Ariza AJF, Lue NZ, Grob P, Kaeser B, Fang J, Kassube SA, Nogales E
bioRxiv (2025) [ Pubmed: 39975028 DOI: doi:10.1101/2025.01.29.634372 ]
- Dna-directed rna polymerase ii subunit rpb7 (19 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc3 (17 kDa, Protein from Homo sapiens)
- Magnesium ion (24 Da, Ligand)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc4 (7 kDa, Protein from Homo sapiens)
- Template dna, nucleic acid scaffold (8 kDa, DNA from Homo sapiens)
- Zinc ion (65 Da, Ligand)
- Stalled human rna polymerase ii elongation complex bound to an apo recql5 helicase (490 kDa, Complex from Homo sapiens)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc1 (24 kDa, Protein from Homo sapiens)
- Rna, nucleic acid scaffold (6 kDa, RNA from Homo sapiens)
- Dna-directed rna polymerase ii subunit rpb2 (134 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase ii subunit rpb4 (16 kDa, Protein from Homo sapiens)
- Atp-dependent dna helicase q5 (108 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase ii subunit rpb3 (31 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc5 (7 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc2 (14 kDa, Protein from Homo sapiens)
- Non-template dna, nucleic acid scaffold (13 kDa, DNA from Homo sapiens)
- Dna-directed rna polymerase ii subunit rpb9 (14 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase ii subunit rpb11-a (13 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase ii subunit rpb1 (217 kDa, Protein from Homo sapiens)
Ariza AJF, Lue NZ, Grob P, Kaeser B, Fang J, Kassube SA, Nogales E
bioRxiv (2025) [ Pubmed: 39975028 DOI: doi:10.1101/2025.01.29.634372 ]
- Dna-directed rna polymerase ii subunit rpb7 (19 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc3 (17 kDa, Protein from Homo sapiens)
- Atp-dependent dna helicase q5 (109 kDa, Protein from Homo sapiens)
- Magnesium ion (24 Da, Ligand)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc4 (7 kDa, Protein from Homo sapiens)
- Phosphoaminophosphonic acid-adenylate ester (506 Da, Ligand)
- Template dna, nucleic acid scaffold (8 kDa, DNA from Homo sapiens)
- Zinc ion (65 Da, Ligand)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc1 (24 kDa, Protein from Homo sapiens)
- Rna, nucleic acid scaffold (6 kDa, RNA from Homo sapiens)
- Dna-directed rna polymerase ii subunit rpb2 (134 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase ii subunit rpb4 (16 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase ii subunit rpb3 (31 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc5 (7 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc2 (14 kDa, Protein from Homo sapiens)
- Non-template dna, nucleic acid scaffold (13 kDa, DNA from Homo sapiens)
- Dna-directed rna polymerase ii subunit rpb9 (14 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase ii subunit rpb11-a (13 kDa, Protein from Homo sapiens)
- Stalled human rna polymerase ii elongation complex bound to an amppnp-bound recql5 helicase (490 kDa, Complex from Homo sapiens)
- Dna-directed rna polymerase ii subunit rpb1 (217 kDa, Protein from Homo sapiens)
Ariza AJF, Lue NZ, Grob P, Kaeser B, Fang J, Kassube SA, Nogales E
bioRxiv (2025) [ Pubmed: 39975028 DOI: doi:10.1101/2025.01.29.634372 ]
- Dna-directed rna polymerase ii subunit rpb7 (19 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc3 (17 kDa, Protein from Homo sapiens)
- Atp-dependent dna helicase q5 (109 kDa, Protein from Homo sapiens)
- Magnesium ion (24 Da, Ligand)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc4 (7 kDa, Protein from Homo sapiens)
- Adenosine-5'-diphosphate (427 Da, Ligand)
