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PDB:2CME

Protein Name

SARS coronavirus ORF-9b protein

Species

Human severe acute respiratory syndrome (SARS) virus

Biological Context

Viruses can replicate themselves only by infecting a host cell. They therefore cannot reproduce on their own. Some viruses use multiple start codons and produce more than two proteins from a gene. Each codon consists of three nucleotides, corresponding to a single amino acid. Therefore a gene can be read by three ways.

For example, a DNA sequence with ATGTCTGSTSSTGGSCCC can be read as
ATG-TCT-GAT-AAT-GGA-CCC-C..., or
A-TGT-CTG-ATA-ATG-GAC-CCC...
Each includes a start codon ATG, encodes a different protein.

This different reading frame is called alternative open reading frame (alternative ORF). To explain how alternative ORFs have originated, the following model has been proposed. At first, only one reading frame was used, but a peptide was accidentally translated from another reading frame. Then this peptide partially became structured and obtained some function. The disordered regions remained as a trace of the past history.

SARS coronaviruses (SARS-CoVs), known as the pathogen for the severe acute respiratory syndrome (SARS), are viruses that have alternative ORFs. SARS-CoV's N gene that codes nucleocapsid is translated into two reading frame ORF-9a and ORF-9b. ORF-9b proteins probably code virus assembly, a step of virus replicating pathway combine a replicated gene material and a capsid.

Structure Description

2cme2cme_x2cme_y
The structure shown here is a ORF-9b protein of SARS coronavirus complexed with a part of lipid molecule. This protein is homodimer and has a hydrophobic cavity that binds lipid molecules between two monomers. The ligand is an unbranched chain of about 25 carbon atoms but only 10 carbon atoms are shown.

It is suggested that the ligand actually bound to the hydrophobic tunnel is a phospholipids of intracellular vesicle membrane of host cell and serves as an attachment point for components of the nascent virus. According to this model, the nascent virus enters into the vesicle, is assembled, and is excreted by exocytosis.

The protein is built up from twisted chains of ORF-9b dimers that form an open three-dimensional mesh, via end-to-end packing of dimers via the beta4-beta5 and beta6-beta7 loops. These chains are suggested to cover the surface of vesicle of host cell.

Protein Data Bank (PDB)

References

Source

  • Meier, C. Aricescu, A.R. Assenberg, R. Aplin, R.T. Gilbert, R.J.C. Grimes, J.M. Stuart, D.I.; "The Crystal Structure of Orf-9B, a Lipid Binding Protein from the Sars Coronavirus."; Structure; (2006) 14:1157-1165 PubMed:16843897.

Others

author: Takahiro Kudou


Japanese version:PDB:2CME