XBB 1.0 RBD bound to P4J15 (Local)
Resolution: 3.85 Å
EM Method: Single-particle
Fitted PDBs: 8pq2
Q-score: 0.481
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 ]
- P4j15 fragment antigen-binding light chain (11 kDa, Protein from Homo sapiens)
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
- P4j15 fragment antigen-binding heavy chain (13 kDa, Protein from Homo sapiens)
- Spike protein s2' (21 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Spike xbb.1 rbd up - p4j15 fab (local) (72 MDa, Complex from Severe acute respiratory syndrome coronavirus 2)
XBB 1.0 RBD bound to P4J15 (Global)
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 ]
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, full map
Resolution: 2.8 Å
EM Method: Single-particle
Fitted PDBs: 7zrv
Q-score: 0.4
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 [ DOI: doi:10.1038/s41586-023-05993-x Pubmed: 37100904 ]
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
- Spike glycoprotein,envelope glycoprotein (142 kDa, Protein from Tequatrovirus T4)
- Omicron spike (Complex from Severe acute respiratory syndrome coronavirus 2)
- De novo designed binder (Complex from Drosophila melanogaster)
- De novo designed binder (8 kDa, Protein from Drosophila melanogaster)
- Omicron spike in complex with de novo designed binder, full map (Complex)
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 [ DOI: doi:10.1038/s41586-023-05993-x Pubmed: 37100904 ]
- Omicron spike (Complex from Severe acute respiratory syndrome coronavirus 2)
- Spike glycoprotein (22 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- De novo designed binder (Complex from Drosophila melanogaster)
- Omicron spike in complex with de novo designed binder (450 kDa, Complex)
- De novo designed binder (8 kDa, Protein 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 [ DOI: doi:10.1038/s41586-023-05993-x Pubmed: 37100904 ]
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
- De novo designed binder (Complex from Drosophila melanogaster)
- Spike glycoprotein (126 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- De novo designed binder (8 kDa, Protein from Drosophila melanogaster)
- D614g spike in complex with de novo designed binder (450 kDa, Complex)
- D614g spike (Complex from Severe acute respiratory syndrome coronavirus 2)
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 ]
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
- P2g3 light chain (23 kDa, Protein from Homo sapiens)
- P2g3 heavy chain (24 kDa, Protein from Homo sapiens)
- Spike omicron trimer with fabs (Complex)
- P5c3 heavy chain (23 kDa, Protein from Homo sapiens)
- P5c3 light chain (23 kDa, Protein from Homo sapiens)
- Spike glycoprotein,envelope glycoprotein (142 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Omicron spike (Complex from Homo sapiens)
- Fabs (Complex from Severe acute respiratory syndrome coronavirus 2)
SARS-CoV-2 S Omicron Spike B.1.1.529 - RBD up - 1-P2G3 and 1-P5C3 Fabs (Local)
Resolution: 4.01 Å
EM Method: Single-particle
Fitted PDBs: 7qtj
Q-score: 0.344
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 ]
- P2g3 light chain (23 kDa, Protein from Homo sapiens)
- P2g3 heavy chain (24 kDa, Protein from Homo sapiens)
- P5c3 heavy chain (23 kDa, Protein from Homo sapiens)
- P5c3 light chain (23 kDa, Protein from Homo sapiens)
- Spike omicron trimer with fabs (Complex from Severe acute respiratory syndrome coronavirus 2)
- Surface glycoprotein (142 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
SARS-CoV-2 S Omicron Spike B.1.1.529 - RBD down - 1-P2G3 Fab (Local)
Resolution: 3.84 Å
EM Method: Single-particle
Fitted PDBs: 7qtk
Q-score: 0.393
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 ]
- Spike omicron trimer with fabs (Complex from Severe acute respiratory syndrome coronavirus 2)
- Surface glycoprotein (142 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- P2g3 light chain (23 kDa, Protein from Homo sapiens)
- 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)