- Template dna, nucleic acid scaffold (8 kDa, DNA from Homo sapiens)
- Zinc ion (65 Da, Ligand)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc1 (24 kDa, Protein from Homo sapiens)
- Stalled human rna polymerase ii elongation complex bound to an adp-bound recql5 helicase (490 kDa, Complex from Homo sapiens)
- Rna, nucleic acid scaffold (6 kDa, RNA from Homo sapiens)
- Dna-directed rna polymerase ii subunit rpb2 (134 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase ii subunit rpb4 (16 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase ii subunit rpb3 (31 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc5 (7 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc2 (14 kDa, Protein from Homo sapiens)
- Non-template dna, nucleic acid scaffold (13 kDa, DNA from Homo sapiens)
- Dna-directed rna polymerase ii subunit rpb9 (14 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase ii subunit rpb11-a (13 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase ii subunit rpb1 (217 kDa, Protein from Homo sapiens)
Resolution: 3.1 Å
EM Method: Single-particle
Fitted PDBs: 8pfg
Q-score: 0.471
Zuber PK, Said N, Hilal T, Wang B, Loll B, Gonzalez-Higueras J, Ramirez-Sarmiento CA, Belogurov GA, Artsimovitch I, Wahl MC, Knauer SH
Nat Commun (2024) 15 pp. 3040-3040 [ DOI: doi:10.1038/s41467-024-47368-4 Pubmed: 38589445 ]
- Dna and rna (Complex from Escherichia coli)
- Magnesium ion (24 Da, Ligand)
- Non-template dna (12 kDa, DNA from Escherichia coli)
- Transcription antitermination protein rfah (18 kDa, Protein from Escherichia coli)
- Dna-directed rna polymerase subunit beta' (156 kDa, Protein from Escherichia coli)
- Template dna (12 kDa, DNA from Escherichia coli)
- Rna (5 kDa, RNA from Escherichia coli)
- Transcription complex paused at ops site, assembled on not fully complementary nucleic acid scaffold, bound to disulfide-bridged (autoinhibited) rfah (417 kDa, Complex)
- Zinc ion (65 Da, Ligand)
- Dna-directed rna polymerase subunit alpha (36 kDa, Protein from Escherichia coli)
- Transcription complex (Complex from Escherichia coli)
- Dna-directed rna polymerase subunit omega (10 kDa, Protein from Escherichia coli)
- Dna-directed rna polymerase subunit beta (150 kDa, Protein from Escherichia coli)
Resolution: 3.4 Å
EM Method: Single-particle
Fitted PDBs: 8pfj
Q-score: 0.434
Zuber PK, Said N, Hilal T, Wang B, Loll B, Gonzalez-Higueras J, Ramirez-Sarmiento CA, Belogurov GA, Artsimovitch I, Wahl MC, Knauer SH
Nat Commun (2024) 15 pp. 3040-3040 [ DOI: doi:10.1038/s41467-024-47368-4 Pubmed: 38589445 ]
- Dna and rna (Complex from Escherichia coli)
- Magnesium ion (24 Da, Ligand)
- Non-template dna (12 kDa, DNA from Escherichia coli)
- Dna-directed rna polymerase subunit beta' (156 kDa, Protein from Escherichia coli)
- Template dna (12 kDa, DNA from Escherichia coli)
- Rna (5 kDa, RNA from Escherichia coli)
- Zinc ion (65 Da, Ligand)
- Dna-directed rna polymerase subunit alpha (36 kDa, Protein from Escherichia coli)
- Transcription complex (Complex from Escherichia coli)
- Dna-directed rna polymerase subunit omega (10 kDa, Protein from Escherichia coli)
- Transcription antitermination protein rfah (18 kDa, Protein from Escherichia coli)
- Dna-directed rna polymerase subunit beta (150 kDa, Protein from Escherichia coli)
- Transcription complex paused at ops site, bound to fully activated rfah, assembled on not fully complementary nucleic acid scaffold (417 kDa, Complex)
E. coli transcription complex paused at ops site and bound to RfaH and NusA
Resolution: 3.2 Å
EM Method: Single-particle
Fitted PDBs: 8pil
Q-score: 0.421
Zuber PK, Said N, Hilal T, Wang B, Loll B, Gonzalez-Higueras J, Ramirez-Sarmiento CA, Belogurov GA, Artsimovitch I, Wahl MC, Knauer SH
