Dimer of SARS-CoV-2 S1 in complex with H18 and R1-32 Fabs
Yan Q, Gao X, Liu B, Hou R, He P, Ma Y, Zhang Y, Zhang Y, Li Z, Chen Q, Wang J, Huang X, Liang H, Zheng H, Yao Y, Chen X, Niu X, He J, Chen L, Zhao J, Xiong X
Nat Commun (2024) 15 pp. 7585-7585 [ DOI: doi:10.1038/s41467-024-51770-3 Pubmed: 39217172 ]
- Heavy chain of h18 fab (25 kDa, Protein from Homo sapiens)
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
- Light chain of r1-32 fab (22 kDa, Protein from Homo sapiens)
- Dimer of sars-cov-2 s1 in complex with h18 and r1-32 fabs (Complex from Severe acute respiratory syndrome coronavirus 2)
- H18 fab (Complex from Homo sapiens)
- Light chain of h18 fab (25 kDa, Protein from Homo sapiens)
- Spike glycoprotein (74 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Heavy chain of r1-32 fab (23 kDa, Protein from Homo sapiens)
- Sars-cov-2 s1 (Complex from Severe acute respiratory syndrome coronavirus 2)
- R1-32 fab (Complex from Homo sapiens)
Cryo-EM structure of Thogoto virus polymerase in transcription pre-initiation conformation 1
Resolution: 2.3 Å
EM Method: Single-particle
Fitted PDBs: 8z85
Q-score: 0.597
Xue L, Chang T, Li Z, Wang C, Zhao H, Li M, Tang P, Wen X, Yu M, Wu J, Bao X, Wang X, Gong P, He J, Chen X, Xiong X
Nat Commun (2024) 15 pp. 4620-4620 [ DOI: doi:10.1038/s41467-024-48848-3 Pubmed: 38816392 ]
- Rna-directed rna polymerase catalytic subunit (81 kDa, Protein from Thogoto virus (isolate SiAr 126))
- Polymerase acidic protein (71 kDa, Protein from Thogoto virus (isolate SiAr 126))
- Rna (5'-r(*ap*gp*ap*gp*ap*ap*ap*up*cp*ap*ap*gp*gp*cp*ap*gp*up*u)-3') (5 kDa, RNA from Thogoto virus (isolate SiAr 126))
- Rna (5'-r(*gp*ap*cp*up*gp*cp*cp*up*gp*up*up*up*up*up*gp*cp*u)-3') (5 kDa, RNA from Thogoto virus (isolate SiAr 126))
- Cryo-em structure of thogoto virus polymerase in transcription pre-initiation conformation 1 (Complex from Thogoto virus (isolate SiAr 126))
- Polymerase basic protein 2 (94 kDa, Protein from Thogoto virus (isolate SiAr 126))
Cryo-EM structure of Thogoto virus polymerase in transcription pre-initiation conformation 2
Resolution: 3.16 Å
EM Method: Single-particle
Fitted PDBs: 8z8j
Q-score: 0.515
Xue L, Chang T, Li Z, Wang C, Zhao H, Li M, Tang P, Wen X, Yu M, Wu J, Bao X, Wang X, Gong P, He J, Chen X, Xiong X
Nat Commun (2024) 15 pp. 4620-4620 [ DOI: doi:10.1038/s41467-024-48848-3 Pubmed: 38816392 ]
- Rna-directed rna polymerase catalytic subunit (81 kDa, Protein from Thogoto virus (isolate SiAr 126))
- Polymerase acidic protein (71 kDa, Protein from Thogoto virus (isolate SiAr 126))
- Rna (5'-r(*ap*gp*ap*gp*ap*ap*ap*up*cp*ap*ap*gp*gp*cp*ap*gp*up*u)-3') (5 kDa, RNA from Thogoto virus (isolate SiAr 126))
- Cryo-em structure of thogoto virus polymerase in transcription pre-initiation conformation 2 (Complex from Thogoto virus (isolate SiAr 126))
- Rna (5'-r(*gp*ap*cp*up*gp*cp*cp*up*gp*up*up*up*up*up*gp*cp*u)-3') (5 kDa, RNA from Thogoto virus (isolate SiAr 126))
- Polymerase basic protein 2 (94 kDa, Protein from Thogoto virus (isolate SiAr 126))
Cryo-EM structure of Thogoto virus polymerase in transcription pre-initiation conformation 3
Resolution: 2.79 Å
EM Method: Single-particle
Fitted PDBs: 8z8n
Q-score: 0.532
