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Cryo-EM structure of Pyrococcus furiosus transcription elongation complex bound to Spt4/5
Resolution: 3.45 Å
EM Method: Single-particle
Fitted PDBs: 8oki
Q-score: 0.48
Tarau D, Grunberger F, Pilsl M, Reichelt R, Heiss F, Konig S, Urlaub H, Hausner W, Engel C, Grohmann D
Nucleic Acids Res (2024) [ DOI: doi:10.1093/nar/gkae282 Pubmed: 38709902 ]
- Dna-directed rna polymerase subunit rpo1c (44 kDa, Protein from Pyrococcus furiosus DSM 3638)
- Nucleotide strands (Complex from Pyrococcus furiosus DSM 3638)
- Spt4/5 (Complex from Pyrococcus furiosus DSM 3638)
- Pyrococcus furiosus rna polymerase (Complex from Pyrococcus furiosus DSM 3638)
- Dna-directed rna polymerase subunit rpo5 (9 kDa, Protein from Pyrococcus furiosus DSM 3638)
- Dna non-template strand (7 kDa, DNA from Pyrococcus furiosus DSM 3638)
- Zinc ion (65 Da, Ligand)
- Dna-directed rna polymerase subunit beta (127 kDa, Protein from Pyrococcus furiosus DSM 3638)
- Dna-directed rna polymerase subunit rpo7 (21 kDa, Protein from Pyrococcus furiosus DSM 3638)
- Dna-directed rna polymerase subunit rpo4 (14 kDa, Protein from Pyrococcus furiosus DSM 3638)
- Dna-directed rna polymerase subunit rpo12 (5 kDa, Protein from Pyrococcus furiosus DSM 3638)
- Transcription elongation complex with spt4/5 (Complex)
- Dna-directed rna polymerase subunit rpo10 (7 kDa, Protein from Pyrococcus furiosus DSM 3638)
- Dna template strand (8 kDa, DNA from Pyrococcus furiosus DSM 3638)
- Dna-directed rna polymerase subunit rpo1n (103 kDa, Protein from Pyrococcus furiosus DSM 3638)
- Rna (2 kDa, RNA from Pyrococcus furiosus DSM 3638)
- Dna-directed rna polymerase subunit rpo6 (6 kDa, Protein from Pyrococcus furiosus DSM 3638)
- Transcription elongation factor spt4 (6 kDa, Protein from Pyrococcus furiosus DSM 3638)
- Dna-directed rna polymerase subunit rpo3 (31 kDa, Protein from Pyrococcus furiosus DSM 3638)
- Transcription elongation factor spt5 (16 kDa, Protein from Pyrococcus furiosus DSM 3638)
- Magnesium ion (24 Da, Ligand)
- Dna-directed rna polymerase subunit rpo11 (11 kDa, Protein from Pyrococcus furiosus DSM 3638)
E. coli RNA polymerase paused at ops site
Resolution: 2.8 Å
EM Method: Single-particle
Fitted PDBs: 8pdy
Q-score: 0.409
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 ]
- Non-template dna (35-mer) (12 kDa, DNA from Escherichia coli)
- Rna (5'-r(p*up*gp*gp*cp*gp*gp*up*ap*gp*cp*gp*u)-3') (5 kDa, RNA from Escherichia coli)
- Template dna (35-mer) (12 kDa, DNA from Escherichia coli)
- Dna-directed rna polymerase subunit beta (150 kDa, Protein from Escherichia coli)
- Dna-directed rna polymerase subunit alpha (36 kDa, Protein from Escherichia coli)
- Dna-directed rna polymerase subunit beta' (156 kDa, Protein from Escherichia coli)
- Dna and rna (Complex from Escherichia coli)
- Transcription elongation complex paused at ops site, assembled on fully complementary nucleic acid scaffold (399 kDa, Complex)
- Zinc ion (65 Da, Ligand)
- Transcription complex (Complex from Escherichia coli)
- Magnesium ion (24 Da, Ligand)
- Dna-directed rna polymerase subunit omega (10 kDa, Protein from Escherichia coli)
backtracked E. coli transcription complex paused at ops site and bound to RfaH
Resolution: 3.0 Å
EM Method: Single-particle
Fitted PDBs: 8pid
Q-score: 0.469
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-directed rna polymerase subunit beta (150 kDa, Protein from Escherichia coli)
- Dna-directed rna polymerase subunit beta' (156 kDa, Protein from Escherichia coli)
- Dna-directed rna polymerase subunit alpha (36 kDa, Protein from Escherichia coli)
- Rna (5'-r(p*up*gp*gp*cp*gp*gp*up*ap*gp*cp*gp*up*gp*c)-3') (6 kDa, RNA from Escherichia coli)
- Dna and rna (Complex from Escherichia coli)
- Transcription antitermination protein rfah (18 kDa, Protein from Escherichia coli)
