Cryo-EM structure of neutralizing antibody 8G3 in complex with BA.1 RBD
Resolution: 3.8 Å
EM Method: Single-particle
Fitted PDBs: 9js4
Q-score: 0.434
Liao Y, Ma H, Wang Z, Wang S, He Y, Chang Y, Zong H, Tang H, Wang L, Ke Y, Cai H, Li P, Tang J, Chen H, Drelich A, Peng BH, Hsu J, Tat V, Tseng CK, Song J, Yuan Y, Wu M, Liu J, Yue Y, Zhang X, Wang Z, Yang L, Li J, Ni X, Li H, Xiang Y, Bian Y, Zhang B, Yin H, Dimitrov DS, Gilly J, Han L, Jiang H, Xie Y, Zhu J
PNAS (2025) 122 pp. e2406659122-e2406659122 [ Pubmed: 39908098 DOI: doi:10.1073/pnas.2406659122 ]
- Cryo-em structure of neutralizing antibody 8g3 in complex with ba.1 rbd (Complex from Severe acute respiratory syndrome coronavirus 2)
- Spike glycoprotein (137 kDa, Protein from Severe acute respiratory syndrome coronavirus)
- Heavy chain of 8g3 (23 kDa, Protein from Homo heidelbergensis)
- Light chain of 8g3 (23 kDa, Protein from Homo sapiens)
Cryo-EM structure of SARS-CoV-2 Omicron BA.1 spike protein in complex with white-tailed deer ACE2
Resolution: 2.98 Å
EM Method: Single-particle
Fitted PDBs: 8hfx
Q-score: 0.46
Han P, Meng Y, Zhang D, Xu Z, Li Z, Pan X, Zhao Z, Li L, Tang L, Qi J, Liu K, Gao GF
J Virol (2023) 97 pp. e0050523-e0050523 [ Pubmed: 37676003 DOI: doi:10.1128/jvi.00505-23 ]
- Angiotensin-converting enzyme (71 kDa, Protein from Odocoileus virginianus texanus)
- Zinc ion (65 Da, Ligand)
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
- Spike glycoprotein,envelope glycoprotein (139 kDa, Protein from Human immunodeficiency virus 1)
- Sars-cov-2 omicron ba.1 spike protein, envelope glycoprotein chimera in complex with white-tailed deer ace2 (Complex from Severe acute respiratory syndrome coronavirus 2)
SARS-CoV-2 Omicron BA.1 spike protein receptor-binding domain in complex with white-tailed deer ACE2
Resolution: 3.21 Å
EM Method: Single-particle
Fitted PDBs: 8hfy
Q-score: 0.506
Han P, Meng Y, Zhang D, Xu Z, Li Z, Pan X, Zhao Z, Li L, Tang L, Qi J, Liu K, Gao GF
J Virol (2023) 97 pp. e0050523-e0050523 [ Pubmed: 37676003 DOI: doi:10.1128/jvi.00505-23 ]
- Zinc ion (65 Da, Ligand)
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
- Sars-cov-2 omicron ba.1 spike protein receptor-binding domain in complex with white-tailed deer ace2 (Complex from Severe acute respiratory syndrome coronavirus 2)
- Angiotensin-converting enzyme (69 kDa, Protein from Odocoileus virginianus texanus)
- Spike protein s1 (22 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
SARS-CoV-2 Omicron BA.1 spike trimer (6P) in complex with 1 YB9-258 Fab (1 RBD up)
Resolution: 6.21 Å
EM Method: Single-particle
Fitted PDBs: 8hc2
Q-score: 0.154
Yu H, Liu B, Zhang Y, Gao X, Wang Q, Xiang H, Peng X, Xie C, Wang Y, Hu P, Shi J, Shi Q, Zheng P, Feng C, Tang G, Liu X, Guo L, Lin X, Li J, Liu C, Huang Y, Yang N, Chen Q, Li Z, Su M, Yan Q, Pei R, Chen X, Liu L, Hu F, Liang D, Ke B, Ke C, Li F, He J, Wang M, Chen L, Xiong X, Tang X
Nat Commun (2023) 14 pp. 1058-1058 [ DOI: doi:10.1038/s41467-023-36761-0 Pubmed: 36828833 ]
- Heavy chain of yb9-258 fab (23 kDa, Protein from Homo sapiens)
- Yb9-258 fab (Complex from Homo sapiens)
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
- Sars-cov-2 omicron ba.1 spike trimer (Complex from Severe acute respiratory syndrome coronavirus 2)