Nat Commun (2024) 15 pp. 3040-3040 [ DOI: doi:10.1038/s41467-024-47368-4 Pubmed: 38589445 ]
- Dna and rna (Complex from Escherichia coli)
- Magnesium ion (24 Da, Ligand)
- Transcription complex paused at ops site, assembled on a fully complementary nucleic acid scaffold, bound to rfah and nusa (472 kDa, Complex)
- Rna (5 kDa, RNA from Escherichia coli)
- Non-template dna (12 kDa, DNA from Escherichia coli)
- Dna-directed rna polymerase subunit beta' (156 kDa, Protein from Escherichia coli)
- Template dna (12 kDa, DNA from Escherichia coli)
- Zinc ion (65 Da, Ligand)
- Dna-directed rna polymerase subunit alpha (36 kDa, Protein from Escherichia coli)
- Transcription complex (Complex from Escherichia coli)
- Dna-directed rna polymerase subunit omega (10 kDa, Protein from Escherichia coli)
- Transcription termination/antitermination protein nusa (55 kDa, Protein from Escherichia coli)
- Transcription antitermination protein rfah (18 kDa, Protein from Escherichia coli)
- Dna-directed rna polymerase subunit beta (150 kDa, Protein from Escherichia coli)
Helical reconstruction of influenza A virus M1 in complex with nucleic acid
Resolution: 3.8 Å
EM Method: Helical reconstruction
Fitted PDBs: 6z5l
Q-score: 0.435
Peukes J, Xiong X, Erlendsson S, Qu K, Wan W, Calder LJ, Schraidt O, Kummer S, Freund SMV, Krausslich HG, Briggs JAG
Nature (2020) 587 pp. 495-498 [ Pubmed: 32908308 DOI: doi:10.1038/s41586-020-2696-8 ]
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- [ DOI: doi:10.1016/j.cell.2020.03.061 Pubmed: 32304664 ]
- Bat influenza a polymerase stuttering complex using 44-mer vrna template with intact oligo(u) sequence (Complex)
- Nucleic acid (Complex from synthetic construct)
- Magnesium ion (24 Da, Ligand)
- Polymerase acidic protein (85 kDa, Protein 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)))
- Polymerase (Complex from Influenza A virus (A/little yellow-shouldered bat/Guatemala/060/2010(H17N10)))
- Rna-directed rna polymerase catalytic subunit (87 kDa, Protein from Influenza A virus (A/little yellow-shouldered bat/Guatemala/060/2010(H17N10)))
- Mrna (3 kDa, RNA from synthetic construct)
- Vrna (13 kDa, RNA from synthetic construct)
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- [ DOI: doi:10.1016/j.cell.2020.03.061 Pubmed: 32304664 ]
- Polymerase acidic protein (85 kDa, Protein 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)))
- Polymerase (Complex from Influenza A virus (A/little yellow-shouldered bat/Guatemala/060/2010(H17N10)))
- Rna-directed rna polymerase catalytic subunit (87 kDa, Protein from Influenza A virus (A/little yellow-shouldered bat/Guatemala/060/2010(H17N10)))
- Vrna (13 kDa, RNA from Influenza B virus)
- Bat influenza a polymerase product dissociation complex using 44-mer vrna template with intact oligo(u) sequence (Complex)
- Nucleic acid (Complex from Influenza B virus)
Human Influenza B polymerase recycling complex
Resolution: 3.18 Å
EM Method: Single-particle
Fitted PDBs: 6t0w
Q-score: 0.546
Wandzik JM, Kouba T, Karuppasamy M, Pflug A, Drncova P, Provaznik J, Azevedo N, Cusack S
Cell (2020) 181 pp. 877- [ DOI: doi:10.1016/j.cell.2020.03.061 Pubmed: 32304664 ]
- Human influenza b polymerase recycling complex (Complex)
- Polymerase (Complex from Influenza B virus)
- Polymerase pb2 (90 kDa, Protein from Influenza B virus)
- Polymerase acidic protein (85 kDa, Protein from Influenza B virus)
- Vrna (10 kDa, RNA from Influenza B virus)
- Rna-directed rna polymerase catalytic subunit (86 kDa, Protein from Influenza B virus)
- Nucleic acid (Complex from Influenza B virus)