Biological Assembly 1  

 3D View: Structure | 1D-3D View | Validation Report

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 9.91 kDa 
• Atom Count: 697 
• Modelled Residue Count: 87 
• Deposited Residue Count: 87 
• Unique protein chains: 1

1YO4

Solution Structure of the SARS Coronavirus ORF 7a coded X4 protein

• PDB DOI: 10.2210/pdb1YO4/pdb

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


• Deposited: 2005-01-26 Released: 2006-01-17 
• Deposition Author(s): Haenel, K., Stangler, T., Stoldt, M., Willbold, D.

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Experimental Data Snapshot

• Method: SOLUTION NMR
• Conformers Calculated: 100 
• Conformers Submitted: 10 
• Selection Criteria: structures with the lowest energy 

Literature

Solution structure of the X4 protein coded by the SARS related coronavirus reveals an immunoglobulin like fold and suggests a binding activity to integrin I domains.

Haenel, K., Stangler, T., Stoldt, M., Willbold, D.

(2006) J Biomed Sci 13: 281-293

• PubMed: 16328780 
• DOI: 10.1007/s11373-005-9043-9
• Primary Citation of Related Structures:  
  1YO4


• PubMed Abstract: 
  

The SARS related Coronavirus genome contains a variety of novel accessory genes. One of these, called ORF7a or ORF8, code for a protein, known as 7a, U122 or X4. We set out to determine the three-dimensional structure of the soluble ectodomain of this type-I transmembrane protein by nuclear magnetic resonance spectroscopy. The fold of the protein is the first member of a further variation of the immunoglobulin like beta-sandwich fold. Because X4 does not reveal significant sequence homologies to proteins in the data bases, we carried out a structure based similarity search for proteins with known function. High structural similarity to Dl domains of ICAM-1 and ICAM-2, and common features in amino acid sequence between X4 and ICAM-1, suggest X4 to possess binding activity for the alpha(L) integrin I domain of LFA-1. Further, based on this structure based prediction, potential functions of X4 in virus replication and pathogenesis are discussed.

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Organizational Affiliation: 

Forschungszentrum Jülich, Institut für Biologische Informationsverarbeitung (IBI-2), Germany.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Hypothetical protein X4	A	87	Severe acute respiratory syndrome-related coronavirus	Mutation(s): 0  Gene Names: 7a
UniProt
Find proteins for P59635 (Severe acute respiratory syndrome coronavirus) Explore P59635  Go to UniProtKB:  P59635

Experimental Data & Validation

Experimental Data

• Method: SOLUTION NMR
• Conformers Calculated: 100 
• Conformers Submitted: 10 
• Selection Criteria: structures with the lowest energy 
• OLDERADO: 1YO4 Olderado

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2005-01-26 
• Released Date: 2006-01-17 
Deposition Author(s): Haenel, K., Stangler, T., Stoldt, M., Willbold, D.

Revision History  

• Version 1.0: 2006-01-17
  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: 2022-03-02
  Changes: Database references, Derived calculations