- Zinc ion (65 Da, Ligand)
- Transcription elongation complex paused at ops site with bound rfah after nucleotide addition, assembled on fully complementary scaffold (417 kDa, Complex)
- Non-template dna (12 kDa, DNA from Escherichia coli)
- Magnesium ion (24 Da, Ligand)
- Template dna (12 kDa, DNA from Escherichia coli)
- Transcription elongation complex (Complex from Escherichia coli)
- Dna-directed rna polymerase subunit omega (10 kDa, Protein from Escherichia coli)
Cryo-EM structure of Pyrococcus furiosus transcription elongation complex
Resolution: 3.1 Å
EM Method: Single-particle
Fitted PDBs: 8cro
Q-score: 0.462
Tarau D, Grunberger F, Pilsl M, Reichelt R, Heiss F, Konig S, Urlaub H, Hausner W, Engel C, Grohmann D
Nucleic Acids Res (2024) [ DOI: doi:10.1093/nar/gkae282 Pubmed: 38709902 ]
- Dna-directed rna polymerase subunit rpo1c (44 kDa, Protein from Pyrococcus furiosus DSM 3638)
- Nucleotide strands (Complex from Pyrococcus furiosus DSM 3638)
- Pyrococcus furiosus rna polymerase (Complex from Pyrococcus furiosus DSM 3638)
- Dna-directed rna polymerase subunit rpo5 (9 kDa, Protein from Pyrococcus furiosus DSM 3638)
- Zinc ion (65 Da, Ligand)
- Dna-directed rna polymerase subunit beta (127 kDa, Protein from Pyrococcus furiosus DSM 3638)
- Dna-directed rna polymerase subunit rpo7 (21 kDa, Protein from Pyrococcus furiosus DSM 3638)
- Dna-directed rna polymerase subunit rpo4 (14 kDa, Protein from Pyrococcus furiosus DSM 3638)
- Dna-directed rna polymerase subunit rpo12 (5 kDa, Protein from Pyrococcus furiosus DSM 3638)
- Transcription elongation complex (tec) (Complex)
- Dna-directed rna polymerase subunit rpo10 (7 kDa, Protein from Pyrococcus furiosus DSM 3638)
- Dna non-template strand (2 kDa, DNA from Pyrococcus furiosus DSM 3638)
- Dna-directed rna polymerase subunit rpo1n (103 kDa, Protein from Pyrococcus furiosus DSM 3638)
- Rna (2 kDa, RNA from Pyrococcus furiosus DSM 3638)
- Dna-directed rna polymerase subunit rpo3 (29 kDa, Protein from Pyrococcus furiosus DSM 3638)
- Dna-directed rna polymerase subunit rpo6 (6 kDa, Protein from Pyrococcus furiosus DSM 3638)
- Magnesium ion (24 Da, Ligand)
- Dna template strand (6 kDa, DNA from Pyrococcus furiosus DSM 3638)
- Dna-directed rna polymerase subunit rpo11 (11 kDa, Protein from Pyrococcus furiosus DSM 3638)
Plastid-encoded RNA polymerase transcription elongation complex (consensus map)
Vergara-Cruces A, Pramanick I, Pearce D, Vogirala VK, Byrne MJ, Low JKK, Webster MW
Cell (2024) 187 pp. 1145-1159.e21 [ DOI: doi:10.1016/j.cell.2024.01.036 Pubmed: 38428394 ]
Plastid-encoded RNA polymerase transcription elongation complex (Region 1)
Vergara-Cruces A, Pramanick I, Pearce D, Vogirala VK, Byrne MJ, Low JKK, Webster MW
Cell (2024) 187 pp. 1145-1159.e21 [ DOI: doi:10.1016/j.cell.2024.01.036 Pubmed: 38428394 ]
Plastid-encoded RNA polymerase transcription elongation complex (Region 2)
Vergara-Cruces A, Pramanick I, Pearce D, Vogirala VK, Byrne MJ, Low JKK, Webster MW
Cell (2024) 187 pp. 1145-1159.e21 [ DOI: doi:10.1016/j.cell.2024.01.036 Pubmed: 38428394 ]
Plastid-encoded RNA polymerase transcription elongation complex (Region 3)
Vergara-Cruces A, Pramanick I, Pearce D, Vogirala VK, Byrne MJ, Low JKK, Webster MW
Cell (2024) 187 pp. 1145-1159.e21 [ DOI: doi:10.1016/j.cell.2024.01.036 Pubmed: 38428394 ]
Plastid-encoded RNA polymerase transcription elongation complex (Region 4)
Vergara-Cruces A, Pramanick I, Pearce D, Vogirala VK, Byrne MJ, Low JKK, Webster MW
Cell (2024) 187 pp. 1145-1159.e21 [ DOI: doi:10.1016/j.cell.2024.01.036 Pubmed: 38428394 ]
Plastid-encoded RNA polymerase transcription elongation complex (PAP2-mRNA)
Vergara-Cruces A, Pramanick I, Pearce D, Vogirala VK, Byrne MJ, Low JKK, Webster MW
Cell (2024) 187 pp. 1145-1159.e21 [ DOI: doi:10.1016/j.cell.2024.01.036 Pubmed: 38428394 ]