› 3iyd

Electron Microscopy
19.8Å resolution

Three-dimensional EM structure of an intact activator-dependent transcription initiation complex

Released:
DOI: 10.2210/pdb3iyd/pdb
PDB entry 3iyd coloured by chain, front view.
PDB entry 3iyd coloured by chain, side view.
PDB entry 3iyd coloured by chain, top view.
Source organism: Escherichia coli K-12
Primary publication:
Three-dimensional EM structure of an intact activator-dependent transcription initiation complex.
Hudson BP, Quispe J, Lara-González S, Kim Y, Berman HM, Arnold E, Ebright RH, Lawson CL
Proc Natl Acad Sci U S A 106 19830-5 (2009)
PMID: 19903881
Related structures: EMD-5127

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 decamer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-116423 (preferred)
Entry contents:
6 distinct polypeptide molecules
2 distinct DNA molecules
Macromolecules (8 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 K-12
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 K-12
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: 1413 amino acids
Theoretical weight: 156.2 KDa
Source organism: Escherichia coli K-12
Expression system: Not provided
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: 90 amino acids
Theoretical weight: 10.12 KDa
Source organism: Escherichia coli K-12
Expression system: Escherichia coli
UniProt:
  • Canonical: P0A800 (Residues: 2-91; Coverage: 99%)
Gene names: JW3624, b3649, rpoZ
Sequence domains: RNA polymerase Rpb6
RNA polymerase sigma factor RpoD Chain: F
Molecule details ›
Chain: F
Length: 613 amino acids
Theoretical weight: 70.33 KDa
Source organism: Escherichia coli K-12
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: 209 amino acids
Theoretical weight: 23.54 KDa
Source organism: Escherichia coli K-12
Expression system: Escherichia coli
UniProt:
  • Canonical: P0ACJ8 (Residues: 2-210; Coverage: 100%)
Gene names: JW5702, b3357, cap, crp, csm
Sequence domains:
DNA (98-MER) Chain: I
Molecule details ›
Chain: I
Length: 98 nucleotides
Theoretical weight: 30.22 KDa
DNA (98-MER) Chain: J
Molecule details ›
Chain: J
Length: 98 nucleotides
Theoretical weight: 30.1 KDa

Ligands and Environments

1 bound ligand:
Ligand CMP 2 x CMP
No modified residues

Experiments and Validation Details

Entry percentile scores
Resolution: 19.8Å
Relevant EMDB volumes: EMD-5127
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

8 review citations

Activating transcription in bacteria.
Lee et al. (2012)
7 more

15 mentions without citation

Structural biology of bacterial RNA polymerase.
Murakami KS. (2015)
14 more