› 6pb4

Electron Microscopy
4.35Å resolution

The E. coli class-II CAP-dependent transcription activation complex with de novo RNA transcript at the state 2

Released:
DOI: 10.2210/pdb6pb4/pdb
PDB entry 6pb4 coloured by chain, front view.
PDB entry 6pb4 coloured by chain, side view.
PDB entry 6pb4 coloured by chain, top view.
Source organism: Escherichia coli
Primary publication:
Visualization of two architectures in class-II CAP-dependent transcription activation
Shi W, Jiang Y, Deng Y, Dong Z, Liu B
PLoS Biol. 18 e3000706- (2020)
Related structures: EMD-20286

Function and Biology Details

Reaction catalysed: 
Nucleoside triphosphate + RNA(n) = diphosphate + RNA(n+1)
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero undecamer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-199495 (preferred)
Entry contents:
6 distinct polypeptide molecules
2 distinct DNA molecules
1 distinct RNA molecule
Macromolecules (9 distinct):
DNA-directed RNA polymerase subunit alpha Chains: A, B
Molecule details ›
Chains: A, B
Length: 329 amino acids
Theoretical weight: 36.56 KDa
Source organism: Escherichia coli
Expression system: Escherichia coli
UniProt:
  • Canonical: P0A7Z4 (Residues: 1-329; Coverage: 100%)
Gene names: JW3257, b3295, pez, phs, rpoA, sez
Sequence domains:
DNA-directed RNA polymerase subunit beta Chain: C
Molecule details ›
Chain: C
Length: 1342 amino acids
Theoretical weight: 150.82 KDa
Source organism: Escherichia coli
Expression system: Escherichia coli
UniProt:
  • Canonical: P0A8V2 (Residues: 1-1342; Coverage: 100%)
Gene names: JW3950, b3987, groN, nitB, rif, ron, rpoB, stl, stv, tabD
Sequence domains:
DNA-directed RNA polymerase subunit beta' Chain: D
Molecule details ›
Chain: D
Length: 1407 amino acids
Theoretical weight: 155.37 KDa
Source organism: Escherichia coli
Expression system: Escherichia coli
UniProt:
  • Canonical: P0A8T7 (Residues: 1-1407; Coverage: 100%)
Gene names: JW3951, b3988, rpoC, tabB
Sequence domains:
DNA-directed RNA polymerase subunit omega Chain: E
Molecule details ›
Chain: E
Length: 91 amino acids
Theoretical weight: 10.25 KDa
Source organism: Escherichia coli
Expression system: Escherichia coli
UniProt:
  • Canonical: P0A800 (Residues: 1-91; Coverage: 100%)
Gene names: JW3624, b3649, rpoZ
Sequence domains: RNA polymerase Rpb6
RNA polymerase sigma factor RpoD Chain: F
Molecule details ›
Chain: F
Length: 628 amino acids
Theoretical weight: 72.21 KDa
Source organism: Escherichia coli
Expression system: Escherichia coli
UniProt:
  • Canonical: P00579 (Residues: 1-613; Coverage: 100%)
Gene names: JW3039, alt, b3067, rpoD
Sequence domains:
DNA-binding transcriptional dual regulator CRP Chains: G, H
Molecule details ›
Chains: G, H
Length: 210 amino acids
Theoretical weight: 23.67 KDa
Source organism: Escherichia coli
Expression system: Escherichia coli
UniProt:
  • Canonical: P0ACJ8 (Residues: 1-210; Coverage: 100%)
Gene names: JW5702, b3357, cap, crp, csm
Sequence domains:
SYNTHETIC NONTEMPLATE STRAND DNA (78-MER) Chain: 1
Molecule details ›
Chain: 1
Length: 78 nucleotides
Theoretical weight: 23.98 KDa
SYNTHETIC TEMPLATE STRAND DNA (78-MER) Chain: 2
Molecule details ›
Chain: 2
Length: 78 nucleotides
Theoretical weight: 24.19 KDa
Nascent RNA Chain: 3
Molecule details ›
Chain: 3
Length: 3 nucleotides
Theoretical weight: 1.13 KDa

Ligands and Environments

3 bound ligands:
Ligand ZN 2 x ZN
Ligand MG 1 x MG
Ligand CMP 2 x CMP
1 modified residue:
Ligand GTP 1 x GTP

Experiments and Validation Details

Entry percentile scores
Resolution: 4.35Å
Relevant EMDB volumes: EMD-20286
Expression system: Escherichia coli

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