1KHV

Crystal Structure of Rabbit Hemorrhagic Disease Virus RNA-dependent RNA polymerase complexed with Lu3+


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.265 
  • R-Value Work: 0.217 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Crystal structures of active and inactive conformations of a caliciviral RNA-dependent RNA polymerase.

Ng, K.K.Cherney, M.M.Vazquez, A.L.Machin, A.Alonso, J.M.Parra, F.James, M.N.

(2002) J.Biol.Chem. 277: 1381-1387

  • DOI: 10.1074/jbc.M109261200
  • Primary Citation of Related Structures:  1KHW

  • PubMed Abstract: 
  • The structure of the RNA-dependent RNA polymerase (RdRP) from the rabbit hemorrhagic disease virus has been determined by x-ray crystallography to a 2.5-A resolution. The overall structure resembles a "right hand," as seen before in other polymerases ...

    The structure of the RNA-dependent RNA polymerase (RdRP) from the rabbit hemorrhagic disease virus has been determined by x-ray crystallography to a 2.5-A resolution. The overall structure resembles a "right hand," as seen before in other polymerases, including the RdRPs of polio virus and hepatitis C virus. Two copies of the polymerase are present in the asymmetric unit of the crystal, revealing active and inactive conformations within the same crystal form. The fingers and palm domains form a relatively rigid unit, but the thumb domain can adopt either "closed" or "open" conformations differing by a rigid body rotation of approximately 8 degrees. Metal ions bind at different positions in the two conformations and suggest how structural changes may be important to enzymatic function in RdRPs. Comparisons between the structures of the alternate conformational states of rabbit hemorrhagic disease virus RdRP and the structures of RdRPs from hepatitis C virus and polio virus suggest novel structure-function relationships in this medically important class of enzymes.


    Organizational Affiliation

    Canadian Institutes for Health Research Group in Protein Structure and Function, Department of Biochemistry, University of Alberta, Edmonton, Alberta T6G 2H7, Canada.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
RNA-DIRECTED RNA POLYMERASE
A, B
516Rabbit hemorrhagic disease virus (strain Rabbit/Germany/FRG/1989)EC: 3.6.1.15, 3.4.22.66, 2.7.7.48
Find proteins for P27410 (Rabbit hemorrhagic disease virus (strain Rabbit/Germany/FRG/1989))
Go to UniProtKB:  P27410
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
LU
Query on LU

Download SDF File 
Download CCD File 
A, B
LUTETIUM (III) ION
LU
Lu
PSDMOPINLDTFSZ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.265 
  • R-Value Work: 0.217 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 70.300α = 90.00
b = 119.100β = 90.00
c = 158.700γ = 90.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
CNSphasing
REFMACrefinement
DENZOdata reduction
CNSrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2002-01-16
    Type: Initial release
  • Version 1.1: 2007-10-16
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Advisory, Version format compliance