PDBsum entry 4ejr

Viral protein

PDB id: 4ejr

Contents

Protein chains

163 a.a.

Waters ×78

PDB id:

4ejr

Name:

Viral protein

Title:

Crystal structure of major capsid protein s domain from rabbit hemorrhagic disease virus

Structure:

Major capsid protein vp60. Chain: a, b. Fragment: s (inner shell) domain (unp residues 1-230). Engineered: yes

Source:

Rabbit hemorrhagic disease virus. Rhdv. Organism_taxid: 11976. Strain: jx/cha/97. Gene: vp60. Expressed in: escherichia coli. Expression_system_taxid: 511693.

Resolution:

2.00Å R-factor: 0.203 R-free: 0.241

Authors:

F.Xu,J.Ma,K.Zhang,X.Wang,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

Date:

07-Apr-12 Release date: 30-Jan-13

Protein chains

Q3HNQ2  (Q3HNQ2_RHDV) -  Genome polyprotein from Rabbit hemorrhagic disease virus

Seq: 2344 a.a.

Struc: 163 a.a.

Enzyme reactions

• Enzyme class: E.C.3.6.1.15 - nucleoside-triphosphate phosphatase.
• Reaction: a ribonucleoside 5'-triphosphate + H2O = a ribonucleoside 5'-diphosphate + phosphate + H⁺

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

Key reference

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.