- Light chain of yb9-258 fab (23 kDa, Protein from Homo sapiens)
- Sars-cov-2 omicron ba.1 spike trimer with one rbd up in complex with one yb9-258 fab (Complex)
- Spike glycoprotein (138 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
SARS-CoV-2 Omicron BA.1 spike trimer (6P) in complex with 2 YB9-258 Fabs (2 RBD up)
Resolution: 4.35 Å
EM Method: Single-particle
Fitted PDBs: 8hc3
Q-score: 0.224
Yu H, Liu B, Zhang Y, Gao X, Wang Q, Xiang H, Peng X, Xie C, Wang Y, Hu P, Shi J, Shi Q, Zheng P, Feng C, Tang G, Liu X, Guo L, Lin X, Li J, Liu C, Huang Y, Yang N, Chen Q, Li Z, Su M, Yan Q, Pei R, Chen X, Liu L, Hu F, Liang D, Ke B, Ke C, Li F, He J, Wang M, Chen L, Xiong X, Tang X
Nat Commun (2023) 14 pp. 1058-1058 [ DOI: doi:10.1038/s41467-023-36761-0 Pubmed: 36828833 ]
- Sars-cov-2 omicron ba.1 spike trimer with two rbd up in complex with two yb9-258 fab (Complex)
- Yb9-258 fab (Complex from Homo sapiens)
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
- Sars-cov-2 omicron ba.1 spike trimer (Complex from Severe acute respiratory syndrome coronavirus 2)
- Heavy chain of yb9-258 (23 kDa, Protein from Homo sapiens)
- Light chain of yb9-258 (23 kDa, Protein from Homo sapiens)
- Spike glycoprotein (138 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
Resolution: 4.69 Å
EM Method: Single-particle
Fitted PDBs: 8hc6
Q-score: 0.221
Yu H, Liu B, Zhang Y, Gao X, Wang Q, Xiang H, Peng X, Xie C, Wang Y, Hu P, Shi J, Shi Q, Zheng P, Feng C, Tang G, Liu X, Guo L, Lin X, Li J, Liu C, Huang Y, Yang N, Chen Q, Li Z, Su M, Yan Q, Pei R, Chen X, Liu L, Hu F, Liang D, Ke B, Ke C, Li F, He J, Wang M, Chen L, Xiong X, Tang X
Nat Commun (2023) 14 pp. 1058-1058 [ DOI: doi:10.1038/s41467-023-36761-0 Pubmed: 36828833 ]
- Heavy chain of yb9-258 fab (23 kDa, Protein from Homo sapiens)
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
- Spike protein s1 (30 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Yb13-292 fab (Complex from Homo sapiens)
- Spike protein s1 (31 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Light chain of yb9-258 (23 kDa, Protein from Homo sapiens)
- Sars-cov-2 omicron ba.1 spike protein (Complex from Severe acute respiratory syndrome coronavirus 2)
- Sars-cov-2 omicron ba.1 spike (6p) in complex with yb13-292 fab, focused refinement of rbd region (Complex)
Resolution: 4.54 Å
EM Method: Single-particle
Fitted PDBs: 8hc7
Q-score: 0.234
Yu H, Liu B, Zhang Y, Gao X, Wang Q, Xiang H, Peng X, Xie C, Wang Y, Hu P, Shi J, Shi Q, Zheng P, Feng C, Tang G, Liu X, Guo L, Lin X, Li J, Liu C, Huang Y, Yang N, Chen Q, Li Z, Su M, Yan Q, Pei R, Chen X, Liu L, Hu F, Liang D, Ke B, Ke C, Li F, He J, Wang M, Chen L, Xiong X, Tang X
Nat Commun (2023) 14 pp. 1058-1058 [ DOI: doi:10.1038/s41467-023-36761-0 Pubmed: 36828833 ]
- Yb9-258 fab (Complex from Homo sapiens)
- Sars-cov_2 omicron ba.1 spike protein (Complex from Severe acute respiratory syndrome coronavirus 2)
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
- Spike protein s1 (30 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Light chain variable region of yb9-258 (11 kDa, Protein from Homo sapiens)
- Sars-cov-2 omicron ba.1 spike trimer with in complex with yb9-258 fab, focused refinement of 2 rbd region (Complex)
