SARS-CoV-2 Omicron BA.2 spike trimer (6P) in complex with D1F6 Fab, head-to-head aggregate
Resolution: 7.82 Å
EM Method: Single-particle
Fitted PDBs: 8zc2
Q-score: 0.103
Liu B, Niu X, Deng Y, Zhang Z, Wang Y, Gao X, Liang H, Li Z, Wang Q, Cheng Y, Chen Q, Huang S, Pan Y, Su M, Lin X, Niu C, Chen Y, Yang W, Zhang Y, Yan Q, He J, Zhao J, Chen L, Xiong X
Cell Rep (2024) 43 pp. 114265-114265 [ DOI: doi:10.1016/j.celrep.2024.114265 Pubmed: 38805396 ]
- Spike glycoprotein (137 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
- Light chain of d1f6 fab (23 kDa, Protein from Homo sapiens)
- Sars-cov-2 omicron ba.2 spike trimer (6p) in complex with d1f6 fab, head-to-head aggregate (Complex from Severe acute respiratory syndrome coronavirus 2)
- Heavy chain of d1f6 fab (24 kDa, Protein from Homo sapiens)
SARS-CoV-2 Omicron BA.4 spike trimer (6P) in complex with D1F6 Fab, head-to-head aggregate
Resolution: 6.85 Å
EM Method: Single-particle
Fitted PDBs: 8zc6
Q-score: 0.116
Liu B, Niu X, Deng Y, Zhang Z, Wang Y, Gao X, Liang H, Li Z, Wang Q, Cheng Y, Chen Q, Huang S, Pan Y, Su M, Lin X, Niu C, Chen Y, Yang W, Zhang Y, Yan Q, He J, Zhao J, Chen L, Xiong X
Cell Rep (2024) 43 pp. 114265-114265 [ DOI: doi:10.1016/j.celrep.2024.114265 Pubmed: 38805396 ]
- Spike glycoprotein (137 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
- Light chain of d1f6 fab (23 kDa, Protein from Homo sapiens)
- Sars-cov-2 omicron ba.4 spike trimer (6p) in complex with d1f6 fab, head-to-head aggregate (Complex from Severe acute respiratory syndrome coronavirus 2)
- Heavy chain of d1f6 fab (24 kDa, Protein from Homo sapiens)
SARS-CoV-2 Omicron BA.1 spike trimer (x2-4P) in complex with 3 D1F6 Fabs (0 RBD up)
Resolution: 3.67 Å
EM Method: Single-particle
Fitted PDBs: 8zby
Q-score: 0.372
Liu B, Niu X, Deng Y, Zhang Z, Wang Y, Gao X, Liang H, Li Z, Wang Q, Cheng Y, Chen Q, Huang S, Pan Y, Su M, Lin X, Niu C, Chen Y, Yang W, Zhang Y, Yan Q, He J, Zhao J, Chen L, Xiong X
Cell Rep (2024) 43 pp. 114265-114265 [ DOI: doi:10.1016/j.celrep.2024.114265 Pubmed: 38805396 ]
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
- Light chain of d1f6 fab (23 kDa, Protein from Homo sapiens)
- Sars-cov-2 omicron ba.1 spike trimer (x2-4p) in complex with 3 d1f6 fabs (0 rbd up) (Complex from Severe acute respiratory syndrome coronavirus 2)
- Spike glycoprotein (138 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Heavy chain of d1f6 fab (24 kDa, Protein from Homo sapiens)
SARS-CoV-2 Omicron BA.2 spike trimer (6P) in complex with 3 D1F6 Fabs (1 RBD up)
Resolution: 4.71 Å
EM Method: Single-particle
Fitted PDBs: 8zbz
Q-score: 0.272
Liu B, Niu X, Deng Y, Zhang Z, Wang Y, Gao X, Liang H, Li Z, Wang Q, Cheng Y, Chen Q, Huang S, Pan Y, Su M, Lin X, Niu C, Chen Y, Yang W, Zhang Y, Yan Q, He J, Zhao J, Chen L, Xiong X
