1UF2

The Atomic Structure of Rice dwarf Virus (RDV)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.50 Å
  • R-Value Free: 0.306 
  • R-Value Work: 0.303 
  • R-Value Observed: 0.303 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

The atomic structure of rice dwarf virus reveals the self-assembly mechanism of component proteins.

Nakagawa, A.Miyazaki, N.Taka, J.Naitow, H.Ogawa, A.Fujimoto, Z.Mizuno, H.Higashi, T.Watanabe, Y.Omura, T.Cheng, R.H.Tsukihara, T.

(2003) Structure 11: 1227-1238

  • DOI: 10.1016/j.str.2003.08.012
  • Primary Citation of Related Structures:  
    1UF2

  • PubMed Abstract: 
  • Rice dwarf virus (RDV), the causal agent of rice dwarf disease, is a member of the genus Phytoreovirus in the family Reoviridae. RDV is a double-shelled virus with a molecular mass of approximately 70 million Dalton. This virus is widely prevalent an ...

    Rice dwarf virus (RDV), the causal agent of rice dwarf disease, is a member of the genus Phytoreovirus in the family Reoviridae. RDV is a double-shelled virus with a molecular mass of approximately 70 million Dalton. This virus is widely prevalent and is one of the viruses that cause the most economic damage in many Asian countries. The atomic structure of RDV was determined at 3.5 A resolution by X-ray crystallography. The double-shelled structure consists of two different proteins, the core protein P3 and the outer shell protein P8. The atomic structure shows structural and electrostatic complementarities between both homologous (P3-P3 and P8-P8) and heterologous (P3-P8) interactions, as well as overall conformational changes found in P3-P3 dimer caused by the insertion of amino-terminal loop regions of one of the P3 protein into the other. These interactions suggest how the 900 protein components are built into a higher-ordered virus core structure.


    Organizational Affiliation

    Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka 565-0871, Japan. atsushi@protein.osaka-u.ac.jp



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Core protein P3AB1019Rice dwarf virusMutation(s): 0 
Find proteins for P22472 (Rice dwarf virus (isolate Akita))
Explore P22472 
Go to UniProtKB:  P22472
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Outer capsid protein P8CDEFGHIJPQRST421Rice dwarf virusMutation(s): 0 
Find proteins for P17379 (Rice dwarf virus (isolate O))
Explore P17379 
Go to UniProtKB:  P17379
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Structural protein P7K506Rice dwarf virusMutation(s): 0 
Find proteins for P22473 (Rice dwarf virus (isolate O))
Explore P22473 
Go to UniProtKB:  P22473
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.50 Å
  • R-Value Free: 0.306 
  • R-Value Work: 0.303 
  • R-Value Observed: 0.303 
  • Space Group: I 2 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 770α = 90
b = 795β = 90
c = 814γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALAdata scaling
RAVEmodel building
CCP4model building
other jiffy programsmodel building
CNSrefinement
CCP4data scaling
RAVEphasing
CCP4phasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2003-10-14
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2017-10-04
    Changes: Refinement description