CryoEM structure of compound HNC-1664 bound with RdRP-RNA complex of SARS-CoV-2
Resolution: 3.29 Å
EM Method: Single-particle
Fitted PDBs: 8xko
Q-score: 0.486
Jia X, Jing X, Li M, Gao M, Zhong Y, Li E, Liu Y, Li R, Yao G, Liu Q, Zhou M, Hou Y, An L, Hong Y, Li S, Zhang J, Wang W, Zhang K, Gong P, Chiu S
Nat Commun (2024) 15 pp. 10750-10750 [ DOI: doi:10.1038/s41467-024-54918-3 Pubmed: 39737930 ]
- Rna (5'-r(p*up*up*cp*ap*up*gp*cp*up*ap*cp*gp*cp*gp*up*ap*g)-3') (5 kDa, RNA from synthetic construct)
- Cryoem structure of compound hnc-1644 bound with rdrp-rna (150 kDa, Complex from Severe acute respiratory syndrome coronavirus)
- Non-structural protein 7 (10 kDa, Protein from Severe acute respiratory syndrome coronavirus)
- [[(2~{r},3~{r},4~{s},5~{r})-4-fluoranyl-5-(5-iodanyl-4-methyl-pyrrolo[2,3-d]pyrimidin-7-yl)-3-oxidanyl-oxolan-2-yl]methoxy-oxidanyl-phosphoryl] phosphono hydrogen phosphate (633 Da, Ligand)
- Rna (5'-r(p*cp*up*ap*cp*gp*cp*gp*up*ap*gp*cp*ap*up*g)-3') (4 kDa, RNA from synthetic construct)
- Magnesium ion (24 Da, Ligand)
- Non-structural protein 8 (23 kDa, Protein from Severe acute respiratory syndrome coronavirus)
- Rna-directed rna polymerase nsp12 (108 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
Cryo-EM map of SARS-CoV-2 Omicron BA.2 spike in complex with 2130-1-0114-112
Resolution: 3.6 Å
EM Method: Single-particle
Fitted PDBs: 8ekd
Q-score: 0.433
Desautels TA, Arrildt KT, Zemla AT, Lau EY, Zhu F, Ricci D, Cronin S, Zost SJ, Binshtein E, Scheaffer SM, Dadonaite B, Petersen BK, Engdahl TB, Chen E, Handal LS, Hall L, Goforth JW, Vashchenko D, Nguyen S, Weilhammer DR, Lo JK, Rubinfeld B, Saada EA, Weisenberger T, Lee TH, Whitener B, Case JB, Ladd A, Silva MS, Haluska RM, Grzesiak EA, Earnhart CG, Hopkins S, Bates TW, Thackray LB, Segelke BW, Lillo AM, Sundaram S, Bloom JD, Diamond MS, Crowe Jr JE, Carnahan RH, Faissol DM
Nature (2024) 629 pp. 878-885 [ Pubmed: 38720086 DOI: doi:10.1038/s41586-024-07385-1 ]
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
- Fab llnl-199 lc (12 kDa, Protein from Homo sapiens)
- Sars cov2 omicron ba.2 rbd complex with fab llnl-199 (Complex)
- Sars cov2 omicron ba.2 rbd (Complex from Severe acute respiratory syndrome coronavirus)
- Fab llnl-199 hc (14 kDa, Protein from Homo sapiens)
- Spike protein s2' (20 kDa, Protein from Severe acute respiratory syndrome coronavirus)
- Fab llnl-199 (Complex from Homo sapiens)
SARS-CoV-2 Omicron 1-RBD up Spike trimer complexed with three XG005 molecules
Resolution: 3.74 Å
EM Method: Single-particle
Fitted PDBs: 7ycy
Q-score: 0.26
To Be Published
- Spike glycoprotein (142 kDa, Protein from Severe acute respiratory syndrome coronavirus)
- Xg005-vh (13 kDa, Protein from Homo sapiens)
- Omicron rbd with xg005 (Complex from Severe acute respiratory syndrome coronavirus 2)
- Xg005-vl (11 kDa, Protein from Homo sapiens)
SARS-CoV-2 Omicron 2-RBD up Spike trimer complexed with three XG005 molecules
Resolution: 3.24 Å
EM Method: Single-particle
Fitted PDBs: 7ycz
Q-score: 0.352
To Be Published
- Spike glycoprotein (142 kDa, Protein from Severe acute respiratory syndrome coronavirus)
- Xg005-vl (21 kDa, Protein from Homo sapiens)
- Omicron rbd with xg005 (Complex from Severe acute respiratory syndrome coronavirus 2)
- Xg005-vh (23 kDa, Protein from Homo sapiens)
SARS-CoV-2 Omicron 1-RBD up spike trimer complexed with two XG005 Fab
Resolution: 3.58 Å
EM Method: Single-particle
Fitted PDBs: 7yd0
Q-score: 0.267
To Be Published
- Spike glycoprotein (142 kDa, Protein from Severe acute respiratory syndrome coronavirus)
- Xg005-vl (21 kDa, Protein from Homo sapiens)
- Omicron rbd with xg005 (Complex from Severe acute respiratory syndrome coronavirus 2)
- Xg005-vh (23 kDa, Protein from Homo sapiens)
Resolution: 3.1 Å
EM Method: Single-particle
Fitted PDBs: 8fxb
Q-score: 0.469
