› 3n4m

X-ray diffraction
2.99Å resolution

E. coli RNA polymerase alpha subunit C-terminal domain in complex with CAP and DNA

Released:
DOI: 10.2210/pdb3n4m/pdb
PDB entry 3n4m coloured by chain, front view.
PDB entry 3n4m coloured by chain, side view.
PDB entry 3n4m coloured by chain, top view.
Source organism: Escherichia coli K-12
Primary publication:
The RNA Polymerase α Subunit Recognizes the DNA Shape of the Upstream Promoter Element.
Lara-Gonzalez S, Dantas Machado AC, Rao S, Napoli AA, Birktoft J, Di Felice R, Rohs R, Lawson CL
Biochemistry 59 4523-4532 (2020)
PMID: 33205945

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-116599 (preferred)
Entry contents:
2 distinct polypeptide molecules
2 distinct DNA molecules
Macromolecules (4 distinct):
DNA-binding transcriptional dual regulator CRP Chain: A
Molecule details ›
Chain: A
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:
Structure domains:
DNA-directed RNA polymerase subunit alpha Chains: B, C
Molecule details ›
Chains: B, C
Length: 84 amino acids
Theoretical weight: 9.36 KDa
Source organism: Escherichia coli K-12
Expression system: Escherichia coli
UniProt:
  • Canonical: P0A7Z4 (Residues: 246-329; Coverage: 26%)
Gene names: JW3257, b3295, pez, phs, rpoA, sez
Sequence domains: Bacterial RNA polymerase, alpha chain C terminal domain
Structure domains: 5' to 3' exonuclease, C-terminal subdomain
DNA (5'-D(*CP*TP*TP*TP*TP*TP*TP*CP*CP*TP*AP*AP*AP*AP*TP*GP*TP*GP*AP*T)-3') Chain: D
Molecule details ›
Chain: D
Length: 20 nucleotides
Theoretical weight: 6.09 KDa
DNA (5'-D(*CP*TP*AP*GP*AP*TP*CP*AP*CP*AP*TP*TP*TP*TP*AP*GP*GP*AP*AP*AP*AP*AP*AP*G)-3') Chain: E
Molecule details ›
Chain: E
Length: 24 nucleotides
Theoretical weight: 7.41 KDa

Ligands and Environments

2 bound ligands:
Ligand CMP 2 x CMP
Ligand PEG 2 x PEG
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: NSLS BEAMLINE X29A
Spacegroup: P6222
Unit cell:
a: 175.73Å b: 175.73Å c: 160.1Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.199 0.198 0.224
Expression system: Escherichia coli

Quick links

Citations

1 review citation

Elucidating the biology of transcription factor-DNA interaction for accurate identification of cis-regulatory elements.
Hajheidari et al. (2022)
8 other articles

6 mentions without citation

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