Cell Rep (2024) 43 pp. 114265-114265 [ DOI: doi:10.1016/j.celrep.2024.114265 Pubmed: 38805396 ]
- Spike glycoprotein (137 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
- Light chain of d1f6 fab (23 kDa, Protein from Homo sapiens)
- Sars-cov-2 omicron ba.2 spike trimer (6p) in complex with 3 d1f6 fabs (1 rbd up) (Complex from Severe acute respiratory syndrome coronavirus 2)
- Heavy chain of d1f6 fab (24 kDa, Protein from Homo sapiens)
SARS-CoV-2 Omicron BA.2 spike trimer (6P) in complex with 3 D1F6 Fabs (2 RBD up)
Resolution: 4.17 Å
EM Method: Single-particle
Fitted PDBs: 8zc0
Q-score: 0.338
Liu B, Niu X, Deng Y, Zhang Z, Wang Y, Gao X, Liang H, Li Z, Wang Q, Cheng Y, Chen Q, Huang S, Pan Y, Su M, Lin X, Niu C, Chen Y, Yang W, Zhang Y, Yan Q, He J, Zhao J, Chen L, Xiong X
Cell Rep (2024) 43 pp. 114265-114265 [ DOI: doi:10.1016/j.celrep.2024.114265 Pubmed: 38805396 ]
- Sars-cov-2 omicron ba.2 spike trimer (6p) in complex with 3 d1f6 fabs (2 rbd up) (Complex from Severe acute respiratory syndrome coronavirus 2)
- Spike glycoprotein (137 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
- Light chain of d1f6 fab (23 kDa, Protein from Homo sapiens)
- Heavy chain of d1f6 fab (24 kDa, Protein from Homo sapiens)
SARS-CoV-2 Omicron BA.2 spike trimer (6P) in complex with D1F6 Fab, focused refinement of RBD region
Resolution: 4.17 Å
EM Method: Single-particle
Fitted PDBs: 8zc1
Q-score: 0.335
Liu B, Niu X, Deng Y, Zhang Z, Wang Y, Gao X, Liang H, Li Z, Wang Q, Cheng Y, Chen Q, Huang S, Pan Y, Su M, Lin X, Niu C, Chen Y, Yang W, Zhang Y, Yan Q, He J, Zhao J, Chen L, Xiong X
Cell Rep (2024) 43 pp. 114265-114265 [ DOI: doi:10.1016/j.celrep.2024.114265 Pubmed: 38805396 ]
- Light chain of d1f6 fab (23 kDa, Protein from Homo sapiens)
- Heavy chain of d1f6 fab (24 kDa, Protein from Homo sapiens)
- Sars-cov-2 omicron ba.2 spike trimer (6p) in complex with d1f6 fab, focused refinement of rbd region (Complex from Severe acute respiratory syndrome coronavirus 2)
- Spike protein s1 (22 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
SARS-CoV-2 Omicron BA.4 spike trimer (6P) in complex with 3 D1F6 Fabs (1 RBD up)
Resolution: 4.69 Å
EM Method: Single-particle
Fitted PDBs: 8zc3
Q-score: 0.29
Liu B, Niu X, Deng Y, Zhang Z, Wang Y, Gao X, Liang H, Li Z, Wang Q, Cheng Y, Chen Q, Huang S, Pan Y, Su M, Lin X, Niu C, Chen Y, Yang W, Zhang Y, Yan Q, He J, Zhao J, Chen L, Xiong X
Cell Rep (2024) 43 pp. 114265-114265 [ DOI: doi:10.1016/j.celrep.2024.114265 Pubmed: 38805396 ]
- Spike glycoprotein (137 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
- Light chain of d1f6 fab (23 kDa, Protein from Homo sapiens)
- Sars-cov-2 omicron ba.4 spike trimer (6p) in complex with 3 d1f6 fabs (1 rbd up) (Complex from Severe acute respiratory syndrome coronavirus 2)
