2CME

The crystal structure of SARS coronavirus ORF-9b protein


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.289 
  • R-Value Work: 0.266 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

The Crystal Structure of Orf-9B, a Lipid Binding Protein from the Sars Coronavirus.

Meier, C.Aricescu, A.R.Assenberg, R.Aplin, R.T.Gilbert, R.J.C.Grimes, J.M.Stuart, D.I.

(2006) Structure 14: 1157

  • DOI: 10.1016/j.str.2006.05.012

  • PubMed Abstract: 
  • To achieve the greatest output from their limited genomes, viruses frequently make use of alternative open reading frames, in which translation is initiated from a start codon within an existing gene and, being out of frame, gives rise to a distinct ...

    To achieve the greatest output from their limited genomes, viruses frequently make use of alternative open reading frames, in which translation is initiated from a start codon within an existing gene and, being out of frame, gives rise to a distinct protein product. These alternative protein products are, as yet, poorly characterized structurally. Here we report the crystal structure of ORF-9b, an alternative open reading frame within the nucleocapsid (N) gene from the SARS coronavirus. The protein has a novel fold, a dimeric tent-like beta structure with an amphipathic surface, and a central hydrophobic cavity that binds lipid molecules. This cavity is likely to be involved in membrane attachment and, in mammalian cells, ORF-9b associates with intracellular vesicles, consistent with a role in the assembly of the virion. Analysis of ORF-9b and other overlapping genes suggests that they provide snapshots of the early evolution of novel protein folds.


    Organizational Affiliation

    Division of Structural Biology, The Henry Wellcome Building for Genomic Medicine, Oxford University, Roosevelt Drive, Oxford OX3 7BN, United Kingdom.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
HYPOTHETICAL PROTEIN 5
A
78Human SARS coronavirusMutation(s): 0 
Find proteins for P59636 (Human SARS coronavirus)
Go to UniProtKB:  P59636
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
HYPOTHETICAL PROTEIN 5
B
79Human SARS coronavirusMutation(s): 0 
Gene Names: ORF9b
Find proteins for Q19QV9 (Human SARS coronavirus)
Go to UniProtKB:  Q19QV9
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
HYPOTHETICAL PROTEIN 5
C, D, F, H
76Human SARS coronavirusMutation(s): 0 
Find proteins for P59636 (Human SARS coronavirus)
Go to UniProtKB:  P59636
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
HYPOTHETICAL PROTEIN 5
E, G
77Human SARS coronavirusMutation(s): 0 
Gene Names: ORF9b
Find proteins for Q19QV9 (Human SARS coronavirus)
Go to UniProtKB:  Q19QV9
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
D10
Query on D10

Download SDF File 
Download CCD File 
B, C, F, H
DECANE
C10 H22
DIOQZVSQGTUSAI-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.289 
  • R-Value Work: 0.266 
  • Space Group: P 42
Unit Cell:
Length (Å)Angle (°)
a = 140.028α = 90.00
b = 140.028β = 90.00
c = 45.146γ = 90.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
DENZOdata reduction
SHELXphasing
CNSrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2006-07-19
    Type: Initial release
  • Version 1.1: 2011-05-08
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance