Infectious bronchitis virus core polymerase complex
Resolution: 3.5 Å
EM Method: Single-particle
Fitted PDBs: 9cpo
Q-score: 0.477
Hoferle PJ, Anderson TK, Kirchdoerfer RN
bioRxiv (2024) [ DOI: doi:10.1101/2024.07.23.604833 Pubmed: 39091740 ]
- Rna primer (9 kDa, RNA from Severe acute respiratory syndrome coronavirus 2)
- Core polymerase complex of the infectious bronchitis virus composed of nsp12, nsp8, nsp7, and an dsrna substrate (194 kDa, Complex from Infectious bronchitis virus)
- Zinc ion (65 Da, Ligand)
- Rna-directed rna polymerase nsp12 (107 kDa, Protein from Infectious bronchitis virus)
- Non-structural protein 8 (21 kDa, Protein from Infectious bronchitis virus)
- Non-structural protein 7 (8 kDa, Protein from Infectious bronchitis virus)
- Rna template (10 kDa, RNA from Severe acute respiratory syndrome coronavirus 2)
Porcine epidemic diarrhea virus complete core polymerase complex
Resolution: 3.4 Å
EM Method: Single-particle
Fitted PDBs: 8urb
Q-score: 0.49
Anderson TK, Hoferle PJ, Lee KW, Coon JJ, Kirchdoerfer RN
bioRxiv (2023) [ DOI: doi:10.1101/2023.03.15.532841 Pubmed: 36993498 ]
- Nsp7 (9 kDa, Protein from Porcine epidemic diarrhea virus)
- Zinc ion (65 Da, Ligand)
- Nsp12 (108 kDa, Protein from Porcine epidemic diarrhea virus)
- Core polymerase complex of the porcine epidemic diarrhea virus composed of nsp12, nsp7, nsp8, and a short rna substrate (185 kDa, Complex from Porcine epidemic diarrhea virus)
- Rna (55-mer) (17 kDa, RNA from synthetic construct)
- Nsp8 (21 kDa, Protein from Porcine epidemic diarrhea virus)
- Rna (33-mer) (10 kDa, RNA from synthetic construct)
Porcine epidemic diarrhea virus core polymerase complex
Resolution: 3.3 Å
EM Method: Single-particle
Fitted PDBs: 8g6r
Q-score: 0.435
Anderson TK, Hoferle PJ, Lee KW, Coon JJ, Kirchdoerfer RN
bioRxiv (2023) [ DOI: doi:10.1101/2023.03.15.532841 Pubmed: 36993498 ]
- Zinc ion (65 Da, Ligand)
- Nsp12 (104 kDa, Protein from Porcine epidemic diarrhea virus)
- Nsp7 (6 kDa, Protein from Porcine epidemic diarrhea virus)
- Rna (5'-r(p*gp*gp*up*up*gp*up*gp*ap*up*up*up*up*ap*ap*up*ap*gp*cp*up*u)-3') (6 kDa, RNA from synthetic construct)
- Core replication complex of porcine epidemic diarrhea virus composed of nsp12, nsp7, nsp8, and a short rna substrate (185 kDa, Complex from Porcine epidemic diarrhea virus)
- Nsp8 (12 kDa, Protein from Porcine epidemic diarrhea virus)
- Rna (5'-r(p*ap*ap*gp*ap*ap*gp*cp*up*ap*up*up*ap*ap*ap*ap*up*cp*ap*cp*a)-3') (6 kDa, RNA from synthetic construct)
BG505 SOSIP.v5.2 in complex with the polyclonal Fab pAbC-1 from animal Rh.4O9
Resolution: 3.6 Å
EM Method: Single-particle
Fitted PDBs: 7mdt
Q-score: 0.481
Antanasijevic A, Bowman CA, Kirchdoerfer RN, Cottrell CA, Ozorowski G, Upadhyay AA, Cirelli KM, Carnathan DG, Enemuo CA, Sewall LM, Nogal B, Zhao F, Groschel B, Schief WR, Sok D, Silvestri G, Crotty S, Bosinger SE, Ward AB
Sci Adv (2022) 8 pp. eabk2039-eabk2039 [ DOI: doi:10.1126/sciadv.abk2039 Pubmed: 35044813 ]
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
- Transmembrane protein gp41 (17 kDa, Protein from Human immunodeficiency virus 1)
- Bg505 sosip.v5.2 in complex with the polyclonal fab sample isolated from animal rh4o9. (Complex from Human immunodeficiency virus)
- Surface protein gp120 (57 kDa, Protein from Human immunodeficiency virus 1)
- Rh4o9.8 monoclonal antibody heavy chain (12 kDa, Protein from Macaca mulatta)
- Rh4o9.8 monoclonal antibody light chain (11 kDa, Protein from Macaca mulatta)
BG505 SOSIP MD39 in complex with the monoclonal antibodies Rh.33104 mAb.1 and RM20A3
Resolution: 3.3 Å
EM Method: Single-particle
Fitted PDBs: 7mdu
Q-score: 0.517
Antanasijevic A, Bowman CA, Kirchdoerfer RN, Cottrell CA, Ozorowski G, Upadhyay AA, Cirelli KM, Carnathan DG, Enemuo CA, Sewall LM, Nogal B, Zhao F, Groschel B, Schief WR, Sok D, Silvestri G, Crotty S, Bosinger SE, Ward AB
