5Y6Z

Crystal structure of the coxsackievirus A16 polymerase elongation complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.259 
  • R-Value Work: 0.218 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Crystal structure of the coxsackievirus A16 RNA-dependent RNA polymerase elongation complex reveals novel features in motif A dynamics

Bi, P.Shu, B.Gong, P.

(2017) Virol Sin 32: 548-552

  • DOI: 10.1007/s12250-017-4066-8

  • PubMed Abstract: 
  • The RNA-dependent RNA polymerases (RdRPs) encoded by RNA viruses represent a unique class of nucleic acid polymerases. Unlike other classes of single-subunit polymerases, viral RdRPs have evolved a unique conformational change in their palm domain to ...

    The RNA-dependent RNA polymerases (RdRPs) encoded by RNA viruses represent a unique class of nucleic acid polymerases. Unlike other classes of single-subunit polymerases, viral RdRPs have evolved a unique conformational change in their palm domain to close the active site during catalysis. The hallmark of this conformational change is the backbone shift of the polymerase motif A from an "open" state to a "closed" state, allowing two universally conserved aspartic acid residues to orient toward each other for divalent metal binding and catalysis. The "closed" motif A conformation was only observed upon the binding of correct NTP in RdRP catalytic complexes or under rare conditions such as induced by a bound lutetium ion or a bound glutamate molecule. By solving the crystal structure of the catalytic elongation complex of the coxsackievirus RdRP, we in this work observed for the first time the "closed" motif A conformation in the absence of an NTP substrate or other conformational-change-inducing factors. This observation emphasizes the intrinsic dynamic features of viral RdRP motif A, and solidifies the structural basis for how this important structural element participates in catalytic events of the RdRPs.


    Organizational Affiliation

    Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, 430071, China.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Genome polyprotein
A, E
468N/AN/A
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 2
MoleculeChainsLengthOrganism
Template RNA (33-MER)B,F33synthetic construct
Entity ID: 3
MoleculeChainsLengthOrganism
Product RNA (14-MER)C,G14synthetic construct
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PO4
Query on PO4

Download SDF File 
Download CCD File 
A, B, C, G
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
GOL
Query on GOL

Download SDF File 
Download CCD File 
A, B, C, E, F
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

Download SDF File 
Download CCD File 
E
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.259 
  • R-Value Work: 0.218 
  • Space Group: P 31
Unit Cell:
Length (Å)Angle (°)
a = 93.724α = 90.00
b = 93.724β = 90.00
c = 167.512γ = 120.00
Software Package:
Software NamePurpose
d*TREKdata reduction
PDB_EXTRACTdata extraction
PHENIXrefinement
PHASERphasing
d*TREKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2017-08-15 
  • Released Date: 2017-12-27 
  • Deposition Author(s): Bi, P., Shu, B., Gong, P.

Revision History 

  • Version 1.0: 2017-12-27
    Type: Initial release
  • Version 1.1: 2018-01-17
    Type: Database references