› 4k4y

X-ray diffraction
2.72Å resolution

Coxsackievirus B3 polymerase elongation complex (r2+1_form)

Released:
DOI: 10.2210/pdb4k4y/pdb
PDB entry 4k4y coloured by chain, front view.
PDB entry 4k4y coloured by chain, side view.
PDB entry 4k4y coloured by chain, top view.
Source organism: Coxsackievirus B3
Primary publication:
Structures of coxsackievirus, rhinovirus, and poliovirus polymerase elongation complexes solved by engineering RNA mediated crystal contacts.
Gong P, Kortus MG, Nix JC, Davis RE, Peersen OB
PLoS One 8 e60272 (2013)
PMID: 23667424

Function and Biology Details

Reactions catalysed: 
Nucleoside triphosphate + RNA(n) = diphosphate + RNA(n+1)
Selective cleavage of Gln-|-Gly bond in the poliovirus polyprotein. In other picornavirus reactions Glu may be substituted for Gln, and Ser or Thr for Gly.
Selective cleavage of Tyr-|-Gly bond in picornavirus polyprotein.
NTP + H(2)O = NDP + phosphate
Biochemical function:
Biological process:
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
hetero tetramer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-238516 (preferred)
Entry contents:
1 distinct polypeptide molecule
2 distinct RNA molecules
1 distinct DNA/RNA hybrid molecule
Macromolecules (4 distinct):
RNA-dependent RNA polymerase Chains: A, E, I, M
Molecule details ›
Chains: A, E, I, M
Length: 472 amino acids
Theoretical weight: 53.62 KDa
Source organism: Coxsackievirus B3
Expression system: Escherichia coli
UniProt:
  • Canonical: Q5UEA2 (Residues: 1724-2185; Coverage: 21%)
Sequence domains: Viral RNA-dependent RNA polymerase
Structure domains:
RNA (5'-R(*AP*AP*GP*UP*CP*UP*CP*CP*AP*GP*GP*UP*CP*UP*CP*UP*CP*GP*UP*CP*GP*AP*AP*A)-3') Chains: B, F, J, N
Molecule details ›
Chains: B, F, J, N
Length: 24 nucleotides
Theoretical weight: 7.63 KDa
Source organism: Coxsackievirus B3
Expression system: Not provided
RNA (5'-R(*GP*GP*GP*AP*GP*AP*UP*GP*A)-3') Chains: D, H, L, P
Molecule details ›
Chains: D, H, L, P
Length: 9 nucleotides
Theoretical weight: 2.97 KDa
Source organism: Coxsackievirus B3
Expression system: Not provided
DNA/RNA (5'-R(*UP*GP*UP*UP*CP*GP*AP*CP*GP*AP*GP*AP*GP*AP*(DOC))-3') Chains: C, G, K, O
Molecule details ›
Chains: C, G, K, O
Length: 15 nucleotides
Theoretical weight: 4.8 KDa
Source organism: Coxsackievirus B3
Expression system: Not provided

Ligands and Environments

3 bound ligands:
Ligand DCT 4 x DCT
Ligand ACT 3 x ACT
Ligand GOL 12 x GOL
1 modified residue:
Ligand DOC 4 x DOC

Experiments and Validation Details

Entry percentile scores
X-ray source: ALS BEAMLINE 4.2.2
Spacegroup: P1
Unit cell:
a: 60.373Å b: 60.402Å c: 194.026Å
α: 89.92° β: 89.96° γ: 79.75°
R-values:
R R work R free
0.202 0.199 0.247
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

10 review citations

RNA Dependent RNA Polymerases: Insights from Structure, Function and Evolution.
Venkataraman et al. (2018)
9 more

4 mentions without citation

Visualizing the Nucleotide Addition Cycle of Viral RNA-Dependent RNA Polymerase.
Wu et al. (2018)
3 more