3HHZ

Complex of the vesicular stomatitis virus nucleocapsid and the nucleocapsid-binding domain of the phosphoprotein


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.5 Å
  • R-Value Free: 0.323 
  • R-Value Work: 0.254 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structure of the vesicular stomatitis virus nucleocapsid in complex with the nucleocapsid-binding domain of the small polymerase cofactor, P.

Green, T.J.Luo, M.

(2009) Proc.Natl.Acad.Sci.USA 106: 11713-11718

  • DOI: 10.1073/pnas.0903228106
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The negative-strand RNA viruses (NSRVs) are unique because their nucleocapsid, not the naked RNA, is the active template for transcription and replication. The viral polymerase of nonsegmented NSRVs contains a large polymerase catalytic subunit (L) a ...

    The negative-strand RNA viruses (NSRVs) are unique because their nucleocapsid, not the naked RNA, is the active template for transcription and replication. The viral polymerase of nonsegmented NSRVs contains a large polymerase catalytic subunit (L) and a nonenzymatic cofactor, the phosphoprotein (P). Insight into how P delivers the polymerase complex to the nucleocapsid has long been pursued by reverse genetics and biochemical approaches. Here, we present the X-ray crystal structure of the C-terminal domain of P of vesicular stomatitis virus, a prototypic nonsegmented NSRV, bound to nucleocapsid-like particles. P binds primarily to the C-terminal lobe of 2 adjacent N proteins within the nucleocapsid. This binding mode is exclusive to the nucleocapsid, not the nucleocapsid (N) protein in other existing forms. Localization of phosphorylation sites within P and their proximity to the RNA cavity give insight into how the L protein might be oriented to access the RNA template.


    Organizational Affiliation

    Department of Microbiology, University of Alabama School of Medicine, Birmingham, AL 35294, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Phosphoprotein
A, B, C, D, E
87Vesicular stomatitis Indiana virus (strain Mudd-Summers)Mutation(s): 0 
Gene Names: P
Find proteins for P04880 (Vesicular stomatitis Indiana virus (strain Mudd-Summers))
Go to UniProtKB:  P04880
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Nucleoprotein
K, L, M, N, O
421Vesicular stomatitis Indiana virus (strain 98COE North America)Mutation(s): 0 
Gene Names: N
Find proteins for Q77E03 (Vesicular stomatitis Indiana virus (strain 98COE North America))
Go to UniProtKB:  Q77E03
Entity ID: 3
MoleculeChainsLengthOrganism
RNA (45-MER)R45Escherichia coli
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.5 Å
  • R-Value Free: 0.323 
  • R-Value Work: 0.254 
  • Space Group: P 21 21 2
Unit Cell:
Length (Å)Angle (°)
a = 166.568α = 90.00
b = 235.248β = 90.00
c = 96.138γ = 90.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
Blu-Icedata collection
HKL-2000data reduction
COMOphasing
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2009-05-18 
  • Released Date: 2009-07-28 
  • Deposition Author(s): Green, T.J., Luo, M.

Revision History 

  • Version 1.0: 2009-07-28
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Advisory, Version format compliance
  • Version 1.2: 2017-11-01
    Type: Refinement description