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Cryo-EM structure of E.coli transcription initiation complex with transcription factor GcvA
Resolution: 3.97 Å
EM Method: Single-particle
Fitted PDBs: 8y6u
Q-score: 0.318
Biochem Biophys Res Commun (2024) 691 pp. 149327-149327 [ DOI: doi:10.1016/j.bbrc.2023.149327 Pubmed: 38039839 ]
- Dna-directed rna polymerase subunit beta' (155 kDa, Protein from Escherichia coli K-12)
- Non-template promoter dna (28 kDa, DNA from Escherichia coli)
- Dna-directed rna polymerase subunit alpha (36 kDa, Protein from Escherichia coli)
- Template promoter dna (28 kDa, DNA from Escherichia coli)
- Dna-directed rna polymerase subunit beta (150 kDa, Protein from Escherichia coli K-12)
- Dna-directed rna polymerase subunit omega (10 kDa, Protein from Escherichia coli K-12)
- E.coli transcription initiation complex with gcva (Complex from Escherichia coli K-12)
- Rna polymerase sigma factor rpod (70 kDa, Protein from Escherichia coli)
- Glycine cleavage system transcriptional activator (34 kDa, Protein from Escherichia coli K-12)
Gustavsson E, Grunewald K, Elias P, Hallberg BM
Nucleic Acids Res (2024) [ Pubmed: 38806233 DOI: doi:10.1093/nar/gkae374 ]
- Dna polymerase catalytic subunit (Protein from Human alphaherpesvirus 1 strain KOS)
- Dna (Complex from synthetic construct)
- Template dna (DNA from synthetic construct)
- Primer dna (DNA from synthetic construct)
- Hsv-1 dna polymerase-processivity factor complex in exonuclease state with 1-bp dna mismatch (Complex)
- Dna polymerase-processivity factor (Complex from Human alphaherpesvirus 1 strain KOS)
Gustavsson E, Grunewald K, Elias P, Hallberg BM
Nucleic Acids Res (2024) [ Pubmed: 38806233 DOI: doi:10.1093/nar/gkae374 ]
- Dna (Complex from synthetic construct)
- Template dna (DNA from synthetic construct)
- Primer dna (DNA from synthetic construct)
- Hsv-1 dna polymerase-processivity factor complex in exonuclease state with 1-bp dna mismatch (Complex)
- Dna polymerase-processivity factor (Complex from Human alphaherpesvirus 1 strain KOS)
- Dna polymerase processivity factor (Protein from Human alphaherpesvirus 1 strain KOS)
Grimm C, Jungwirth S, Fischer U
To Be Published
- Vaccinia dna-directed rna polymerase open promoter intermediate pre-initiation complex (Complex from Vaccinia virus)
- Mrna-capping enzyme catalytic subunit (96 kDa, Protein from Vaccinia virus)
- Zinc ion (65 Da, Ligand)
- Vaccinia dna-directed rna polymerase open promoter intermediate pre-initiation complex (750 kDa, Complex)
- Dna-directed rna polymerase 133 kda polypeptide (133 kDa, Protein from Vaccinia virus)
- Template dna oligomer (21 kDa, DNA from Vaccinia virus)
- Dna-directed rna polymerase 18 kda subunit (17 kDa, Protein from Vaccinia virus)
- Dna-directed rna polymerase 7 kda subunit (7 kDa, Protein from Vaccinia virus)
- Dna-directed rna polymerase 147 kda polypeptide (146 kDa, Protein from Vaccinia virus)
- Non-template dna oligomer and template dna oligomer (Complex from Vaccinia virus)
- Dna-directed rna polymerase 22 kda subunit (21 kDa, Protein from Vaccinia virus)
- Dna-directed rna polymerase 19 kda subunit (19 kDa, Protein from Vaccinia virus)
- Intermediate transcription factor 3 large subunit (44 kDa, Protein from Vaccinia virus)
- Dna-directed rna polymerase 30 kda polypeptide (29 kDa, Protein from Vaccinia virus)
- Mrna-capping enzyme regulatory subunit opg124 (33 kDa, Protein from Vaccinia virus)
- Dna-directed rna polymerase 35 kda subunit (35 kDa, Protein from Vaccinia virus)
- Intermediate transcription factor 3 small subunit (33 kDa, Protein from Vaccinia virus)
- Non-template dna oligomer (21 kDa, DNA from Vaccinia virus)
- Water (18 Da, Ligand)
- Magnesium ion (24 Da, Ligand)
Grimm C, Jungwirth S, Fischer U
To Be Published
- Dna-directed rna polymerase 18 kda subunit (17 kDa, Protein from Vaccinia virus)
- Intermediate transcription factor 3 large subunit (44 kDa, Protein from Vaccinia virus)
- Dna-directed rna polymerase 147 kda polypeptide (146 kDa, Protein from Vaccinia virus)
