Locally refined region of SARS-CoV-2 spike in complex with antibodies 9G11 and 3E2.
Resolution: 3.46 Å
EM Method: Single-particle
Fitted PDBs: 9lae
Q-score: 0.522
Jiang W, Jiang Y, Sun H, Deng T, Yu K, Fang Q, Ge H, Lan M, Lin Y, Fang Z, Zhang Y, Zhou L, Li T, Yu H, Zheng Q, Li S, Xia N, Gu Y
Emerg Microbes Infect (2024) 13 pp. 2406300- [ DOI: doi:10.1038/s41467-023-39265-z Pubmed: 39470577 ]
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
- Sars-cov-2 spike in complex with antibodies 9g11 and 3e2 (Complex)
- Light chain of 9g11 (11 kDa, Protein from Mus musculus)
- Heavy chain of 3e2 (13 kDa, Protein from Mus musculus)
- The fab of 3e2 (Complex from Mus musculus)
- Heavy chain of 9g11 (13 kDa, Protein from Mus musculus)
- Sars-cov-2 spike (Complex from Severe acute respiratory syndrome coronavirus 2)
- Light chain of 3e2 (11 kDa, Protein from Mus musculus)
- The fab of 9g11 (Complex from Mus musculus)
- Spike protein s1 (25 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
Resolution: 3.6 Å
EM Method: Single-particle
Fitted PDBs: 8via
Q-score: 0.302
Clark JJ, Hoxie I, Adelsberg DC, Sapse IA, Andreata-Santos R, Yong JS, Amanat F, Tcheou J, Raskin A, Singh G, Gonzalez-Dominguez I, Edgar JE, Bournazos S, Sun W, Carreno JM, Simon V, Ellebedy AH, Bajic G, Krammer F
Cell Rep (2024) 43 pp. 114922-114922 [ DOI: doi:10.1016/j.celrep.2024.114922 Pubmed: 39504245 ]
- Spike protein s1 (74 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
- Pvi.v5-4 light chain (23 kDa, Protein from Homo sapiens)
- Sars-cov-2 spike in complex with pvi.v5-4 fab (500 MDa, Complex from Homo sapiens)
- Pvi.v5-4 heavy chain (25 kDa, Protein from Homo sapiens)
- Spike protein s2 (62 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
Cryo-EM structure of SARS-CoV-2 spike in complex with VHH14
Resolution: 4.6 Å
EM Method: Single-particle
Fitted PDBs: 7xy3
Q-score: 0.278
Wang K, Cao D, Liu L, Fan X, Wang H, Zhang X, Yang P
To Be Published
- Vhh14 (17 kDa, Protein from Camelus bactrianus)
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
- Spike glycoprotein (125 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Vhh14 (Complex from Camelus bactrianus)
- Sars-cov-2 spike in complex with vhh14 (Complex)
- Sars-cov-2 spike (Complex from Severe acute respiratory syndrome coronavirus 2)
Cryo-EM structure of SARS-CoV-2 spike in complex with VHH21
Resolution: 3.3 Å
EM Method: Single-particle
Fitted PDBs: 7xy4
Q-score: 0.43
Wang K, Cao D, Liu L, Fan X, Wang H, Zhang X, Yang P
To Be Published
- Vhh21 (Complex from Camelus bactrianus)
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
- Spike glycoprotein (125 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Vhh21 (16 kDa, Protein from Camelus bactrianus)
- Sars-cov-2 spike (Complex from Severe acute respiratory syndrome coronavirus 2)
- Sars-cov-2 spike in complex with vhh21 (Complex)
SARS-CoV-2 WT Spike in complex with R15 Fab and P14 Nanobody
Resolution: 3.8 Å
EM Method: Single-particle
Fitted PDBs: 7y0n
Q-score: 0.333
To Be Published
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
- R15-f7 (Complex)
- Complex of sars-cov-2 spike in complex with r15-f7 and p14-f18-35 (Complex from Severe acute respiratory syndrome coronavirus 2)
- Light chain of r15-f7 (11 kDa, Protein from Homo sapiens)
- P14 (Complex from Homo sapiens)
- Spike glycoprotein (127 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- P14 nanobody (13 kDa, Protein from Vicugna pacos)
- Heavy chain of r15-f7 (12 kDa, Protein from Homo sapiens)
- Sars-cov-2 spike (Complex from Vicugna pacos)
Interface of SARS-CoV-2 WT Spike in complex with R15 Fab and P14 Nanobody
Resolution: 4.4 Å
EM Method: Single-particle
Fitted PDBs: 7y0o
Q-score: 0.3
To Be Published
- Spike protein s1 (21 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- P14 nanobody (13 kDa, Protein from Vicugna pacos)
