein (138 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Ace2 ectodomain (Complex)
- Zinc ion (65 Da, Ligand)
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
- Sars-cov-2 omicron spike protein (Complex from Homo sapiens)
Cryo-EM structure of SARS-CoV-2 Omicron RBD in complex with human ACE2 ectodomain (local refinement)
Resolution: 3.2 Å
EM Method: Single-particle
Fitted PDBs: 7xci
Q-score: 0.478
Zhao Z, Zhou J, Tian M, Huang M, Liu S, Xie Y, Han P, Bai C, Han P, Zheng A, Fu L, Gao Y, Peng Q, Li Y, Chai Y, Zhang Z, Zhao X, Song H, Qi J, Wang Q, Wang P, Gao GF
Nat Commun (2022) 13 pp. 4958- [ DOI: doi:10.1038/s41467-022-32665-7 ]
- Ace2 (Complex from Severe acute respiratory syndrome coronavirus 2)
- Processed angiotensin-converting enzyme 2 (69 kDa, Protein from Homo sapiens)
- Spike glycoprotein (22 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Cryo-em structure of sars-cov-2 omicron rbd in complex with human ace2 ectodomain(local refinement) (Complex from Homo sapiens)
- Zinc ion (65 Da, Ligand)
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
- Sars-cov-2 omicron rbd (Complex)
Cryo-EM structure of SARS-CoV-2 Omicron RBD in complex with S309 fab (local refinement)
Resolution: 2.5 Å
EM Method: Single-particle
Fitted PDBs: 7xck
Q-score: 0.548
Zhao Z, Zhou J, Tian M, Huang M, Liu S, Xie Y, Han P, Bai C, Han P, Zheng A, Fu L, Gao Y, Peng Q, Li Y, Chai Y, Zhang Z, Zhao X, Song H, Qi J, Wang Q, Wang P, Gao GF
Nat Commun (2022) 13 pp. 4958- [ DOI: doi:10.1038/s41467-022-32665-7 ]
- Spike protein s1 (30 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Cryo-em structure of sars-cov-2 omicron rbd in complex with s309 fab (local refinement) (Complex from Homo sapiens)
- Sars-cov-2 omicron rbd (Complex)
- S309 fab (Complex from Severe acute respiratory syndrome coronavirus 2)
- S309 heavy chain (24 kDa, Protein from Homo sapiens)
- S309 light chain (23 kDa, Protein from Homo sapiens)
Cryo-EM structure of Omicron RBD complexed with ACE2 and 304 Fab
Resolution: 3.05 Å
EM Method: Single-particle
Fitted PDBs: 7xcp
Q-score: 0.457
Zhao Z, Zhou J, Tian M, Huang M, Liu S, Xie Y, Han P, Bai C, Han P, Zheng A, Fu L, Gao Y, Peng Q, Li Y, Chai Y, Zhang Z, Zhao X, Song H, Qi J, Wang Q, Wang P, Gao GF
Nat Commun (2022) 13 pp. 4958-4958 [ DOI: doi:10.1038/s41467-022-32665-7 ]
- Ace2 (Complex from Homo sapiens)
- Omicron rbd (Complex from Severe acute respiratory syndrome coronavirus 2)
- Processed angiotensin-converting enzyme 2 (69 kDa, Protein from Homo sapiens)
- Lignt chain of 304 fab (23 kDa, Protein from Homo sapiens)
- 304 fab (Complex from Homo sapiens)
- Heavy chain of 304 fab (23 kDa, Protein from Homo sapiens)
- Zinc ion (65 Da, Ligand)
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
- Cryoem structure of omicron rbd complexed with ace2 and 304 fab (Complex)
- Spike protein s1 (22 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
Cryo-EM structure of apo SARS-CoV-2 Omicron spike protein (S-2P-GSAS)
Resolution: 3.0 Å
EM Method: Single-particle
Fitted PDBs: 7y9s
Q-score: 0.457