Xue L, Chang T, Li Z, Wang C, Zhao H, Li M, Tang P, Wen X, Yu M, Wu J, Bao X, Wang X, Gong P, He J, Chen X, Xiong X
Nat Commun (2024) 15 pp. 4620-4620 [ DOI: doi:10.1038/s41467-024-48848-3 Pubmed: 38816392 ]
- Rna-directed rna polymerase catalytic subunit (81 kDa, Protein from Thogoto virus (isolate SiAr 126))
- Polymerase acidic protein (71 kDa, Protein from Thogoto virus (isolate SiAr 126))
- Cryo-em structure of thogoto virus polymerase in transcription pre-initiation conformation 3 (Complex from Thogoto virus (isolate SiAr 126))
- Rna (5'-r(*ap*gp*ap*gp*ap*ap*ap*up*cp*ap*ap*gp*gp*cp*ap*gp*up*u)-3') (5 kDa, RNA from Thogoto virus (isolate SiAr 126))
- Rna (5'-r(*gp*ap*cp*up*gp*cp*cp*up*gp*up*up*up*up*up*gp*cp*u)-3') (5 kDa, RNA from Thogoto virus (isolate SiAr 126))
- Polymerase basic protein 2 (94 kDa, Protein from Thogoto virus (isolate SiAr 126))
Cryo-EM structure of Thogoto virus polymerase in a transcription initiation conformation
Resolution: 3.06 Å
EM Method: Single-particle
Fitted PDBs: 8z8x
Q-score: 0.525
Xue L, Chang T, Li Z, Wang C, Zhao H, Li M, Tang P, Wen X, Yu M, Wu J, Bao X, Wang X, Gong P, He J, Chen X, Xiong X
Nat Commun (2024) 15 pp. 4620-4620 [ DOI: doi:10.1038/s41467-024-48848-3 Pubmed: 38816392 ]
- Phosphomethylphosphonic acid guanylate ester (521 Da, Ligand)
- Rna-directed rna polymerase catalytic subunit (81 kDa, Protein from Thogoto virus (isolate SiAr 126))
- Polymerase acidic protein (71 kDa, Protein from Thogoto virus (isolate SiAr 126))
- Rna (5'-r(*ap*gp*ap*gp*ap*ap*ap*up*cp*ap*ap*gp*gp*cp*ap*gp*up*u)-3') (5 kDa, RNA from Thogoto virus (isolate SiAr 126))
- Rna (5'-r(*gp*ap*cp*up*gp*cp*cp*up*gp*up*up*up*up*up*gp*cp*u)-3') (5 kDa, RNA from Thogoto virus (isolate SiAr 126))
- Polymerase basic protein 2 (94 kDa, Protein from Thogoto virus (isolate SiAr 126))
- Cryo-em structure of thogoto virus polymerase in a transcription initiation conformation (Complex from Thogoto virus (isolate SiAr 126))
Cryo-EM structure of Thogoto virus polymerase in transcription initiation conformation 2
Resolution: 2.87 Å
EM Method: Single-particle
Fitted PDBs: 8z90
Q-score: 0.55
Xue L, Chang T, Li Z, Wang C, Zhao H, Li M, Tang P, Wen X, Yu M, Wu J, Bao X, Wang X, Gong P, He J, Chen X, Xiong X
Nat Commun (2024) 15 pp. 4620-4620 [ DOI: doi:10.1038/s41467-024-48848-3 Pubmed: 38816392 ]
- Phosphomethylphosphonic acid guanylate ester (521 Da, Ligand)
- Rna-directed rna polymerase catalytic subunit (81 kDa, Protein from Thogoto virus (isolate SiAr 126))
- Polymerase acidic protein (71 kDa, Protein from Thogoto virus (isolate SiAr 126))
- Cryo-em structure of thogoto virus polymerase in transcription initiation conformation 2 (Complex from Thogoto virus (isolate SiAr 126))
- Rna (5'-r(*ap*gp*ap*gp*ap*ap*ap*up*cp*ap*ap*gp*gp*cp*ap*gp*up*u)-3') (5 kDa, RNA from Thogoto virus (isolate SiAr 126))
- Rna (5'-r(*gp*ap*cp*up*gp*cp*cp*up*gp*up*up*up*up*up*gp*cp*u)-3') (5 kDa, RNA from Thogoto virus (isolate SiAr 126))
- Polymerase basic protein 2 (94 kDa, Protein from Thogoto virus (isolate SiAr 126))
Cryo-EM structure of Thogoto virus polymerase in a transcription elongation conformation
Resolution: 2.65 Å
EM Method: Single-particle
Fitted PDBs: 8z97
Q-score: 0.566
Xue L, Chang T, Li Z, Wang C, Zhao H, Li M, Tang P, Wen X, Yu M, Wu J, Bao X, Wang X, Gong P, He J, Chen X, Xiong X
