BA.4/5 SARS-CoV-2 Spike bound to mouse ACE2 (local)
Resolution: 3.3 Å
EM Method: Single-particle
Fitted PDBs: 8aqw
Q-score: 0.452
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 ]
- Ba.4/5 sars-cov-2 spike bound to mouse ace2 (local) (430 kDa, Complex)
- Processed angiotensin-converting enzyme 2,ig gamma-2a chain c region, a allele (101 kDa, Protein from Mus musculus)
- Sars-cov-2 ba.4/5 spike protein (Complex from Severe acute respiratory syndrome coronavirus 2)
- Mouse ace2 (Complex from Mus musculus)
- Spike glycoprotein,fibritin (142 kDa, Protein from Enterobacteria phage T4)
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
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 [ Pubmed: 37100904 DOI: doi:10.1038/s41586-023-05993-x ]
- Spike glycoprotein,envelope glycoprotein (142 kDa, Protein from Tequatrovirus T4)
- De novo designed binder (8 kDa, Protein from Drosophila melanogaster)
- Omicron spike (Complex from Severe acute respiratory syndrome coronavirus 2)
- Omicron spike in complex with de novo designed binder, full map (Complex)
- De novo designed binder (Complex from Drosophila melanogaster)
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
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)
Beta SARS-CoV-2 Spike bound to mouse ACE2 (local)
Resolution: 4.4 Å
EM Method: Single-particle
Fitted PDBs: 8aqt
Q-score: 0.212
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 ]
- Spike glycoprotein,fibritin (142 kDa, Protein from Enterobacteria phage T4)
- Processed angiotensin-converting enzyme 2,ig gamma-2a chain c region, membrane-bound form (101 kDa, Protein from Mus musculus)
- Mouse ace2 (Complex from Homo sapiens)
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
- Beta sars-cov-2 spike (Complex from Severe acute respiratory syndrome coronavirus 2)
- Beta sars-cov-2 spike bound to mouse ace2 (430 kDa, Complex)
BA.1 SARS-CoV-2 Spike bound to mouse ACE2 (local)
Resolution: 3.22 Å
EM Method: Single-particle
Fitted PDBs: 8aqu
Q-score: 0.332
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 ]
- Processed angiotensin-converting enzyme 2,ig gamma-2a chain c region, membrane-bound form (101 kDa, Protein from Mus musculus)
- Sars-cov2 ba1 bound to mouse ace2 (430 kDa, Complex)
- Mouse ace2 (Complex from Mus musculus)
- Sars-cov-2 ba.1 spike protein (Complex from Severe acute respiratory syndrome coronavirus 2)
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
- Spike glycoprotein,fibritin (142 kDa, Protein from Enterobacteria phage T4)
BA.2.12.1 SARS-CoV-2 Spike bound to mouse ACE2 (local)
Resolution: 2.96 Å
EM Method: Single-particle
Fitted PDBs: 8aqv
Q-score: 0.513
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 ]
- Sars-cov-2 ba.2.12.1 spike protein (Complex from Severe acute respiratory syndrome coronavirus 2)
- Processed angiotensin-converting enzyme 2,ig gamma-2a chain c region, membrane-bound form (101 kDa, Protein from Mus musculus)
- Mouse ace2 (Complex from Mus musculus)
- Spike glycoprotein,fibritin (142 kDa, Protein from Enterobacteria phage T4)
- Sars-cov2 ba.2.12.1 bound to mouse ace2 (430 kDa, Complex)
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
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)