Addetia A, Piccoli L, Case JB, Park YJ, Beltramello M, Guarino B, Dang H, de Melo GD, Pinto D, Sprouse K, Scheaffer SM, Bassi J, Silacci-Fregni C, Muoio F, Dini M, Vincenzetti L, Acosta R, Johnson D, Subramanian S, Saliba C, Giurdanella M, Lombardo G, Leoni G, Culap K, McAlister C, Rajesh A, Dellota Jr E, Zhou J, Farhat N, Bohan D, Noack J, Chen A, Lempp FA, Quispe J, Kergoat L, Larrous F, Cameroni E, Whitener B, Giannini O, Cippa P, Ceschi A, Ferrari P, Franzetti-Pellanda A, Biggiogero M, Garzoni C, Zappi S, Bernasconi L, Kim MJ, Rosen LE, Schnell G, Czudnochowski N, Benigni F, Franko N, Logue JK, Yoshiyama C, Stewart C, Chu H, Bourhy H, Schmid MA, Purcell LA, Snell G, Lanzavecchia A, Diamond MS, Corti D, Veesler D
Nature (2023) 621 pp. 592-601 [ DOI: doi:10.1038/s41586-023-06487-6 Pubmed: 37648855 ]
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
- Sars-cov-2 xbb.1 spike rbd bound to the human ace2 ectodomain and the s309 neutralizing antibody fab fragment (Complex from Severe acute respiratory syndrome coronavirus 2)
- S309 heavy chain (50 kDa, Protein from Homo sapiens)
- Processed angiotensin-converting enzyme 2 (74 kDa, Protein from Homo sapiens)
- Sars-cov-2 xbb.1 spike rbd bound to the human ace2 ectodomain and the s309 neutralizing antibody fab fragment (Complex from Severe acute respiratory syndrome coronavirus 2)
- S309 light chain (23 kDa, Protein from Homo sapiens)
- Spike protein s1 (28 kDa, Protein from Severe acute respiratory syndrome coronavirus)
Resolution: 3.0 Å
EM Method: Single-particle
Fitted PDBs: 8s9g
Q-score: 0.473
Addetia A, Piccoli L, Case JB, Park YJ, Beltramello M, Guarino B, Dang H, de Melo GD, Pinto D, Sprouse K, Scheaffer SM, Bassi J, Silacci-Fregni C, Muoio F, Dini M, Vincenzetti L, Acosta R, Johnson D, Subramanian S, Saliba C, Giurdanella M, Lombardo G, Leoni G, Culap K, McAlister C, Rajesh A, Dellota Jr E, Zhou J, Farhat N, Bohan D, Noack J, Chen A, Lempp FA, Quispe J, Kergoat L, Larrous F, Cameroni E, Whitener B, Giannini O, Cippa P, Ceschi A, Ferrari P, Franzetti-Pellanda A, Biggiogero M, Garzoni C, Zappi S, Bernasconi L, Kim MJ, Rosen LE, Schnell G, Czudnochowski N, Benigni F, Franko N, Logue JK, Yoshiyama C, Stewart C, Chu H, Bourhy H, Schmid MA, Purcell LA, Snell G, Lanzavecchia A, Diamond MS, Corti D, Veesler D
Nature (2023) 621 pp. 592-601 [ DOI: doi:10.1038/s41586-023-06487-6 Pubmed: 37648855 ]
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
- Sars-cov-2 bn.1 spike rbd bound to the human ace2 ectodomain and the s309 neutralizing antibody fab fragment (Complex from Severe acute respiratory syndrome coronavirus 2)
- Sars-cov-2 bn.1 spike rbd bound to the human ace2 ectodomain and the s309 neutralizing antibody fab fragment (Complex from Severe acute respiratory syndrome coronavirus 2)
- Processed angiotensin-converting enzyme 2 (74 kDa, Protein from Homo sapiens)
- Spike glycoprotein (28 kDa, Protein from Severe acute respiratory syndrome coronavirus)
- S309 fab light chain (23 kDa, Protein from Homo sapiens)
- S309 fab heavy chain (24 kDa, Protein from Homo sapiens)
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)
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 ]
- Spike glycoprotein (143 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- 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+antibody (Complex from Severe acute respiratory syndrome coronavirus 2)
Cryo-EM structure of SARS-CoV-2 postfusion spike in membrane
Resolution: 2.9 Å
EM Method: Single-particle
Fitted PDBs: 8fdw
Q-score: 0.327
Shi W, Cai Y, Zhu H, Peng H, Voyer J, Rits-Volloch S, Cao H, Mayer ML, Song K, Xu C, Lu J, Zhang J, Chen B
Nature (2023) 619 pp. 403-409 [ DOI: doi:10.1038/s41586-023-06273-4 Pubmed: 37285872 ]
- Alpha-d-mannopyranose (180 Da, Ligand)
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
- Spike protein s2 (68 kDa, Protein from Severe acute respiratory syndrome coronavirus)
- Sras-cov-2 postfusion spike protein in nanodisc (210 kDa, Complex from Severe acute respiratory syndrome coronavirus 2)