Sci Adv (2022) 8 pp. eabk2039-eabk2039 [ DOI: doi:10.1126/sciadv.abk2039 Pubmed: 35044813 ]
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
- Transmembrane protein gp41 (17 kDa, Protein from Human immunodeficiency virus 1)
- Surface protein gp120 (57 kDa, Protein from Human immunodeficiency virus 1)
- Rm20a3 mab heavy chain (13 kDa, Protein from Macaca mulatta)
- Rh.33104 mab.1 light chain (11 kDa, Protein from Macaca mulatta)
- Rm20a3 mab light chain (11 kDa, Protein from Macaca mulatta)
- Rh.33104 mab.1 heavy chain (12 kDa, Protein from Macaca mulatta)
- Bg505 sosip md39 in complex with the monoclonal antibodies rh.33104 mab.1 and rm20a3 (Complex from Macaca mulatta)
BG505 SOSIP.v5.2(7S) in complex with the monoclonal antibodies Rh.33172 mAb.1 and RM19R
Resolution: 3.5 Å
EM Method: Single-particle
Fitted PDBs: 7mep
Q-score: 0.486
Antanasijevic A, Bowman CA, Kirchdoerfer RN, Cottrell CA, Ozorowski G, Upadhyay AA, Cirelli KM, Carnathan DG, Enemuo CA, Sewall LM, Nogal B, Zhao F, Groschel B, Schief WR, Sok D, Silvestri G, Crotty S, Bosinger SE, Ward AB
Sci Adv (2022) 8 pp. eabk2039-eabk2039 [ DOI: doi:10.1126/sciadv.abk2039 Pubmed: 35044813 ]
- Rm19r mab heavy chain (13 kDa, Protein from Macaca mulatta)
- Monoclonal antibodies rh.33172 mab.1 and rm19r (Complex from Macaca mulatta)
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
- Bg505 sosipv5.2(7s) - gp120 (74 kDa, Protein from Human immunodeficiency virus)
- Rm19r mab light chain (11 kDa, Protein from Macaca mulatta)
- Bg505 sosip.v5.2(7s) (Complex from Human immunodeficiency virus)
- Bg505 sosip.v5.2(7s) in complex with the monoclonal antibodies rh.33172 mab.1 and rm19r (Complex)
- Rh.33172 mab.1 heavy chain (14 kDa, Protein from Macaca mulatta)
- Rh.33172 mab.1 light chain (11 kDa, Protein from Macaca mulatta)
Cryo-EM structure of porcine epidemic diarrhea virus (PEDV) spike protein
Resolution: 3.5 Å
EM Method: Single-particle
Fitted PDBs: 6vv5
Q-score: 0.474
Kirchdoerfer RN, Bhandari M, Martini O, Sewall LM, Bangaru S, Yoon KJ, Ward AB
Structure (2021) 29 pp. 385-392.e5 [ Pubmed: 33378641 DOI: doi:10.1016/j.str.2020.12.003 ]
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
- Porcine epidemic diarrhea virus spike protein (600 kDa, Complex from Porcine epidemic diarrhea virus)
- Palmitoleic acid (254 Da, Ligand)
- Spike glycoprotein (148 kDa, Protein from Porcine epidemic diarrhea virus)
SARS-Coronavirus NSP12 bound to NSP7 and NSP8 co-factors
Resolution: 3.1 Å
EM Method: Single-particle
Fitted PDBs: 6nur
Q-score: 0.491
Nat Commun (2019) 10 pp. 2342-2342 [ Pubmed: 31138817 DOI: doi:10.1038/s41467-019-10280-3 ]
- Zinc ion (65 Da, Ligand)
- Nsp7 (9 kDa, Protein from Human SARS coronavirus)
- Sars-coronavirus nsp12 bound to nsp7 and nsp8 co-factors (160 kDa, Complex from SARS coronavirus)
- Nsp12 (109 kDa, Protein from Human SARS coronavirus)
- Nsp8 (21 kDa, Protein from Human SARS coronavirus)
SARS-Coronavirus NSP12 bound to NSP8 co-factor
Resolution: 3.5 Å
EM Method: Single-particle
Fitted PDBs: 6nus
Q-score: 0.383
Nat Commun (2019) 10 pp. 2342-2342 [ Pubmed: 31138817 DOI: doi:10.1038/s41467-019-10280-3 ]
- Sars-coronavirus nsp12 bound to nsp7 and nsp8 co-factors (130 kDa, Complex from SARS coronavirus)
- Zinc ion (65 Da, Ligand)
- Nsp8 (21 kDa, Protein from Human SARS coronavirus)
- Nsp12 (109 kDa, Protein from Human SARS coronavirus)
SARS Spike Glycoprotein, Stabilized variant, C3 symmetry
Resolution: 3.2 Å
EM Method: Single-particle
Fitted PDBs: 6crv
Q-score: 0.466
Kirchdoerfer RN, Wang N, Pallesen J, Wrapp D, Turner HL, Cottrell CA, Corbett KS, Graham BS, McLellan JS, Ward AB
Sci Rep (2018) 8 pp. 15701-15701 [ DOI: doi:10.1038/s41598-018-34171-7 Pubmed: 30356097 ]
- Sars spike glycoprotein, stabilized ectodomain (540 kDa, Complex from SARS coronavirus)
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
- Spike glycoprotein,fibritin (137 kDa, Protein from Enterobacteria phage T4)