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Structure of Escherichia coli CedA in complex with transcription initiation complex
Resolution: 2.76 Å
EM Method: Single-particle
Fitted PDBs: 8ftd
Q-score: 0.456
Vasilyev N, Liu MMJ, Epshtein V, Shamovsky I, Nudler E
Nat Struct Mol Biol (2024) 31 pp. 141-149 [ DOI: doi:10.1038/s41594-023-01154-w Pubmed: 38177674 ]
- Chapso (631 Da, Ligand)
- Dna-directed rna polymerase subunit beta' (155 kDa, Protein from Escherichia coli)
- Rna polymerase sigma factor rpod (69 kDa, Protein from Escherichia coli)
- Transcription unit ssra promoter non-template dna (26 kDa, DNA from Escherichia coli)
- Dna-directed rna polymerase subunit beta (150 kDa, Protein from Escherichia coli)
- Cell division activator ceda (9 kDa, Protein from Escherichia coli)
- Escherichia coli ceda in complex with initiation complex (520 kDa, Complex from Escherichia coli)
- Dna-directed rna polymerase subunit alpha (36 kDa, Protein from Escherichia coli)
- Magnesium ion (24 Da, Ligand)
- Transcription unit ssra promoter template dna (26 kDa, DNA from Escherichia coli)
- Dna-directed rna polymerase subunit omega (10 kDa, Protein from Escherichia coli)
- Zinc ion (65 Da, Ligand)
CryoEM Structure of E. coli Transcription-Coupled Ribonucleotide Excision Repair (TC-RER) complex
Resolution: 2.9 Å
EM Method: Single-particle
Fitted PDBs: 7uwe
Q-score: 0.413
Hao Z, Gowder M, Proshkin S, Bharati BK, Epshtein V, Svetlov V, Shamovsky I, Nudler E
Cell (2023) 186 pp. 2425- [ DOI: doi:10.1016/j.cell.2023.04.029 Pubmed: 37196657 ]
- Dna-directed rna polymerase subunit beta' (155 kDa, Protein from Escherichia coli)
- Dna (29-mer) (8 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)
- Rna (18-mer) (5 kDa, RNA from Escherichia coli)
- Magnesium ion (24 Da, Ligand)
- Dna (29-mer) (8 kDa, DNA from Escherichia coli)
- Dna-directed rna polymerase subunit omega (10 kDa, Protein from Escherichia coli)
- Elongation complex(ec)-rnaseh2 complex (Complex from Escherichia coli)
- Zinc ion (65 Da, Ligand)
- Ribonuclease hii (21 kDa, Protein from Escherichia coli)
Resolution: 3.1 Å
EM Method: Single-particle
Fitted PDBs: 7uwh
Q-score: 0.458
Hao Z, Gowder M, Proshkin S, Bharati BK, Epshtein V, Svetlov V, Shamovsky I, Nudler E
Cell (2023) 186 pp. 2425- [ DOI: doi:10.1016/j.cell.2023.04.029 Pubmed: 37196657 ]
- Dna/rna (59-mer) (18 kDa, Macromolecule from Escherichia coli)
- Dna-directed rna polymerase subunit beta' (155 kDa, Protein from Escherichia coli)
- Dna-directed rna polymerase subunit beta (150 kDa, Protein from Escherichia coli)
- Ribonuclease hii (21 kDa, Protein from Escherichia coli)
- Dna (59-mer) (18 kDa, DNA from Escherichia coli)
- Dna-directed rna polymerase subunit alpha (36 kDa, Protein from Escherichia coli)
- Rna (18-mer) (5 kDa, RNA from Escherichia coli)
- Magnesium ion (24 Da, Ligand)
- Elongation complex(ec)-rnaseh2 complex bound to ribonucleotide substrate (Complex from Escherichia coli)
- Dna-directed rna polymerase subunit omega (10 kDa, Protein from Escherichia coli)
- Zinc ion (65 Da, Ligand)
CryoEM structure of E.coli transcription elongation complex
Resolution: 2.42 Å
EM Method: Single-particle
Fitted PDBs: 8fvr
Q-score: 0.566
Weaver JW, Proshkin S, Duan W, Epshtein V, Gowder M, Bharati BK, Afanaseva E, Mironov A, Serganov A, Nudler E
Nat Struct Mol Biol (2023) 30 pp. 600-607 [ DOI: doi:10.1038/s41594-023-00948-2 Pubmed: 36997761 ]
- 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)
- Dna (53-mer) (16 kDa, DNA from Escherichia coli)
- Dna (53-mer) (16 kDa, DNA from Escherichia coli)
- Dna-directed rna polymerase subunit alpha (36 kDa, Protein from Escherichia coli K-12)
- E. coli transcription elongation complex (ec) (Complex from Escherichia coli K-12)
- Rna (16-mer) (5 kDa, RNA from Escherichia coli)
- Magnesium ion (24 Da, Ligand)
