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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 ]
- 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)
- Nsp7 (6 kDa, Protein from Porcine epidemic diarrhea virus)
- Nsp8 (12 kDa, Protein from Porcine epidemic diarrhea virus)
- Zinc ion (65 Da, Ligand)
- 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)
- 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)
- Nsp12 (104 kDa, Protein from Porcine epidemic diarrhea virus)
Cryo-EM structure of POLRMT mutant.
Resolution: 3.24 Å
EM Method: Single-particle
Fitted PDBs: 7zc4
Q-score: 0.328
Zhu X, Xie X, Das H, Tan BG, Shi Y, Al-Behadili A, Peter B, Motori E, Valenzuela S, Posse V, Gustafsson CM, Hallberg BM, Falkenberg M
Cell (2022) 185 pp. 2309-2323.e24 [ DOI: doi:10.1016/j.cell.2022.05.006 Pubmed: 35662414 ]
- Polrmt (137 kDa, Cellular component from Homo sapiens)
- Dna-directed rna polymerase, mitochondrial (134 kDa, Protein from Homo sapiens)
Cryo-EM structure of POLRMT in free form.
Resolution: 3.0 Å
EM Method: Single-particle
Fitted PDBs: 7pzr
Q-score: 0.385
Zhu X, Xie X, Das H, Tan BG, Shi Y, Al-Behadili A, Peter B, Motori E, Valenzuela S, Posse V, Gustafsson CM, Hallberg BM, Falkenberg M
Cell (2022) 185 pp. 2309-2323.e24 [ DOI: doi:10.1016/j.cell.2022.05.006 Pubmed: 35662414 ]
- Dna-directed rna polymerase, mitochondrial (137 kDa, Protein from Homo sapiens)
- Polrmt (137 kDa, Complex from Homo sapiens)
Mitochondrial DNA dependent RNA polymerase homodimer.
Resolution: 3.5 Å
EM Method: Single-particle
Fitted PDBs: 7pzp
Q-score: 0.323
Zhu X, Xie X, Das H, Tan BG, Shi Y, Al-Behadili A, Peter B, Motori E, Valenzuela S, Posse V, Gustafsson CM, Hallberg BM, Falkenberg M
Cell (2022) 185 pp. 2309- [ DOI: doi:10.1016/j.cell.2022.05.006 Pubmed: 35662414 ]
- Dna-directed rna polymerase, mitochondrial (137 kDa, Protein from Homo sapiens)
- Polrmt (137 kDa, Complex)
- Mitochondrial dna-directed rna polymerase dimer. (Complex from Homo sapiens)
SARS-CoV-2 nsp12/7/8 complex with a native N-terminus nsp9
Resolution: 3.18 Å
EM Method: Single-particle
Fitted PDBs: 7thm
Q-score: 0.486
Park GJ, Osinski A, Hernandez G, Eitson JL, Majumdar A, Tonelli M, Henzler-Wildman K, Pawlowski K, Chen Z, Li Y, Schoggins JW, Tagliabracci VS
Nature (2022) 609 pp. 793-800 [ Pubmed: 35944563 DOI: doi:10.1038/s41586-022-05185-z ]
- Non-structural protein 9 (12 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Non-structural protein 7 (9 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Pyrophosphate 2- (175 Da, Ligand)
- Non-structural protein 8 (21 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Rna-directed rna polymerase (106 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Manganese (ii) ion (54 Da, Ligand)
- Zinc ion (65 Da, Ligand)
- Sars-cov-2 replication-transcription complex with a native n-terminus nsp9 bound to niran domain of nsp12. (172 kDa, Complex from Severe acute respiratory syndrome coronavirus 2)
Resolution: 2.5 Å
EM Method: Single-particle
Fitted PDBs: 7aap
Q-score: 0.571
Naydenova K, Muir KW, Wu LF, Zhang Z, Coscia F, Peet MJ, Castro-Hartmann P, Qian P, Sader K, Dent K, Kimanius D, Sutherland JD, Lowe J, Barford D, Russo CJ
PNAS (2021) 118 [ DOI: doi:10.1073/pnas.2021946118 Pubmed: 33526596 ]
- Non-structural protein 7 (9 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Pyrophosphate 2- (175 Da, Ligand)
- Non-structural protein 8 (21 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Rna (5'-r(p*up*up*ap*ap*gp*up*up*ap*u)-3') (7 kDa, RNA from Severe acute respiratory syndrome coronavirus 2)
- Rna (5'-r(p*up*up*cp*ap*up*ap*ap*cp*up*up*ap*a)-3') (9 kDa, RNA from Severe acute respiratory syndrome coronavirus 2)
- Non-structural protein 12 (110 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- [[(2~{r},3~{s},4~{r},5~{r})-5-(3-aminocarbonyl-5-fluoranyl-2-oxidanylidene-pyrazin-1-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] phosphono hydrogen phosphate (529 Da, Ligand)
- Zinc ion (65 Da, Ligand)
- Magnesium ion (24 Da, Ligand)
- Nsp7-nsp8-nsp12 sars-cov2 rna-directed rna polymerase (Complex from Severe acute respiratory syndrome coronavirus 2)
- Rna (Complex from Severe acute respiratory syndrome coronavirus 2)
- Nsp7-nsp8-nsp12 sars-cov2 rna-directed rna polymerase in complex with template:primer dsrna and favipiravir-rtp (Complex)
Structure of DNA Polymerase Zeta (Apo)
Resolution: 4.1 Å
EM Method: Single-particle
Fitted PDBs: 6v8p
Q-score: 0.369
Malik R, Kopylov M, Gomez-Llorente Y, Jain R, Johnson RE, Prakash L, Prakash S, Ubarretxena-Belandia I, Aggarwal AK
Nat Struct Mol Biol (2020) 27 pp. 913-924 [ DOI: doi:10.1038/s41594-020-0476-7 Pubmed: 32807989 ]
- Dna polymerase delta small subunit (55 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Dna polymerase zeta catalytic subunit (177 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Dna polymerase zeta processivity subunit (28 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Dna polymerase delta subunit 3 (40 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Apo (Complex from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Iron/sulfur cluster (351 Da, Ligand)