3G80

Nodamura virus protein b2, RNA-binding domain


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.297 
  • R-Value Work: 0.233 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structure of the RNA-Binding Domain of Nodamura Virus Protein B2, a Suppressor of RNA Interference.

Korber, S.Shaik Syed Ali, P.Chen, J.C.

(2009) Biochemistry 48: 2307-2309

  • DOI: 10.1021/bi900126s

  • PubMed Abstract: 
  • Protein B2 from Nodamura virus (NMV B2), a member of the Nodavirus family, acts as a suppressor of RNA interference (RNAi). The N-terminal domain of NMV B2, consisting of residues 1-79, recognizes double-stranded RNA (dsRNA). The 2.5 A crystal struct ...

    Protein B2 from Nodamura virus (NMV B2), a member of the Nodavirus family, acts as a suppressor of RNA interference (RNAi). The N-terminal domain of NMV B2, consisting of residues 1-79, recognizes double-stranded RNA (dsRNA). The 2.5 A crystal structure of the RNA-binding domain of NMV B2 shows a dimeric, helical bundle structure. The structure shows a conserved set of RNA-binding residues compared with flock house virus B2, despite limited sequence identity. The crystal packing places the RNA-binding residues along one face of symmetry-related molecules, suggesting a potential platform for recognition of dsRNA.


    Organizational Affiliation

    Institute of Biophysical Chemistry, Goethe University Frankfurt, Max-von-Laue-Strasse 9, 60438 Frankfurt, Germany.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Protein B2
A, B
97Nodamura virus (strain Mag115)Mutation(s): 0 
Gene Names: B2
Find proteins for Q9IMM3 (Nodamura virus (strain Mag115))
Go to UniProtKB:  Q9IMM3
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.297 
  • R-Value Work: 0.233 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 32.190α = 90.00
b = 56.600β = 90.00
c = 98.560γ = 90.00
Software Package:
Software NamePurpose
MOSFLMdata reduction
MOLREPphasing
SCALAdata scaling
CNSrefinement
PDB_EXTRACTdata extraction
ADSCdata collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2010-01-05
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance