3EKE

Crystal structure of IBV X-domain at pH 5.6


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.231 
  • R-Value Work: 0.199 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Crystal structures of the X-domains of a Group-1 and a Group-3 coronavirus reveal that ADP-ribose-binding may not be a conserved property.

Piotrowski, Y.Hansen, G.Boomaars-van der Zanden, A.L.Snijder, E.J.Gorbalenya, A.E.Hilgenfeld, R.

(2009) Protein Sci. 18: 6-16

  • DOI: 10.1002/pro.15
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The polyproteins of coronaviruses are cleaved by viral proteases into at least 15 nonstructural proteins (Nsps). Consisting of five domains, Nsp3 is the largest of these (180-210 kDa). Among these domains, the so-called X-domain is believed to act as ...

    The polyproteins of coronaviruses are cleaved by viral proteases into at least 15 nonstructural proteins (Nsps). Consisting of five domains, Nsp3 is the largest of these (180-210 kDa). Among these domains, the so-called X-domain is believed to act as ADP-ribose-1''-phosphate phosphatase or to bind poly(ADP-ribose). However, here we show that the X-domain of Infectious Bronchitis Virus (strain Beaudette), a Group-3 coronavirus, fails to bind ADP-ribose. This is explained on the basis of the crystal structure of the protein, determined at two different pH values. For comparison, we also describe the crystal structure of the homologous X-domain from Human Coronavirus 229E, a Group-1 coronavirus, which does bind ADP-ribose.


    Organizational Affiliation

    Institute of Biochemistry, Center for Structural and Cell Biology in Medicine, University of Lübeck, Ratzeburger Allee 160, 23538 Lübeck, Germany.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Non-structural protein 3
A
176Avian infectious bronchitis virus (strain Beaudette)Mutation(s): 0 
Gene Names: rep
Find proteins for P0C6Y1 (Avian infectious bronchitis virus (strain Beaudette))
Go to UniProtKB:  P0C6Y1
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
TLA
Query on TLA

Download SDF File 
Download CCD File 
A
L(+)-TARTARIC ACID
C4 H6 O6
FEWJPZIEWOKRBE-JCYAYHJZSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.231 
  • R-Value Work: 0.199 
  • Space Group: P 32 2 1
Unit Cell:
Length (Å)Angle (°)
a = 78.200α = 90.00
b = 78.200β = 90.00
c = 81.701γ = 120.00
Software Package:
Software NamePurpose
PHASERphasing
MOSFLMdata reduction
REFMACrefinement
SCALAdata scaling
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2008-09-30
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance