2GIC

Crystal Structure of a vesicular stomatitis virus nucleocapsid-RNA complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.92 Å
  • R-Value Free: 0.306 
  • R-Value Work: 0.255 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Structure of the vesicular stomatitis virus nucleoprotein-RNA complex unveils how the RNA is sequestered

Green, T.J.Zhang, X.Wertz, G.W.Luo, M.

(2006) Science 313: 357-360

  • DOI: 10.1126/science.1126953

  • PubMed Abstract: 
  • Vesicular stomatitis virus is a negative-stranded RNA virus. Its nucleoprotein (N) binds the viral genomic RNA and is involved in multiple functions including transcription, replication, and assembly. We have determined a 2.9 angstrom structure of a ...

    Vesicular stomatitis virus is a negative-stranded RNA virus. Its nucleoprotein (N) binds the viral genomic RNA and is involved in multiple functions including transcription, replication, and assembly. We have determined a 2.9 angstrom structure of a complex containing 10 molecules of the N protein and 90 bases of RNA. The RNA is tightly sequestered in a cavity at the interface between two lobes of the N protein. This serves to protect the RNA in the absence of polynucleotide synthesis. For the RNA to be accessed, some conformational change in the N protein should be necessary.


    Organizational Affiliation

    Department of Microbiology, School of Medicine, University of Alabama at Birmingham, 1025 18th Street South, Birmingham, AL 35294, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Nucleocapsid protein
A, B, C, D, E
422Vesicular stomatitis Indiana virus (strain San Juan)Mutation(s): 0 
Gene Names: N
Find proteins for P03521 (Vesicular stomatitis Indiana virus (strain San Juan))
Go to UniProtKB:  P03521
Entity ID: 1
MoleculeChainsLengthOrganism
45-MERR45N/A
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
IUM
Query on IUM

Download SDF File 
Download CCD File 
A, B, C, D, E
URANYL (VI) ION
O2 U
IZLHQJIUOZHTLW-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.92 Å
  • R-Value Free: 0.306 
  • R-Value Work: 0.255 
  • Space Group: P 21 21 2
Unit Cell:
Length (Å)Angle (°)
a = 166.160α = 90.00
b = 236.316β = 90.00
c = 75.651γ = 90.00
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
PDB_EXTRACTdata extraction
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2006-08-22
    Type: Initial release
  • Version 1.1: 2008-05-01
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Advisory, Version format compliance
  • Version 1.3: 2017-10-18
    Type: Refinement description