Local refined cryo-EM reconstruction of Omicron BA.5 RBD in complex with 8-9D Fab
Resolution: 3.3 Å
EM Method: Single-particle
Fitted PDBs: 8j1t
Q-score: 0.455
Tai W, Yang K, Liu Y, Li R, Feng S, Chai B, Zhuang X, Qi S, Shi H, Liu Z, Lei J, Ma E, Wang W, Tian C, Le T, Wang J, Chen Y, Tian M, Xiang Y, Yu G, Cheng G
Nat Commun (2023) 14 pp. 8042-8042 [ Pubmed: 38052844 DOI: doi:10.1038/s41467-023-43798-8 ]
- Spike protein (21 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Severe acute respiratory syndrome coronavirus 2 omicron ba.5 rbd bound 8-9d fab (22 kDa, Complex from Severe acute respiratory syndrome coronavirus 2)
- 8-9d light chain (11 kDa, Protein from Homo sapiens)
- 8-9d fab (Complex from Homo sapiens)
- Sars-cov2 omicron ba.5 rbd (Complex)
- 8-9d heavy chain (12 kDa, Protein from Homo sapiens)
Cryo-EM reconstruction of SARS-CoV2 Omicron BA.5 spike in complex with 8-9D Fabs
Resolution: 3.01 Å
EM Method: Single-particle
Fitted PDBs: 8j1v
Q-score: 0.374
Tai W, Yang K, Liu Y, Li R, Feng S, Chai B, Zhuang X, Qi S, Shi H, Liu Z, Lei J, Ma E, Wang W, Tian C, Le T, Wang J, Chen Y, Tian M, Xiang Y, Yu G, Cheng G
Nat Commun (2023) 14 pp. 8042-8042 [ Pubmed: 38052844 DOI: doi:10.1038/s41467-023-43798-8 ]
- Severe acute respiratory syndrome coronavirus 2 omicron ba.5 spike bound 8-9d fab (369 kDa, Complex from Severe acute respiratory syndrome coronavirus 2)
- 8-9d light chain (11 kDa, Protein from Homo sapiens)
- Spike protein s2' (123 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- 8-9d fab variable region (Complex from Homo sapiens)
- 8-9d heavy chain (12 kDa, Protein from Homo sapiens)
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
- Sars-cov2 omicron ba.5 spike ectodomain (Complex)
SARS-CoV-2 S ectodomain trimer in complex with neutralizing antibody 10-5B
Resolution: 3.3 Å
EM Method: Single-particle
Fitted PDBs: 7xd2
Q-score: 0.367
Liu Y, Wang Z, Zhuang X, Zhang S, Chen Z, Zou Y, Sheng J, Li T, Tai W, Yu J, Wang Y, Zhang Z, Chen Y, Tong L, Yu X, Wu L, Chen D, Zhang R, Jin N, Shen W, Zhao J, Tian M, Wang X, Cheng G
Nat Commun (2023) 14 pp. 2179-2179 [ Pubmed: 37069158 DOI: doi:10.1038/s41467-023-37926-7 ]
- L chian of antibody 10-5b (11 kDa, Protein from Homo sapiens)
- H chain of antibody 10-5b (12 kDa, Protein from Homo sapiens)
- Spike glycoprotein (143 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Spike+antibody (Complex from Severe acute respiratory syndrome coronavirus 2)
SARS-CoV-2 BA.4 variants S ectodomain trimer in complex with neutralizing antibody 10-5B and 6-2C
Resolution: 2.9 Å
EM Method: Single-particle
Fitted PDBs: 8h07
Q-score: 0.298
Liu Y, Wang Z, Zhuang X, Zhang S, Chen Z, Zou Y, Sheng J, Li T, Tai W, Yu J, Wang Y, Zhang Z, Chen Y, Tong L, Yu X, Wu L, Chen D, Zhang R, Jin N, Shen W, Zhao J, Tian M, Wang X, Cheng G
Nat Commun (2023) 14 pp. 2179-2179 [ Pubmed: 37069158 DOI: doi:10.1038/s41467-023-37926-7 ]
- Spike glycoprotein (142 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- 10-5b l chain (11 kDa, Protein from Homo sapiens)
- Sars-cov-2 ba.4 variants spike (Complex)
- Antibody (Cellular component from Homo sapiens)
- 10-5b h chain (12 kDa, Protein from Homo sapiens)
- Sars-cov-2 ba.4 variants spike (Cellular component from Severe acute respiratory syndrome coronavirus 2)
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
- 6-2c l chain (11 kDa, Protein from Homo sapiens)
- 6-2c h chain (13 kDa, Protein from Homo sapiens)
SARS-CoV-2 BA.1 variants S ectodomain trimer in complex with neutralizing antibody 10-5B and 6-2C
Resolution: 3.2 Å
EM Method: Single-particle
Fitted PDBs: 8h08
Q-score: 0.3
Liu Y, Wang Z, Zhuang X, Zhang S, Chen Z, Zou Y, Sheng J, Li T, Tai W, Yu J, Wang Y, Zhang Z, Chen Y, Tong L, Yu X, Wu L, Chen D, Zhang R, Jin N, Shen W, Zhao J, Tian M, Wang X, Cheng G
Nat Commun (2023) 14 pp. 2179-2179 [ Pubmed: 37069158 DOI: doi:10.1038/s41467-023-37926-7 ]
- Sars-cov-2 ba.1 variants spike (Cellular component from Severe acute respiratory syndrome coronavirus 2)
- 6-2c l chain (11 kDa, Protein from Homo sapiens)
- 10-5b l chain (11 kDa, Protein from Homo sapiens)
- Spike glycoprotein (144 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Antibody (Cellular component from Homo sapiens)
- 10-5b h chain (12 kDa, Protein from Homo sapiens)
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
- Sars-cov-2 ba.1 variants spike (Complex)
- 6-2c h chain (13 kDa, Protein from Homo sapiens)
Cryo-EM structure of the SARS-CoV-2 spike glycoprotein in complex with all-trans retinoic acid
Resolution: 3.45 Å
EM Method: Single-particle
Fitted PDBs: 7y42
Q-score: 0.473
Tong L, Wang L, Liao S, Xiao X, Qu J, Wu C, Zhu Y, Tai W, Huang Y, Wang P, Li L, Zhang R, Xiang Y, Cheng G
Mbio (2022) 13 pp. e0148522-e0148522 [ Pubmed: 35862773 DOI: doi:10.1128/mbio.01485-22 ]
- Spike glycoprotein (124 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
- Retinoic acid (300 Da, Ligand)
- Sars-cov-2 spike glycoprotein in complex with atra (Complex from Severe acute respiratory syndrome coronavirus 2)