Structure of mammalian Pol II-DSIF-SPT6-PAF1-TFIIS-hexasome elongation complex
Resolution: 3.3 Å
EM Method: Single-particle
Fitted PDBs: 8a3y
Q-score: 0.231
Farnung L, Ochmann M, Garg G, Vos SM, Cramer P
Mol Cell (2022) 82 pp. 3126-3134.e7 [ Pubmed: 35858621 DOI: doi:10.1016/j.molcel.2022.06.027 ]
- Rna polymerase ii subunit d (16 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerase subunit beta (142 kDa, Protein from Sus scrofa)
- Transcription elongation factor spt5 (121 kDa, Protein from Homo sapiens)
- Rna polymerase-associated protein rtf1 homolog (29 kDa, Protein from Homo sapiens)
- Histone h2b (10 kDa, Protein from Xenopus laevis)
- Histone h4 (11 kDa, Protein from Xenopus laevis)
- Zinc ion (65 Da, Ligand)
- Dna-directed rna polymerase ii subunit rpb3 (30 kDa, Protein from Sus scrofa)
- Rna polymerase-associated protein ctr9 homolog,rna polymerase-associated protein leo1 (210 kDa, Protein from Homo sapiens)
- Rna, template dna (42 kDa, DNA from synthetic construct)
- Transcription elongation factor spt4 (13 kDa, Protein from Homo sapiens)
- Parafibromin (60 kDa, Protein from Homo sapiens)
- Rna polymerase ii-associated factor 1 homolog (36 kDa, Protein from Homo sapiens)
- Histone h3.2 (15 kDa, Protein from Xenopus laevis)
- Non-template dna (39 kDa, DNA from synthetic construct)
- Dna-directed rna polymerase ii subunit rpb7 (19 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc2 (14 kDa, Protein from Sus scrofa)
- Rna, template dna (9 kDa, RNA from synthetic construct)
- Mammalian pol ii-tfiis elongation complex (Complex from Sus scrofa)
- Rna polymerase ii subunit k (7 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerase ii subunit e (24 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerase ii subunit rpb11-a (13 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc5 (7 kDa, Protein from Sus scrofa)
- Magnesium ion (24 Da, Ligand)
- Dna-directed rna polymerase subunit (219 kDa, Protein from Sus scrofa)
- Histone h2a (11 kDa, Protein from Xenopus laevis)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc3 (17 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerase ii subunit rpb9 (14 kDa, Protein from Sus scrofa)
- Spt6 (117 kDa, Protein from Homo sapiens)
- Wd repeat-containing protein 61 (33 kDa, Protein from Homo sapiens)
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 ]
- Non-structural protein 7 (8 kDa, Protein from Infectious bronchitis virus)
- Non-structural protein 8 (21 kDa, Protein from Infectious bronchitis virus)
- Rna-directed rna polymerase nsp12 (107 kDa, Protein from Infectious bronchitis virus)
- Core polymerase complex of the infectious bronchitis virus composed of nsp12, nsp8, nsp7, and an dsrna substrate (194 kDa, Complex from Infectious bronchitis virus)
- Rna template (10 kDa, RNA from Severe acute respiratory syndrome coronavirus 2)
- Rna primer (9 kDa, RNA from Severe acute respiratory syndrome coronavirus 2)
- Zinc ion (65 Da, Ligand)
Structure of LINE-1 ORF2p with template:primer hybrid
Resolution: 3.3 Å
EM Method: Single-particle
Fitted PDBs: 8sxt
Q-score: 0.339
Baldwin ET, van Eeuwen T, Hoyos D, Zalevsky A, Tchesnokov EP, Sanchez R, Miller BD, Di Stefano LH, Ruiz FX, Hancock M, Isik E, Mendez-Dorantes C, Walpole T, Nichols C, Wan P, Riento K, Halls-Kass R, Augustin M, Lammens A, Jestel A, Upla P, Xibinaku K, Congreve S, Hennink M, Rogala KB, Schneider AM, Fairman JE, Christensen SM, Desrosiers B, Bisacchi GS, Saunders OL, Hafeez N, Miao W, Kapeller R, Zaller DM, Sali A, Weichenrieder O, Burns KH, Gotte M, Rout MP, Arnold E, Greenbaum BD, Romero DL, LaCava J, Taylor MS
Nature (2024) 626 pp. 194-206 [ DOI: doi:10.1038/s41586-023-06947-z Pubmed: 38096902 ]
- Long interspersed nuclear element (line)-1 orf2 protein (Complex from Homo sapiens)
- Line-1 retrotransposable element orf2 protein (149 kDa, Protein from Homo sapiens)
- Dna primer (3 kDa, DNA from synthetic construct)
- Rna template (5 kDa, RNA from synthetic construct)
- Magnesium ion (24 Da, Ligand)
- Thymidine-5'-triphosphate (482 Da, Ligand)
