› 3q23

X-ray diffraction
1.8Å resolution

X-ray crystal structure of the N4 mini-VRNAP and P2_7a promoter transcription initiation complex with GMPCPP and Manganese: sustrate complex II

Released:
DOI: 10.2210/pdb3q23/pdb
PDB entry 3q23 coloured by chain, front view.
PDB entry 3q23 coloured by chain, side view.
PDB entry 3q23 coloured by chain, top view.
Source organism: Enquatrovirus N4
Primary publication:
X-ray crystal structures elucidate the nucleotidyl transfer reaction of transcript initiation using two nucleotides.
Gleghorn ML, Davydova EK, Basu R, Rothman-Denes LB, Murakami KS
Proc Natl Acad Sci U S A 108 3566-71 (2011)
PMID: 21321236

Function and Biology Details

Reaction catalysed: 
Nucleoside triphosphate + RNA(n) = diphosphate + RNA(n+1)
Biochemical function:
  • not assigned
Biological process:
  • not assigned
Cellular component:
  • not assigned

Structure analysis Details

Assembly composition:
hetero dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-116736 (preferred)
Entry contents:
1 distinct polypeptide molecule
1 distinct DNA molecule
Macromolecules (2 distinct):
Virion DNA-directed RNA polymerase Chains: A, B
Molecule details ›
Chains: A, B
Length: 1118 amino acids
Theoretical weight: 123.19 KDa
Source organism: Escherichia virus N4
Expression system: Escherichia coli
UniProt:
  • Canonical: Q859P9 (Residues: 998-2103; Coverage: 32%)
Gene name: 50
Sequence domains:
Structure domains:
DNA (5'-D(*TP*GP*CP*CP*TP*CP*CP*CP*AP*GP*GP*CP*AP*TP*CP*CP*AP*AP*AP*AP*GP*AP*AP*GP*CP*GP*GP*AP*GP*CP*TP*TP*CP*TP*TP*C)-3') Chains: C, D
Molecule details ›
Chains: C, D
Length: 36 nucleotides
Theoretical weight: 11.01 KDa
Source organism: Enquatrovirus N4
Expression system: Not provided

Ligands and Environments

3 bound ligands:
Ligand G2P 4 x G2P
Ligand MN 4 x MN
Ligand 2HP 2 x 2HP
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: NSLS BEAMLINE X25
Spacegroup: P212121
Unit cell:
a: 82.834Å b: 111.861Å c: 276.093Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.201 0.2 0.231
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

4 review citations

Basic mechanisms of RNA polymerase II activity and alteration of gene expression in Saccharomyces cerevisiae.
Kaplan CD. (2013)
3 more

57 mentions without citation

Lysine post-translational modifications of collagen.
Yamauchi et al. (2012)
56 more