SARS-CoV-2 XBB 1.0 closed conformation.
Resolution: 2.9 Å
EM Method: Single-particle
Fitted PDBs: 8psd
Q-score: 0.562
Fenwick C, Turelli P, Duhoo Y, Lau K, Herate C, Marlin R, Lamrayah M, Campos J, Esteves-Leuenberger L, Farina A, Raclot C, Genet V, Fiscalini F, Cesborn J, Perez L, Dereuddre-Bosquet N, Contreras V, Lheureux K, Relouzat F, Abdelnabi R, Leyssen P, Levy Y, Pojer F, Le Grand R, Trono D, Pantaleo G
J Infect (2023) 87 pp. 524-537 [ Pubmed: 37852477 DOI: doi:10.1016/j.jinf.2023.10.008 ]
cryo-EM structure of omicron spike in complex with de novo designed binder, local
Resolution: 3.29 Å
EM Method: Single-particle
Fitted PDBs: 7zsd
Q-score: 0.431
Gainza P, Wehrle S, Van Hall-Beauvais A, Marchand A, Scheck A, Harteveld Z, Buckley S, Ni D, Tan S, Sverrisson F, Goverde C, Turelli P, Raclot C, Teslenko A, Pacesa M, Rosset S, Georgeon S, Marsden J, Petruzzella A, Liu K, Xu Z, Chai Y, Han P, Gao GF, Oricchio E, Fierz B, Trono D, Stahlberg H, Bronstein M, Correia BE
Nature (2023) 617 pp. 176-184 [ Pubmed: 37100904 DOI: doi:10.1038/s41586-023-05993-x ]
- Omicron spike in complex with de novo designed binder (450 kDa, Complex)
- De novo designed binder (8 kDa, Protein from Drosophila melanogaster)
- Spike glycoprotein (22 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Omicron spike (Complex from Severe acute respiratory syndrome coronavirus 2)
- De novo designed binder (Complex from Drosophila melanogaster)
Resolution: 2.63 Å
EM Method: Single-particle
Fitted PDBs: 7zss
Q-score: 0.453
Gainza P, Wehrle S, Van Hall-Beauvais A, Marchand A, Scheck A, Harteveld Z, Buckley S, Ni D, Tan S, Sverrisson F, Goverde C, Turelli P, Raclot C, Teslenko A, Pacesa M, Rosset S, Georgeon S, Marsden J, Petruzzella A, Liu K, Xu Z, Chai Y, Han P, Gao GF, Oricchio E, Fierz B, Trono D, Stahlberg H, Bronstein M, Correia BE
Nature (2023) 617 pp. 176-184 [ Pubmed: 37100904 DOI: doi:10.1038/s41586-023-05993-x ]
- Spike glycoprotein (126 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- D614g spike in complex with de novo designed binder (450 kDa, Complex)
- De novo designed binder (8 kDa, Protein from Drosophila melanogaster)
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
- De novo designed binder (Complex from Drosophila melanogaster)
- D614g spike (Complex from Severe acute respiratory syndrome coronavirus 2)
BA.4/5 SARS-CoV-2 Spike bound to human ACE2 (local)
Resolution: 2.92 Å
EM Method: Single-particle
Fitted PDBs: 8aqs
Q-score: 0.549
Ni D, Turelli P, Beckert B, Nazarov S, Uchikawa E, Myasnikov A, Pojer F, Trono D, Stahlberg H, Lau K
PLoS Pathog (2023) 19 pp. e1011206-e1011206 [ DOI: doi:10.1371/journal.ppat.1011206 Pubmed: 37018380 ]
- Water (18 Da, Ligand)
- Ba.4/5 sars-cov-2 spike bound to human ace2 (local) (430 kDa, Complex)
- Processed angiotensin-converting enzyme 2 (101 kDa, Protein from Homo sapiens)
- Zinc ion (65 Da, Ligand)
- Spike glycoprotein,fibritin (142 kDa, Protein from Enterobacteria phage T4)
- Sars-cov-2 ba.4/5 spike protein (Complex from Severe acute respiratory syndrome coronavirus 2)
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
- Human ace2 (Complex from Homo sapiens)
SARS-CoV-2 S Omicron Spike B.1.1.529 - 3-P2G3 and 1-P5C3 Fabs (Global)
Resolution: 3.04 Å
EM Method: Single-particle
Fitted PDBs: 7qti
Q-score: 0.331
Fenwick C, Turelli P, Ni D, Perez L, Lau K, Herate C, Marlin R, Lana E, Pellaton C, Raclot C, Esteves-Leuenberger L, Campos J, Farina A, Fiscalini F, Dereuddre-Bosquet N, Relouzat F, Abdelnabi R, Foo CS, Neyts J, Leyssen P, Levy Y, Pojer F, Stahlberg H, LeGrand R, Trono D, Pantaleo G
Nat Microbiol (2022) 7 pp. 1376-1389 [ Pubmed: 35879526 DOI: doi:10.1038/s41564-022-01198-6 ]
- P5c3 light chain (23 kDa, Protein from Homo sapiens)
- Spike omicron trimer with fabs (Complex)
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
- Spike glycoprotein,envelope glycoprotein (142 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- P5c3 heavy chain (23 kDa, Protein from Homo sapiens)
- P2g3 light chain (23 kDa, Protein from Homo sapiens)
- Omicron spike (Complex from Homo sapiens)
- Fabs (Complex from Severe acute respiratory syndrome coronavirus 2)
- P2g3 heavy chain (24 kDa, Protein from Homo sapiens)
SARS-CoV-2 S Omicron Spike B.1.1.529 - RBD and NTD (Local)
Resolution: 3.88 Å
EM Method: Single-particle
Fitted PDBs: 7qo9
Q-score: 0.38
Ni D, Lau K, Turelli P, Raclot C, Beckert B, Nazarov S, Pojer F, Myasnikov A, Stahlberg H, Trono D
bioRxiv (2021) [ DOI: doi:10.1101/2021.12.27.474250 ]
- Water (18 Da, Ligand)
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
- Spike glycoprotein,sars-cov-2 s omicron spike b.1.1.529 (142 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Spike trimer (752 MDa, Complex from Severe acute respiratory syndrome coronavirus 2)
P5C3 is a potent fab neutralizer
Resolution: 3.5 Å
EM Method: Single-particle
Fitted PDBs: 7p40
Q-score: 0.308
Fenwick C, Turelli P, Perez L, Pellaton C, Esteves-Leuenberger L, Farina A, Campos J, Lana E, Fiscalini F, Raclot C, Pojer F, Lau K, Demurtas D, Descatoire M, Joo VS, Foglierini M, Noto A, Abdelnabi R, Foo CS, Vangeel L, Neyts J, Du W, Bosch BJ, Veldman G, Leyssen P, Thiel V, LeGrand R, Levy Y, Trono D, Pantaleo G
Cell Rep (2021) 37 pp. 109814-109814 [ Pubmed: 34599871 DOI: doi:10.1016/j.celrep.2021.109814 ]
- Spike glycoprotein (141 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Variable light chain p5c3 (vl) (23 kDa, Protein from Homo sapiens)
- Severe acute respiratory syndrome coronavirus 2 (Complex)
- Spike glycoprotein (Complex from Severe acute respiratory syndrome coronavirus 2)
- Variable heavy chain p5c3 (vh) (23 kDa, Protein from Homo sapiens)
- Fab (Complex from Homo sapiens)