Nat Commun (2024) 15 pp. 4620-4620 [ DOI: doi:10.1038/s41467-024-48848-3 Pubmed: 38816392 ]
- Cryo-em structure of thogoto virus polymerase in a transcription elongation conformation (Complex from Thogoto virus (isolate SiAr 126))
- 7-methyl-guanosine-5'-triphosphate-5'-(2'-o-methyl)-adenosine (801 Da, Ligand)
- Rna (5'-r(p*gp*cp*ap*ap*ap*ap*ap*cp*a)-3') (2 kDa, RNA from Thogoto virus (isolate SiAr 126))
- Rna-directed rna polymerase catalytic subunit (81 kDa, Protein from Thogoto virus (isolate SiAr 126))
- Polymerase acidic protein (71 kDa, Protein from Thogoto virus (isolate SiAr 126))
- Rna (5'-r(*ap*gp*ap*gp*ap*ap*ap*up*cp*ap*ap*gp*gp*cp*ap*gp*up*u)-3') (5 kDa, RNA from Thogoto virus (isolate SiAr 126))
- Rna (5'-r(*gp*ap*cp*up*gp*cp*cp*up*gp*up*up*up*up*up*gp*cp*u)-3') (5 kDa, RNA from Thogoto virus (isolate SiAr 126))
- Polymerase basic protein 2 (94 kDa, Protein from Thogoto virus (isolate SiAr 126))
Cryo-EM structure of Thogoto virus polymerase in a transcription reception conformation
Resolution: 2.52 Å
EM Method: Single-particle
Fitted PDBs: 8z98
Q-score: 0.569
Xue L, Chang T, Li Z, Wang C, Zhao H, Li M, Tang P, Wen X, Yu M, Wu J, Bao X, Wang X, Gong P, He J, Chen X, Xiong X
Nat Commun (2024) 15 pp. 4620-4620 [ DOI: doi:10.1038/s41467-024-48848-3 Pubmed: 38816392 ]
- 7-methyl-guanosine-5'-triphosphate-5'-(2'-o-methyl)-adenosine (801 Da, Ligand)
- Cryo-em structure of thogoto virus polymerase in a transcription reception conformation (Complex from Thogoto virus (isolate SiAr 126))
- Rna (5'-r(p*gp*cp*ap*ap*ap*ap*ap*cp*a)-3') (2 kDa, RNA from Thogoto virus (isolate SiAr 126))
- Rna-directed rna polymerase catalytic subunit (81 kDa, Protein from Thogoto virus (isolate SiAr 126))
- Polymerase acidic protein (71 kDa, Protein from Thogoto virus (isolate SiAr 126))
- Polymerase basic protein 2 (94 kDa, Protein from Thogoto virus (isolate SiAr 126))
Cryo-EM structure of Thogoto virus polymerase in a replication reception conformation
Resolution: 2.33 Å
EM Method: Single-particle
Fitted PDBs: 8z9q
Q-score: 0.6
Xue L, Chang T, Li Z, Wang C, Zhao H, Li M, Tang P, Wen X, Yu M, Wu J, Bao X, Wang X, Gong P, He J, Chen X, Xiong X
Nat Commun (2024) 15 pp. 4620-4620 [ DOI: doi:10.1038/s41467-024-48848-3 Pubmed: 38816392 ]
- Cryo-em structure of thogoto virus polymerase in a replication reception conformation (Complex from Thogoto virus (isolate SiAr 126))
- Rna (5'-d(*(atp))-r(p*gp*cp*ap*ap*ap*ap*ap*cp*a)-3') (3 kDa, RNA from Thogoto virus (isolate SiAr 126))
- Rna-directed rna polymerase catalytic subunit (81 kDa, Protein from Thogoto virus (isolate SiAr 126))
- Polymerase acidic protein (71 kDa, Protein from Thogoto virus (isolate SiAr 126))
- Polymerase basic protein 2 (94 kDa, Protein from Thogoto virus (isolate SiAr 126))
Resolution: 2.9 Å
EM Method: Single-particle
Fitted PDBs: 8k98
Q-score: 0.486
Yin H, Li X, Wang X, Zhang C, Gao J, Yu G, He Q, Yang J, Liu X, Wei Y, Li Z, Zhang H
Nat Commun (2024) 15 pp. 2692-2692 [ DOI: doi:10.1038/s41467-024-47030-z Pubmed: 38538592 ]
- A protein (118 kDa, Protein from Bacillus halotolerans)
- Cryo-em structure of a protein (Complex from Bacillus halotolerans)
- A protein (29 kDa, Protein from Bacillus halotolerans)