- Heavy chain of d1f6 fab (24 kDa, Protein from Homo sapiens)
SARS-CoV-2 Omicron BA.4 spike trimer (6P) in complex with 3 D1F6 Fabs (2 RBD up)
Resolution: 3.95 Å
EM Method: Single-particle
Fitted PDBs: 8zc4
Q-score: 0.372
Liu B, Niu X, Deng Y, Zhang Z, Wang Y, Gao X, Liang H, Li Z, Wang Q, Cheng Y, Chen Q, Huang S, Pan Y, Su M, Lin X, Niu C, Chen Y, Yang W, Zhang Y, Yan Q, He J, Zhao J, Chen L, Xiong X
Cell Rep (2024) 43 pp. 114265-114265 [ DOI: doi:10.1016/j.celrep.2024.114265 Pubmed: 38805396 ]
- Spike glycoprotein (137 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
- Sars-cov-2 omicron ba.4 spike trimer (6p) in complex with 3 d1f6 fabs (2 rbd up) (Complex from Severe acute respiratory syndrome coronavirus 2)
- Light chain of d1f6 fab (23 kDa, Protein from Homo sapiens)
- Heavy chain of d1f6 fab (24 kDa, Protein from Homo sapiens)
SARS-CoV-2 Omicron BA.4 spike trimer (6P) in complex with D1F6 Fab, focused refinement of RBD region
Resolution: 3.91 Å
EM Method: Single-particle
Fitted PDBs: 8zc5
Q-score: 0.439
Liu B, Niu X, Deng Y, Zhang Z, Wang Y, Gao X, Liang H, Li Z, Wang Q, Cheng Y, Chen Q, Huang S, Pan Y, Su M, Lin X, Niu C, Chen Y, Yang W, Zhang Y, Yan Q, He J, Zhao J, Chen L, Xiong X
Cell Rep (2024) 43 pp. 114265-114265 [ DOI: doi:10.1016/j.celrep.2024.114265 Pubmed: 38805396 ]
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
- Spike protein s1 (22 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Heavy chain of d1f6 fab (14 kDa, Protein from Homo sapiens)
- Sars-cov-2 omicron ba.4 spike trimer (6p) in complex with d1f6 fab, focused refinement of rbd region (Complex from Severe acute respiratory syndrome coronavirus 2)
- Light chain of d1f6 fab (11 kDa, Protein from Homo sapiens)
Resolution: 2.95 Å
EM Method: Single-particle
Fitted PDBs: 8x90
Q-score: 0.439
Li Z, Cong Y, Wu T, Wang T, Lou X, Yang X, Yan N
Cell Res (2024) 34 pp. 455-457 [ Pubmed: 38443561 DOI: doi:10.1038/s41422-024-00940-5 ]
- 1,2-didecanoyl-sn-glycero-3-[phospho-l-serine] (566 Da, Ligand)
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
- Calcium ion (40 Da, Ligand)
- 1,2-distearoyl-sn-glycerophosphoethanolamine (748 Da, Ligand)
- Voltage-gated p/q type calcium channel (Complex from Homo sapiens)
- Voltage-dependent p/q-type calcium channel subunit alpha-1a (287 kDa, Protein from Homo sapiens)
- [(2r)-1-octadecanoyloxy-3-[oxidanyl-[(1r,2r,3s,4r,5r,6s)-2,3,6-tris(oxidanyl)-4,5-diphosphonooxy-cyclohexyl]oxy-phospho ryl]oxy-propan-2-yl] (8z)-icosa-5,8,11,14-tetraenoate (1 kDa, Ligand)
- Cholesterol hemisuccinate (486 Da, Ligand)
- Cholesterol (386 Da, Ligand)
- Voltage-dependent calcium channel subunit alpha-2/delta-1 (126 kDa, Protein from Homo sapiens)
- Voltage-dependent l-type calcium channel subunit beta-3 (56 kDa, Protein from Homo sapiens)