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 ]
- Bd-604 fab light chain (23 kDa, Protein from Homo sapiens)
- Bd-604 fab heavy chain (24 kDa, Protein from Homo sapiens)
- S304 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)
- S309 fab heavy chain (25 kDa, Protein from Homo sapiens)
- S309 fab light chain (23 kDa, Protein from Homo sapiens)
- S304 fab heavy chain (24 kDa, Protein from Homo sapiens)
- Spike protein s2' (22 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
Cryo-EM structure of SARS-CoV-2 Omicron BA.2.12.1 RBD in complex with human ACE2 (local refinement)
Resolution: 3.09 Å
EM Method: Single-particle
Fitted PDBs: 7yhw
Q-score: 0.516
Zhao Z, Xie Y, Bai B, Luo C, Zhou J, Li W, Meng Y, Li L, Li D, Li X, Li X, Wang X, Sun J, Xu Z, Sun Y, Zhang W, Fan Z, Zhao X, Wu L, Ma J, Li OY, Shang G, Chai Y, Liu K, Wang P, Gao GF, Qi J
Nat Commun (2023) 14 pp. 4405-4405 [ Pubmed: 37479708 DOI: doi:10.1038/s41467-023-39942-z ]
- Zinc ion (65 Da, Ligand)
- Omicron ba.2.12.1 rbd (Complex from Homo sapiens)
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
- Cryo-em structure of sars-cov-2 omicron ba.2.12.1 rbd in complex with human ace2 (local refinement) (Complex from Severe acute respiratory syndrome coronavirus 2)
- Spike protein s1 (22 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Angiotensin-converting enzyme 2 (69 kDa, Protein from Homo sapiens)
- Ace2 (Complex)
Cryo-EM structure of SARS-CoV-2 Omicron BA.2 RBD in complex with human ACE2 (local refinement)
Resolution: 3.14 Å
EM Method: Single-particle
Fitted PDBs: 7yj3
Q-score: 0.468
Zhao Z, Xie Y, Bai B, Luo C, Zhou J, Li W, Meng Y, Li L, Li D, Li X, Li X, Wang X, Sun J, Xu Z, Sun Y, Zhang W, Fan Z, Zhao X, Wu L, Ma J, Li OY, Shang G, Chai Y, Liu K, Wang P, Gao GF, Qi J
Nat Commun (2023) 14 pp. 4405-4405 [ Pubmed: 37479708 DOI: doi:10.1038/s41467-023-39942-z ]
- Spike protein s1 (22 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Zinc ion (65 Da, Ligand)
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
- Omicron ba.2 rbd (Complex)
- Cryo-em structure of sars-cov-2 omicron ba.2 rbd in complex with human ace2 (local refinement) (Complex from Severe acute respiratory syndrome coronavirus 2)
- Angiotensin-converting enzyme 2 (69 kDa, Protein from Homo sapiens)
- Angiotensin-converting enzyme 2 (Complex from Homo sapiens)
Resolution: 2.94 Å
EM Method: Single-particle
Fitted PDBs: 7yv8
Q-score: 0.553
Zhao Z, Xie Y, Bai B, Luo C, Zhou J, Li W, Meng Y, Li L, Li D, Li X, Li X, Wang X, Sun J, Xu Z, Sun Y, Zhang W, Fan Z, Zhao X, Wu L, Ma J, Li OY, Shang G, Chai Y, Liu K, Wang P, Gao GF, Qi J
Nat Commun (2023) 14 pp. 4405-4405 [ Pubmed: 37479708 DOI: doi:10.1038/s41467-023-39942-z ]
- Zinc ion (65 Da, Ligand)
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
- Spike glycoprotein (22 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Cryo-em structure of sars-cov-2 omicron ba.2 rbd in complex with golden hamster ace2 (local refinement) (Complex)
- Omicron ba.2 rbd (Complex from Severe acute respiratory syndrome coronavirus 2)
- Golden hamster angiotensin-converting enzyme 2 (Complex from Mesocricetus auratus)
- Angiotensin-converting enzyme (68 kDa, Protein from Mesocricetus auratus)
Cryo-EM structure of SARS-CoV-2 Omicron BA.2 RBD in complex with mouse ACE2 (local refinement)
Resolution: 3.2 Å
EM Method: Single-particle
Fitted PDBs: 7yvu
Q-score: 0.484
Zhao Z, Xie Y, Bai B, Luo C, Zhou J, Li W, Meng Y, Li L, Li D, Li X, Li X, Wang X, Sun J, Xu Z, Sun Y, Zhang W, Fan Z, Zhao X, Wu L, Ma J, Li OY, Shang G, Chai Y, Liu K, Wang P, Gao GF, Qi J