Yan L, Yang Y, Li M, Zhang Y, Zheng L, Ge J, Huang YC, Liu Z, Wang T, Gao S, Zhang R, Huang YY, Guddat LW, Gao Y, Rao Z, Lou Z
Cell (2021) 184 pp. 3474-3485.e11 [ DOI: doi:10.1016/j.cell.2021.05.033 Pubmed: 34143953 ]
- Primer (8 kDa, RNA from Severe acute respiratory syndrome coronavirus 2)
- Non-structural protein 10 (14 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Non-structural protein 9 (12 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Proofreading exoribonuclease (59 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Primer rna, template rna (Complex)
- Magnesium ion (24 Da, Ligand)
- Non-structural protein 7 (9 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Helicase (66 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Non-structural protein 8 (21 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Nsp 7, 8, 9, 10, 12, 13, 14 (Complex from Severe acute respiratory syndrome coronavirus 2)
- Template (8 kDa, RNA from Severe acute respiratory syndrome coronavirus 2)
- Rna-directed rna polymerase (106 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Zinc ion (65 Da, Ligand)
- Mcap(0)-rtc (Complex from Severe acute respiratory syndrome coronavirus 2)
Resolution: 3.35 Å
EM Method: Single-particle
Fitted PDBs: 7egq
Q-score: 0.384
Yan L, Yang Y, Li M, Zhang Y, Zheng L, Ge J, Huang YC, Liu Z, Wang T, Gao S, Zhang R, Huang YY, Guddat LW, Gao Y, Rao Z, Lou Z
Cell (2021) 184 pp. 3474-3485.e11 [ DOI: doi:10.1016/j.cell.2021.05.033 Pubmed: 34143953 ]
- Cap(0)-rtc (Complex from Severe acute respiratory syndrome coronavirus 2)
- Proofreading exoribonuclease (59 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Non-structural protein 10 (14 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Primer rna, template rna (Complex)
- Magnesium ion (24 Da, Ligand)
- Non-structural protein 7 (9 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Template rna (10 kDa, RNA from Severe acute respiratory syndrome coronavirus 2)
- Helicase (66 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Rna-directed rna polymerase (106 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Nsp 7, 8, 9, 10, 12, 13, 14 (Complex from Severe acute respiratory syndrome coronavirus 2)
- Non-structural protein 8 (21 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Primer rna (8 kDa, RNA from Severe acute respiratory syndrome coronavirus 2)
- Zinc ion (65 Da, Ligand)
- Non-structural protein 9 (12 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
Resolution: 2.41 Å
EM Method: Single-particle
Fitted PDBs: 6szu
Q-score: 0.665
Wandzik JM, Kouba T, Karuppasamy M, Pflug A, Drncova P, Provaznik J, Azevedo N, Cusack S
Cell (2020) 181 pp. 877- [ Pubmed: 32304664 DOI: doi:10.1016/j.cell.2020.03.061 ]
- Pyrophosphate 2- (175 Da, Ligand)
- 5-oxidanyl-4-oxidanylidene-1-[(1-pyrrolo[2,3-b]pyridin-1-ylcyclopentyl)methyl]pyridine-3-carboxylic acid (353 Da, Ligand)
- Vrna (14 kDa, RNA from Influenza B virus)
- Water (18 Da, Ligand)
- Bat influenza a polymerase pre-termination complex with pyrophosphate using 44-mer vrna template with mutated oligo(u) sequence (Complex)
- Mrna (3 kDa, RNA from Influenza B virus)
- Polymerase (Complex from Influenza A virus (A/little yellow-shouldered bat/Guatemala/060/2010(H17N10)))
- Nucleic acids (Complex from Influenza B virus)
- Polymerase basic protein 2 (91 kDa, Protein from Influenza A virus (A/little yellow-shouldered bat/Guatemala/060/2010(H17N10)))
- Magnesium ion (24 Da, Ligand)
- Rna-directed rna polymerase catalytic subunit (87 kDa, Protein from Influenza A virus (A/little yellow-shouldered bat/Guatemala/060/2010(H17N10)))
- Polymerase acidic protein (85 kDa, Protein from Influenza A virus (A/little yellow-shouldered bat/Guatemala/060/2010(H17N10)))
Resolution: 2.82 Å
EM Method: Single-particle
Fitted PDBs: 6t0r
Q-score: 0.563
Wandzik JM, Kouba T, Karuppasamy M, Pflug A, Drncova P, Provaznik J, Azevedo N, Cusack S
Cell (2020) 181 pp. 877- [ Pubmed: 32304664 DOI: doi:10.1016/j.cell.2020.03.061 ]