- Dna-directed rna polymerase 7 kda subunit (7 kDa, Protein from Vaccinia virus)
- Intermediate transcription factor 3 small subunit (33 kDa, Protein from Vaccinia virus)
- Vaccinia dna-directed rna polymerase open promoter intermediate pre-initiation complex (Complex from Vaccinia virus)
- Non-template dna oligomer (21 kDa, DNA from Vaccinia virus)
- Mrna-capping enzyme catalytic subunit (96 kDa, Protein from Vaccinia virus)
- Template dna oligomer (Complex from Vaccinia virus)
- Zinc ion (65 Da, Ligand)
- Magnesium ion (24 Da, Ligand)
- Dna-directed rna polymerase 22 kda subunit (21 kDa, Protein from Vaccinia virus)
- Dna-directed rna polymerase 30 kda polypeptide (29 kDa, Protein from Vaccinia virus)
- Vaccinia dna-directed rna polymerase open promoter intermediate pre-initiation complex (750 kDa, Complex)
- Dna-directed rna polymerase 35 kda subunit (35 kDa, Protein from Vaccinia virus)
- Dna-directed rna polymerase 19 kda subunit (19 kDa, Protein from Vaccinia virus)
- Dna-directed rna polymerase 133 kda polypeptide (133 kDa, Protein from Vaccinia virus)
- Template dna oligomer (21 kDa, DNA from Vaccinia virus)
Grimm C, Jungwirth S, Fischer U
To Be Published
- Dna-directed rna polymerase 18 kda subunit (17 kDa, Protein from Vaccinia virus)
- Intermediate transcription factor 3 large subunit (44 kDa, Protein from Vaccinia virus)
- Dna-directed rna polymerase 147 kda polypeptide (146 kDa, Protein from Vaccinia virus)
- Dna-directed rna polymerase 7 kda subunit (7 kDa, Protein from Vaccinia virus)
- Intermediate transcription factor 3 small subunit (33 kDa, Protein from Vaccinia virus)
- Vaccinia dna-directed rna polymerase open promoter intermediate pre-initiation complex (750 kDa, Complex from Vaccinia virus)
- Non-template dna oligomer (21 kDa, DNA from Vaccinia virus)
- Mrna-capping enzyme catalytic subunit (96 kDa, Protein from Vaccinia virus)
- Zinc ion (65 Da, Ligand)
- Magnesium ion (24 Da, Ligand)
- Dna-directed rna polymerase 22 kda subunit (21 kDa, Protein from Vaccinia virus)
- Dna-directed rna polymerase 30 kda polypeptide (29 kDa, Protein from Vaccinia virus)
- Mrna-capping enzyme regulatory subunit opg124 (33 kDa, Protein from Vaccinia virus)
- Dna-directed rna polymerase 35 kda subunit (35 kDa, Protein from Vaccinia virus)
- Dna-directed rna polymerase 19 kda subunit (19 kDa, Protein from Vaccinia virus)
- Dna-directed rna polymerase 133 kda polypeptide (133 kDa, Protein from Vaccinia virus)
- Template dna oligomer (21 kDa, DNA from Vaccinia virus)
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)
Resolution: 3.1 Å
EM Method: Single-particle
Fitted PDBs: 8pen
Q-score: 0.451
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)
- Dna and rna (Complex from Escherichia coli)
- Transcription antitermination protein rfah (18 kDa, Protein from Escherichia coli)
- Zinc ion (65 Da, Ligand)
- Transcription complex (Complex from Escherichia coli)
- Non-template dna (12 kDa, DNA from Escherichia coli)
- Rna (5 kDa, RNA from Escherichia coli)
- Magnesium ion (24 Da, Ligand)
- Template dna (12 kDa, DNA from Escherichia coli)
- Dna-directed rna polymerase subunit omega (10 kDa, Protein from Escherichia coli)
- Transcription complex paused at ops site with fully recruited rfah (417 kDa, Complex)
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 ]
- Transcription complex paused at ops site, assembled on not fully complementary nucleic acid scaffold, bound to disulfide-bridged (autoinhibited) rfah (417 kDa, Complex)
- Transcription antitermination protein rfah (18 kDa, Protein from Escherichia coli)
- 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 kDa, RNA from Escherichia coli)
- Dna and rna (Complex from Escherichia coli)
- Template dna (12 kDa, DNA from Escherichia coli)
- Zinc ion (65 Da, Ligand)
- Transcription complex (Complex from Escherichia coli)
- Non-template dna (12 kDa, DNA from Escherichia coli)
- Magnesium ion (24 Da, Ligand)
- Dna-directed rna polymerase subunit omega (10 kDa, Protein from Escherichia coli)