2CME

The crystal structure of SARS coronavirus ORF-9b protein


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.289 
  • R-Value Work: 0.266 
  • R-Value Observed: 0.266 

wwPDB Validation   3D Report Full Report


This is version 1.3 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: https://doi.org/10.1016/j.str.2006.05.012
  • Primary Citation of Related Structures:  
    2CME

  • 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 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
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
HYPOTHETICAL PROTEIN 578Severe acute respiratory syndrome-related coronavirusMutation(s): 0 
UniProt
Find proteins for P59636 (Severe acute respiratory syndrome coronavirus)
Explore P59636 
Go to UniProtKB:  P59636
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP59636
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
HYPOTHETICAL PROTEIN 579Severe acute respiratory syndrome-related coronavirusMutation(s): 0 
UniProt
Find proteins for P59636 (Severe acute respiratory syndrome coronavirus)
Explore P59636 
Go to UniProtKB:  P59636
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP59636
Sequence Annotations
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
HYPOTHETICAL PROTEIN 5
C, D, F, H
76Severe acute respiratory syndrome-related coronavirusMutation(s): 0 
UniProt
Find proteins for P59636 (Severe acute respiratory syndrome coronavirus)
Explore P59636 
Go to UniProtKB:  P59636
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP59636
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
HYPOTHETICAL PROTEIN 5
E, G
77Severe acute respiratory syndrome-related coronavirusMutation(s): 0 
UniProt
Find proteins for P59636 (Severe acute respiratory syndrome coronavirus)
Explore P59636 
Go to UniProtKB:  P59636
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP59636
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.289 
  • R-Value Work: 0.266 
  • R-Value Observed: 0.266 
  • Space Group: P 42
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 140.028α = 90
b = 140.028β = 90
c = 45.146γ = 90
Software Package:
Software NamePurpose
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
SHELXphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2006-07-19
    Type: Initial release
  • Version 1.1: 2011-05-08
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2024-05-08
    Changes: Data collection, Database references, Other