- Complex of sars-cov-2 spike in complex with r15-f7 and p14-f18-35 (Complex from Severe acute respiratory syndrome coronavirus 2)
- Light chain of r15 (11 kDa, Protein from Homo sapiens)
- P14 (Complex)
- Heavy chain of r15 (12 kDa, Protein from Homo sapiens)
- Sars-cov-2 spike (Complex from Homo sapiens)
- R15 (Complex from Vicugna pacos)
- Water (18 Da, Ligand)
SARS Cov2 Spike RBD in complex with Fab47
Resolution: 2.64 Å
EM Method: Single-particle
Fitted PDBs: 8a95
Q-score: 0.269
Pushparaj P, Nicoletto A, Sheward DJ, Das H, Castro Dopico X, Perez Vidakovics L, Hanke L, Chernyshev M, Narang S, Kim S, Fischbach J, Ekstrom S, McInerney G, Hallberg BM, Murrell B, Corcoran M, Karlsson Hedestam GB
Immunity (2023) 56 pp. 193-206.e7 [ Pubmed: 36574772 DOI: doi:10.1016/j.immuni.2022.12.005 ]
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
- Sars-cov2 trimeric spike in 1-up conformation in complex with three fab47 (142 kDa, Protein from Severe acute respiratory syndrome coronavirus)
- Fab47 (light chain variable domain) (11 kDa, Protein from Homo sapiens)
- Sars-cov-2 spike in complex with fab47 (629 MDa, Complex from Homo sapiens)
- Fab47 (heavy chain variable domain) (13 kDa, Protein from Homo sapiens)
Cryo-EM structure of SARS-CoV-2 spike in complex with K202.B bispecific antibody
Resolution: 3.1 Å
EM Method: Single-particle
Fitted PDBs: 7yc5
Q-score: 0.284
Kim JW, Heo K, Kim HJ, Yoo Y, Cho HS, Jang HJ, Lee HY, Ko IY, Woo JR, Cho YB, Lee JH, Yang HR, Shin HG, Choi HL, Hwang K, Kim S, Kim H, Chun K, Lee S
Antiviral Res (2023) 212 pp. 105576-105576 [ Pubmed: 36870394 DOI: doi:10.1016/j.antiviral.2023.105576 ]
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
- Spike glycoprotein (133 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Light chain from k202.b, bispecific antibody (49 kDa, Protein from Homo sapiens)
- Heavy chain from k202.b, bispecific antibody (49 kDa, Protein from Homo sapiens)
- Cryo-em structure of sars-cov-2 spike in complex with k202.b bispecific antibody (Complex from Severe acute respiratory syndrome coronavirus 2)
- K202.b bispecific antibody (Complex)
- Sars-cov-2 spike (Complex from Severe acute respiratory syndrome coronavirus 2)
SARS CoV2 Spike in the 2-up state in complex with Fab47
Resolution: 2.4 Å
EM Method: Single-particle
Fitted PDBs: 8a94
Q-score: 0.303
Pushparaj P, Nicoletto A, Sheward DJ, Das H, Castro Dopico X, Perez Vidakovics L, Hanke L, Chernyshev M, Narang S, Kim S, Fischbach J, Ekstrom S, McInerney G, Hallberg BM, Murrell B, Corcoran M, Karlsson Hedestam GB
Immunity (2023) 56 pp. 193-206.e7 [ Pubmed: 36574772 DOI: doi:10.1016/j.immuni.2022.12.005 ]
- Fab47 (heavy chain variable domain) (13 kDa, Protein from Homo sapiens)
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
- Sars-cov-2 spike in complex with fab47 (629 MDa, Complex from Homo sapiens)
- Fab47 (light chain variable domain) (11 kDa, Protein from Homo sapiens)
- Sars-cov2 spike in 2-up conformation in complex with fab47 (142 kDa, Protein from Severe acute respiratory syndrome coronavirus)
Cryo-EM structure of SARS-CoV-2 spike glycoprotein in complex with three F61 Fab
Resolution: 3.62 Å
EM Method: Single-particle
Fitted PDBs: 7xmx
Q-score: -0.013
Li X, Pan Y, Yin Q, Wang Z, Shan S, Zhang L, Yu J, Qu Y, Sun L, Gui F, Lu J, Jing Z, Wu W, Huang T, Shi X, Li J, Li X, Li D, Wang S, Yang M, Zhang L, Duan K, Liang M, Yang X, Wang X
Cell Discov (2022) 8 pp. 87-87 [ DOI: doi:10.1038/s41421-022-00449-4 Pubmed: 36075908 ]
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
- F61 light chain (11 kDa, Protein from Homo sapiens)
- F61 heavy chain (12 kDa, Protein from Homo sapiens)
- S protein of sars-cov-2 spike in complex with f61 fab (Complex from Severe acute respiratory syndrome coronavirus 2)
- Spike glycoprotein (143 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)