- Polymerase (Complex from Influenza A virus (A/little yellow-shouldered bat/Guatemala/060/2010(H17N10)))
- Water (18 Da, Ligand)
- Bat influenza a polymerase product dissociation complex using 44-mer vrna template with mutated oligo(u) sequence (Complex)
- Polymerase basic protein 2 (91 kDa, Protein from Influenza A virus (A/little yellow-shouldered bat/Guatemala/060/2010(H17N10)))
- Nucleic acid (Complex from synthetic construct)
- Vrna (14 kDa, RNA from synthetic construct)
- Rna-directed rna polymerase catalytic subunit (87 kDa, Protein from Influenza A virus (A/little yellow-shouldered bat/Guatemala/060/2010(H17N10)))
- Polymerase acidic protein (85 kDa, Protein from Influenza A virus (A/little yellow-shouldered bat/Guatemala/060/2010(H17N10)))
Resolution: 3.04 Å
EM Method: Single-particle
Fitted PDBs: 6t0s
Q-score: 0.555
Wandzik JM, Kouba T, Karuppasamy M, Pflug A, Drncova P, Provaznik J, Azevedo N, Cusack S
Cell (2020) 181 pp. 877- [ Pubmed: 32304664 DOI: doi:10.1016/j.cell.2020.03.061 ]
- Vrna (13 kDa, RNA from synthetic construct)
- Nucleic acid (Complex from synthetic construct)
- Polymerase acidic protein (85 kDa, Protein from Influenza A virus (A/little yellow-shouldered bat/Guatemala/060/2010(H17N10)))
- Polymerase (Complex from Influenza A virus (A/little yellow-shouldered bat/Guatemala/060/2010(H17N10)))
- Polymerase basic protein 2 (91 kDa, Protein from Influenza A virus (A/little yellow-shouldered bat/Guatemala/060/2010(H17N10)))
- Mrna (3 kDa, RNA from synthetic construct)
- Magnesium ion (24 Da, Ligand)
- Rna-directed rna polymerase catalytic subunit (87 kDa, Protein from Influenza A virus (A/little yellow-shouldered bat/Guatemala/060/2010(H17N10)))
- Bat influenza a polymerase stuttering complex using 44-mer vrna template with intact oligo(u) sequence (Complex)
Resolution: 3.12 Å
EM Method: Single-particle
Fitted PDBs: 6t0u
Q-score: 0.544
Wandzik JM, Kouba T, Karuppasamy M, Pflug A, Drncova P, Provaznik J, Azevedo N, Cusack S
Cell (2020) 181 pp. 877- [ Pubmed: 32304664 DOI: doi:10.1016/j.cell.2020.03.061 ]
- Polymerase (Complex from Influenza A virus (A/little yellow-shouldered bat/Guatemala/060/2010(H17N10)))
- Bat influenza a polymerase product dissociation complex using 44-mer vrna template with intact oligo(u) sequence (Complex)
- Polymerase basic protein 2 (91 kDa, Protein from Influenza A virus (A/little yellow-shouldered bat/Guatemala/060/2010(H17N10)))
- Nucleic acid (Complex from Influenza B virus)
- Rna-directed rna polymerase catalytic subunit (87 kDa, Protein from Influenza A virus (A/little yellow-shouldered bat/Guatemala/060/2010(H17N10)))
- Polymerase acidic protein (85 kDa, Protein from Influenza A virus (A/little yellow-shouldered bat/Guatemala/060/2010(H17N10)))
- Vrna (13 kDa, RNA from Influenza B virus)
Resolution: 2.7 Å
EM Method: Single-particle
Fitted PDBs: 6tw1
Q-score: 0.591
Wandzik JM, Kouba T, Karuppasamy M, Pflug A, Drncova P, Provaznik J, Azevedo N, Cusack S
Cell (2020) [ Pubmed: 32304664 DOI: doi:10.1016/j.cell.2020.03.061 ]
- Polymerase (Complex from Influenza A virus (A/little yellow-shouldered bat/Guatemala/060/2010(H17N10)))
- Nucleic acids (Complex from Influenza B virus)
- Water (18 Da, Ligand)
- Mrna (3 kDa, RNA from Influenza B virus)
- Polymerase basic protein 2 (91 kDa, Protein from Influenza A virus (A/little yellow-shouldered bat/Guatemala/060/2010(H17N10)))
- Magnesium ion (24 Da, Ligand)
- Rna-directed rna polymerase catalytic subunit (87 kDa, Protein from Influenza A virus (A/little yellow-shouldered bat/Guatemala/060/2010(H17N10)))
- Polymerase acidic protein (85 kDa, Protein from Influenza A virus (A/little yellow-shouldered bat/Guatemala/060/2010(H17N10)))
- 5-oxidanyl-4-oxidanylidene-1-[(1-pyrrolo[2,3-b]pyridin-1-ylcyclopentyl)methyl]pyridine-3-carboxylic acid (353 Da, Ligand)
- Vrna (14 kDa, RNA from Influenza B virus)
- Bat influenza a polymerase termination complex with pyrophosphate using 44-mer vrna template with mutated oligo(u) sequence (Complex)
- Pyrophosphate 2- (175 Da, Ligand)