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PDBsum entry 3j1p

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protein Protein-protein interface(s) links
Virus PDB id
3j1p
Jmol
Contents
Protein chains
525 a.a.
PDB id:
3j1p
Name: Virus
Title: Atomic model of rabbit hemorrhagic disease virus
Structure: Major capsid protein vp60. Chain: a, b, c. Fragment: unp residues 1766-2344
Source: Rabbit hemorrhagic disease virus. Rhdv. Organism_taxid: 11976. Strain: hyd
Authors: X.Wang,Y.Liu,F.Sun
Key ref: X.Wang et al. (2013). Atomic model of rabbit hemorrhagic disease virus by cryo-electron microscopy and crystallography. PLoS Pathog, 9, e1003132. PubMed id: 23341770 DOI: 10.1371/journal.ppat.1003132
Date:
09-Apr-12     Release date:   30-Jan-13    
PROCHECK
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 Headers
 References

Protein chains
Pfam   ArchSchema ?
F5BXG7  (F5BXG7_RHDV) -  Polyprotein
Seq:
Struc:
 
Seq:
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Seq:
Struc:
 
Seq:
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Seq:
Struc:
2344 a.a.
525 a.a.
Key:    PfamA domain  PfamB domain  Secondary structure

 

 
DOI no: 10.1371/journal.ppat.1003132 PLoS Pathog 9:e1003132 (2013)
PubMed id: 23341770  
 
 
Atomic model of rabbit hemorrhagic disease virus by cryo-electron microscopy and crystallography.
X.Wang, F.Xu, J.Liu, B.Gao, Y.Liu, Y.Zhai, J.Ma, K.Zhang, T.S.Baker, K.Schulten, D.Zheng, H.Pang, F.Sun.
 
  ABSTRACT  
 
Rabbit hemorrhagic disease, first described in China in 1984, causes hemorrhagic necrosis of the liver. Its etiological agent, rabbit hemorrhagic disease virus (RHDV), belongs to the Lagovirus genus in the family Caliciviridae. The detailed molecular structure of any lagovirus capsid has yet to be determined. Here, we report a cryo-electron microscopic (cryoEM) reconstruction of wild-type RHDV at 6.5 Å resolution and the crystal structures of the shell (S) and protruding (P) domains of its major capsid protein, VP60, each at 2.0 Å resolution. From these data we built a complete atomic model of the RHDV capsid. VP60 has a conserved S domain and a specific P2 sub-domain that differs from those found in other caliciviruses. As seen in the shell portion of the RHDV cryoEM map, which was resolved to ∼5.5 Å, the N-terminal arm domain of VP60 folds back onto its cognate S domain. Sequence alignments of VP60 from six groups of RHDV isolates revealed seven regions of high variation that could be mapped onto the surface of the P2 sub-domain and suggested three putative pockets might be responsible for binding to histo-blood group antigens. A flexible loop in one of these regions was shown to interact with rabbit tissue cells and contains an important epitope for anti-RHDV antibody production. Our study provides a reliable, pseudo-atomic model of a Lagovirus and suggests a new candidate for an efficient vaccine that can be used to protect rabbits from RHDV infection.