- Water (18 Da, Ligand)
- Zinc ion (65 Da, Ligand)
- Dna-directed rna polymerase subunit beta' (156 kDa, Protein from Escherichia coli K-12)
CryoEM structure of E.coli transcription elongation complex bound to ppGpp
Resolution: 2.1 Å
EM Method: Single-particle
Fitted PDBs: 8fvw
Q-score: 0.611
Weaver JW, Proshkin S, Duan W, Epshtein V, Gowder M, Bharati BK, Afanaseva E, Mironov A, Serganov A, Nudler E
Nat Struct Mol Biol (2023) 30 pp. 600-607 [ DOI: doi:10.1038/s41594-023-00948-2 Pubmed: 36997761 ]
- Dna-directed rna polymerase subunit beta (150 kDa, Protein from Escherichia coli K-12)
- Guanosine-5',3'-tetraphosphate (603 Da, Ligand)
- Dna-directed rna polymerase subunit omega (10 kDa, Protein from Escherichia coli K-12)
- Dna (53-mer) (16 kDa, DNA from Escherichia coli)
- Dna (53-mer) (16 kDa, DNA from Escherichia coli)
- Sodium ion (22 Da, Ligand)
- Dna-directed rna polymerase subunit alpha (36 kDa, Protein from Escherichia coli K-12)
- Rna (16-mer) (5 kDa, RNA from Escherichia coli)
- Magnesium ion (24 Da, Ligand)
- Water (18 Da, Ligand)
- E. coli transcription elongation complex bound to ppgpp (ec-ppgpp) (Complex from Escherichia coli K-12)
- Zinc ion (65 Da, Ligand)
- Dna-directed rna polymerase subunit beta' (156 kDa, Protein from Escherichia coli K-12)
CryoEM Structure of E. coli Rho-dependent Transcription Pre-termination Complex
Resolution: 3.8 Å
EM Method: Single-particle
Fitted PDBs: 6xas
Q-score: 0.334
Hao Z, Epshtein V, Kim KH, Proshkin S, Svetlov V, Kamarthapu V, Bharati B, Mironov A, Walz T, Nudler E
Mol Cell (2021) 81 pp. 281- [ DOI: doi:10.1016/j.molcel.2020.11.013 Pubmed: 33296676 ]
- E. coli rho-dependent transcription pre-termination complex (726 kDa, Complex from Escherichia coli (strain K12))
- Transcription termination/antitermination protein nusa (54 kDa, Protein from Escherichia coli (strain K12))
- Dna-directed rna polymerase subunit alpha (36 kDa, Protein from Escherichia coli (strain K12))
- Dna-directed rna polymerase subunit beta' (156 kDa, Protein from Escherichia coli (strain K12))
- Dna (29-mer) (8 kDa, DNA from Escherichia coli (strain K12))
- Dna-directed rna polymerase subunit omega (10 kDa, Protein from Escherichia coli (strain K12))
- Dna-directed rna polymerase subunit beta (150 kDa, Protein from Escherichia coli (strain K12))
- Rna (60-mer) (19 kDa, RNA from Escherichia coli (strain K12))
- Magnesium ion (24 Da, Ligand)
- Transcription termination factor rho (47 kDa, Protein from Escherichia coli (strain K12))
- Zinc ion (65 Da, Ligand)
- Dna (29-mer) (8 kDa, DNA from Escherichia coli (strain K12))
CryoEM Structure of E. coli Rho-dependent Transcription Pre-termination Complex bound with NusG
Resolution: 7.7 Å
EM Method: Single-particle
Fitted PDBs: 6xav
Q-score: 0.103
Hao Z, Epshtein V, Kim KH, Proshkin S, Svetlov V, Kamarthapu V, Bharati B, Mironov A, Walz T, Nudler E
Mol Cell (2021) 81 pp. 281- [ DOI: doi:10.1016/j.molcel.2020.11.013 Pubmed: 33296676 ]
- E. coli rho-dependent transcription pre-termination complex (726 kDa, Complex from Escherichia coli (strain K12))
- Transcription termination factor rho (47 kDa, Protein from Escherichia coli K-12)
- 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)
- Magnesium ion (24 Da, Ligand)
- Dna (29-mer) (8 kDa, DNA from Escherichia coli K-12)
- Dna (29-mer) (9 kDa, DNA from Escherichia coli K-12)
- Rna (18-mer) (5 kDa, RNA from Escherichia coli K-12)
- Dna-directed rna polymerase subunit alpha (36 kDa, Protein from Escherichia coli K-12)
- Transcription termination/antitermination protein nusa (54 kDa, Protein from Escherichia coli K-12)
- Zinc ion (65 Da, Ligand)
- Transcription termination/antitermination protein nusg (20 kDa, Protein from Escherichia coli K-12)
- Dna-directed rna polymerase subunit beta' (156 kDa, Protein from Escherichia coli K-12)