- Spike protein s1 (58 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Heavy chain variable region of yb9-258 (12 kDa, Protein from Homo sapiens)
Resolution: 3.95 Å
EM Method: Single-particle
Fitted PDBs: 8hc8
Q-score: 0.367
Yu H, Liu B, Zhang Y, Gao X, Wang Q, Xiang H, Peng X, Xie C, Wang Y, Hu P, Shi J, Shi Q, Zheng P, Feng C, Tang G, Liu X, Guo L, Lin X, Li J, Liu C, Huang Y, Yang N, Chen Q, Li Z, Su M, Yan Q, Pei R, Chen X, Liu L, Hu F, Liang D, Ke B, Ke C, Li F, He J, Wang M, Chen L, Xiong X, Tang X
Nat Commun (2023) 14 pp. 1058-1058 [ DOI: doi:10.1038/s41467-023-36761-0 Pubmed: 36828833 ]
- Light chain of yb13-292 fab (23 kDa, Protein from Homo sapiens)
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
- Heavy chain of yb13-292 fab (25 kDa, Protein from Homo sapiens)
- Yb13-292 fab (Complex from Homo sapiens)
- Sars-cov-2 omicron ba.1 spike protein (Complex from Severe acute respiratory syndrome coronavirus 2)
- Spike protein s1 (21 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Sars-cov-2 omicron ba.1 spike trimer with in complex with yb13-292 fab, focused refinement of fab region (Complex)
SARS-CoV-2 Omicron BA.1 spike trimer (6P) in complex with 3 YB13-292 Fabs (3 RBD down)
Resolution: 6.03 Å
EM Method: Single-particle
Fitted PDBs: 8hc9
Q-score: 0.156
Yu H, Liu B, Zhang Y, Gao X, Wang Q, Xiang H, Peng X, Xie C, Wang Y, Hu P, Shi J, Shi Q, Zheng P, Feng C, Tang G, Liu X, Guo L, Lin X, Li J, Liu C, Huang Y, Yang N, Chen Q, Li Z, Su M, Yan Q, Pei R, Chen X, Liu L, Hu F, Liang D, Ke B, Ke C, Li F, He J, Wang M, Chen L, Xiong X, Tang X
Nat Commun (2023) 14 pp. 1058-1058 [ DOI: doi:10.1038/s41467-023-36761-0 Pubmed: 36828833 ]
- Light chain of yb13-292 fab (23 kDa, Protein from Homo sapiens)
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
- Heavy chain of yb13-292 fab (25 kDa, Protein from Homo sapiens)
- Yb13-292 fab (Complex from Homo sapiens)
- Sars-cov-2 omicron ba.1 spike protein (Complex from Severe acute respiratory syndrome coronavirus 2)
- Spike glycoprotein (138 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Sars-cov-2 omicron ba.1 spike trimer with three rbd down in complex with three yb13-292 fab (Complex)
SARS-CoV-2 Omicron BA.1 spike trimer (6P) in complex with 3 YB13-292 Fabs (1 RBD up)
Resolution: 4.35 Å
EM Method: Single-particle
Fitted PDBs: 8hca
Q-score: 0.217
Yu H, Liu B, Zhang Y, Gao X, Wang Q, Xiang H, Peng X, Xie C, Wang Y, Hu P, Shi J, Shi Q, Zheng P, Feng C, Tang G, Liu X, Guo L, Lin X, Li J, Liu C, Huang Y, Yang N, Chen Q, Li Z, Su M, Yan Q, Pei R, Chen X, Liu L, Hu F, Liang D, Ke B, Ke C, Li F, He J, Wang M, Chen L, Xiong X, Tang X
Nat Commun (2023) 14 pp. 1058-1058 [ DOI: doi:10.1038/s41467-023-36761-0 Pubmed: 36828833 ]
- Light chain of yb13-292 fab (23 kDa, Protein from Homo sapiens)
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
- Sars-cov-2 ba.1 variant spike protein with one rbd up in complex with three yb13-292 fab (Complex)
- Heavy chain of yb13-292 fab (25 kDa, Protein from Homo sapiens)
- Yb13-292 fab (Complex from Homo sapiens)
- Spike glycoprotein (138 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Sars-cov-2 ba.1 spike protein (Complex from Severe acute respiratory syndrome coronavirus 2)