Nat Commun (2023) 14 pp. 4405-4405 [ Pubmed: 37479708 DOI: doi:10.1038/s41467-023-39942-z ]
- Processed angiotensin-converting enzyme 2 (68 kDa, Protein from Mus musculus)
- Spike protein s1 (22 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
- Zinc ion (65 Da, Ligand)
- Omicron ba.2 rbd (Complex from Severe acute respiratory syndrome coronavirus 2)
- Mouse angiotensin-converting enzyme 2 (Complex from Mus musculus)
- Cryo-em structure of sars-cov-2 omicron ba.2 rbd in complex with mouse ace2 (local refinement) (Complex)
Cryo-EM structure of SARS-CoV-2 Omicron BA.2 RBD in complex with rat ACE2 (local refinement)
Resolution: 3.29 Å
EM Method: Single-particle
Fitted PDBs: 8gry
Q-score: 0.425
Zhao Z, Xie Y, Bai B, Luo C, Zhou J, Li W, Meng Y, Li L, Li D, Li X, Li X, Wang X, Sun J, Xu Z, Sun Y, Zhang W, Fan Z, Zhao X, Wu L, Ma J, Li OY, Shang G, Chai Y, Liu K, Wang P, Gao GF, Qi J
Nat Commun (2023) 14 pp. 4405-4405 [ Pubmed: 37479708 DOI: doi:10.1038/s41467-023-39942-z ]
- Spike protein s1 (22 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Zinc ion (65 Da, Ligand)
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
- Omicron ba.2 rbd (Complex)
- Cryo-em structure of sars-cov-2 omicron ba.2 rbd in complex with mouse ace2 (local refinement) (Complex from Rattus norvegicus)
- Processed angiotensin-converting enzyme 2 (69 kDa, Protein from Rattus norvegicus)
- Rat angiotensin-converting enzyme 2 (Complex from Severe acute respiratory syndrome coronavirus 2)
Cryo-EM structure of SARS-CoV-2 Omicron BA.4/5 RBD in complex with human ACE2 (local refinement)
Resolution: 2.66 Å
EM Method: Single-particle
Fitted PDBs: 8h06
Q-score: 0.566
Zhao Z, Xie Y, Bai B, Luo C, Zhou J, Li W, Meng Y, Li L, Li D, Li X, Li X, Wang X, Sun J, Xu Z, Sun Y, Zhang W, Fan Z, Zhao X, Wu L, Ma J, Li OY, Shang G, Chai Y, Liu K, Wang P, Gao GF, Qi J
Nat Commun (2023) 14 pp. 4405-4405 [ Pubmed: 37479708 DOI: doi:10.1038/s41467-023-39942-z ]
- Processed angiotensin-converting enzyme 2 (69 kDa, Protein from Homo sapiens)
- Zinc ion (65 Da, Ligand)
- Cryo-em structure of sars-cov-2 omicron ba.4/5 rbd in complex with human ace2 (local refinement) (Complex)
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
- Spike protein s1 (22 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Omicron ba.4/5 rbd (Complex from Severe acute respiratory syndrome coronavirus 2)
- Angiotensin-converting enzyme 2 (Complex from Homo sapiens)
The complex structure of Omicron BA.1 RBD with BD604, S309,and S304
Resolution: 2.74 Å
EM Method: Single-particle
Fitted PDBs: 7x1m
Q-score: 0.552
Huang M, Wu L, Zheng A, Xie Y, He Q, Rong X, Han P, Du P, Han P, Zhang Z, Zhao R, Jia Y, Li L, Bai B, Hu Z, Hu S, Niu S, Hu Y, Liu H, Liu B, Cui K, Li W, Zhao X, Liu K, Qi J, Wang Q, Gao GF
Immunity (2022) 55 pp. 1501-1514.e3 [ DOI: doi:10.1016/j.immuni.2022.06.005 Pubmed: 35777362 ]
- S304 fab light chain (23 kDa, Protein from Homo sapiens)
- Spike protein s1 (23 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Bd604 fab, s309 fab and s304 fab complex with omicron ba.1 rbd (Complex)
- Omicron ba.1 rbd (Complex from Severe acute respiratory syndrome coronavirus 2)
- Bd-604 fab heavy chain (23 kDa, Protein from Homo sapiens)
- S309 fab heavy chain (24 kDa, Protein from Homo sapiens)
- Bd604 fab, s309 fab and s304 fab (Complex from Homo sapiens)
- S304 fab haavy chain (23 kDa, Protein from Homo sapiens)
- Bd-604 fab light chain (23 kDa, Protein from Homo sapiens)
- S309 fab light chain (23 kDa, Protein from Homo sapiens)