3PU4

Crystal Structure of a vesicular stomatitis virus nucleocapsid-polyU complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3 Å
  • R-Value Free: 0.288 
  • R-Value Work: 0.251 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Access to RNA Encapsidated in the Nucleocapsid of Vesicular Stomatitis Virus.

Green, T.J.Rowse, M.Tsao, J.Kang, J.Ge, P.Zhou, Z.H.Luo, M.

(2011) J.Virol. 85: 2714-2722

  • DOI: 10.1128/JVI.01927-10
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The genomic RNA of negative-strand RNA viruses, such as vesicular stomatitis virus (VSV), is completely enwrapped by the nucleocapsid protein (N) in every stage of virus infection. During viral transcription/replication, however, the genomic RNA in t ...

    The genomic RNA of negative-strand RNA viruses, such as vesicular stomatitis virus (VSV), is completely enwrapped by the nucleocapsid protein (N) in every stage of virus infection. During viral transcription/replication, however, the genomic RNA in the nucleocapsid must be accessible by the virus-encoded RNA-dependent RNA polymerase in order to serve as the template for RNA synthesis. With the VSV nucleocapsid and a nucleocapsid-like particle (NLP) produced in Escherichia coli, we have found that the RNA in the VSV nucleocapsid can be removed by RNase A, in contrast to what was previously reported. Removal of the RNA did not disrupt the assembly of the N protein, resulting in an empty capsid. Polyribonucleotides were reencapsidated into the empty NLP, and the crystal structures were determined. The crystal structures revealed variable degrees of association of the N protein with a specific RNA sequence.


    Organizational Affiliation

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




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Nucleoprotein
A, B, C, D, E
421Vesicular 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: 2
MoleculeChainsLengthOrganism
RNA (45-MER)R45synthetic construct
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, R
URANYL (VI) ION
O2 U
IZLHQJIUOZHTLW-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3 Å
  • R-Value Free: 0.288 
  • R-Value Work: 0.251 
  • Space Group: P 21 21 2
Unit Cell:
Length (Å)Angle (°)
a = 165.477α = 90.00
b = 235.065β = 90.00
c = 75.498γ = 90.00
Software Package:
Software NamePurpose
MOLREPphasing
PHENIXrefinement
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2011-01-12
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance
  • Version 1.2: 2018-04-04
    Type: Data collection
  • Version 1.3: 2018-04-11
    Type: Data collection, Source and taxonomy