› 2e9r

X-ray diffraction
2.81Å resolution

Foot-and-mouth disease virus RNA-dependent RNA polymerase in complex with a template-primer RNA and with ribavirin

Released:
DOI: 10.2210/pdb2e9r/pdb
PDB entry 2e9r coloured by chain, front view.
PDB entry 2e9r coloured by chain, side view.
PDB entry 2e9r coloured by chain, top view.
Source organism: Foot-and-mouth disease virus C-S8c1
Primary publication:
Sequential structures provide insights into the fidelity of RNA replication.
Ferrer-Orta C, Arias A, Pérez-Luque R, Escarmís C, Domingo E, Verdaguer N
Proc Natl Acad Sci U S A 104 9463-8 (2007)
PMID: 17517631

Function and Biology Details

Reactions catalysed: 
Autocatalytically cleaves itself from the polyprotein of the foot-and-mouth disease virus by hydrolysis of a Lys-|-Gly bond, but then cleaves host cell initiation factor eIF-4G at bonds -Gly-|-Arg- and -Lys-|-Arg-.
NTP + H(2)O = NDP + phosphate
Biochemical function:
Biological process:
Cellular component:
  • not assigned
Sequence domains:
Structure domain:

Structure analysis Details

Assembly composition:
hetero trimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-192994 (preferred)
Entry contents:
1 distinct polypeptide molecule
2 distinct RNA molecules
Macromolecules (3 distinct):
RNA-dependent RNA polymerase Chain: X
Molecule details ›
Chain: X
Length: 476 amino acids
Theoretical weight: 53.49 KDa
Source organism: Foot-and-mouth disease virus C-S8c1
Expression system: Escherichia coli BL21
UniProt:
  • Canonical: Q9QCE4 (Residues: 1858-2327; Coverage: 20%)
Sequence domains: Viral RNA-dependent RNA polymerase
Structure domains:
5'-R(*CP*AP*UP*GP*GP*GP*CP*CP*C)-3' Chain: A
Molecule details ›
Chain: A
Length: 9 nucleotides
Theoretical weight: 2.85 KDa
Source organism: Foot-and-mouth disease virus C-S8c1
Expression system: Not provided
5'-R(*CP*CP*C*GP*GP*GP*CP*CP*C)-3' Chain: B
Molecule details ›
Chain: B
Length: 6 nucleotides
Theoretical weight: 1.91 KDa
Source organism: Foot-and-mouth disease virus C-S8c1
Expression system: Not provided

Ligands and Environments

2 bound ligands:
Ligand MG 1 x MG
Ligand RTP 1 x RTP
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: ESRF BEAMLINE ID29
Spacegroup: P3221
Unit cell:
a: 94.094Å b: 94.094Å c: 99.285Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.245 0.243 0.296
Expression systems:
  • Escherichia coli BL21
  • Not provided

Quick links

Citations

16 review citations

The flavivirus polymerase as a target for drug discovery.
Malet et al. (2008)
15 more

18 mentions without citation

Common and unique features of viral RNA-dependent polymerases.
te Velthuis AJ. (2014)
17 more