3G80 | pdb_00003g80

Nodamura virus protein b2, RNA-binding domain

• PDB DOI: https://doi.org/10.2210/pdb3G80/pdb

• Classification: VIRAL PROTEIN
• Organism(s): Nodamura virus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2009-02-11 Released: 2010-01-05 
• Deposition Author(s): Korber, S., Shaik Syed Ali, P., Chen, J.C.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 
  0.297 (Depositor), 0.286 (DCC) 
• R-Value Work: 
  0.233 (Depositor), 0.226 (DCC) 
• R-Value Observed: 
  0.233 (Depositor) 

Starting Model: experimental

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

• PubMed: 19249868 
• DOI: https://doi.org/10.1021/bi900126s
• Primary Citation Related Structures: 
  3G80


• 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 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.

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

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 22.27 kDa 
• Atom Count: 1,223 
• Modeled Residue Count: 146 
• Deposited Residue Count: 194 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Protein B2	A, B	97	Nodamura virus	Mutation(s): 0  Gene Names: B2
UniProt
Find proteins for Q9IMM3 (Nodamura virus (strain Mag115)) Explore Q9IMM3  Go to UniProtKB:  Q9IMM3

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free:  0.297 (Depositor), 0.286 (DCC) 
• R-Value Work:  0.233 (Depositor), 0.226 (DCC) 
• R-Value Observed: 0.233 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 32.19	α = 90
b = 56.6	β = 90
c = 98.56	γ = 90

Software Package:

Software Name	Purpose
MOLREP	phasing
CNS	refinement
PDB_EXTRACT	data extraction
ADSC	data collection
MOSFLM	data reduction
SCALA	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-01-05 
Deposition Author(s): Korber, S., Shaik Syed Ali, P., Chen, J.C.

Revision History  

• Version 1.0: 2010-01-05
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2023-09-06
  Changes: Data collection, Database references, Refinement description