1XAK | pdb_00001xak

STRUCTURE OF THE SARS-CORONAVIRUS ORF7A ACCESSORY PROTEIN

• PDB DOI: https://doi.org/10.2210/pdb1XAK/pdb

• Classification: VIRAL PROTEIN
• Organism(s): Severe acute respiratory syndrome-related coronavirus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2004-08-26 Released: 2004-10-05 
• Deposition Author(s): Nelson, C.A., Lee, C.A., Fremont, D.H., Midwest Center for Structural Genomics (MCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 
  0.275 (Depositor), 0.278 (DCC) 
• R-Value Work: 
  0.223 (Depositor), 0.222 (DCC) 
• R-Value Observed: 
  0.223 (Depositor) 

Literature

Structure and intracellular targeting of the SARS-coronavirus Orf7a accessory protein.

Nelson, C.A., Pekosz, A., Lee, C.A., Diamond, M.S., Fremont, D.H.

(2005) Structure 13: 75-85

• PubMed: 15642263 
• DOI: https://doi.org/10.1016/j.str.2004.10.010
• Primary Citation Related Structures: 
  1XAK


• PubMed Abstract: 
  

  The open reading frame (ORF) 7a of the SARS-associated coronavirus (SARS-CoV) encodes a unique type I transmembrane protein of unknown function. We have determined the 1.8 A resolution crystal structure of the N-terminal ectodomain of orf7a, revealing a compact seven-stranded beta sandwich unexpectedly similar in fold and topology to members of the Ig superfamily. We also demonstrate that, in SARS-CoV- infected cells, the orf7a protein is expressed and retained intracellularly. Confocal microscopy studies using orf7a and orf7a/CD4 chimeras implicate the short cytoplasmic tail and transmembrane domain in trafficking of the protein within the endoplasmic reticulum and Golgi network. Taken together, our findings provide a structural and cellular framework in which to explore the role of orf7a in SARS-CoV pathogenesis.

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Organizational Affiliation: 
• Department of Pathology and Immunology, 660 South Euclid Avenue, St. Louis, Missouri 63110, USA.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 9.42 kDa 
• Atom Count: 675 
• Modeled Residue Count: 68 
• Deposited Residue Count: 83 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
SARS ORF7A ACCESSORY PROTEIN	A	83	Severe acute respiratory syndrome-related coronavirus	Mutation(s): 0
UniProt
Find proteins for P59635 (Severe acute respiratory syndrome coronavirus) Explore P59635  Go to UniProtKB:  P59635

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free:  0.275 (Depositor), 0.278 (DCC) 
• R-Value Work:  0.223 (Depositor), 0.222 (DCC) 
• R-Value Observed: 0.223 (Depositor) 

Space Group: P 3₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 37.1	α = 90
b = 37.1	β = 90
c = 55.33	γ = 120

Software Package:

Software Name	Purpose
CNS	refinement
HKL-2000	data reduction
SCALEPACK	data scaling
SOLVE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2004-10-05 
Deposition Author(s): Nelson, C.A., Lee, C.A., Fremont, D.H., Midwest Center for Structural Genomics (MCSG)

Revision History  

• Version 1.0: 2004-10-05
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2024-10-30
  Changes: Data collection, Database references, Structure summary