3HHW

Complex of a vesicular stomatitis virus empty capsid with the nucleocapsid-binding domain of the phosphoprotein

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.296 
  • R-Value Work: 0.263 
  • R-Value Observed: 0.264 

wwPDB Validation   3D Report Full Report


This is version 1.1 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 U S A 106: 11713-11718

  • DOI: 10.1073/pnas.0903228106
  • Primary Citation of Related Structures:  
    3HHW, 3HHZ

  • 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) and a nonenzymatic cofactor, the phosphoprotein (P) ...

    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: 
(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Phosphoprotein A, B, C, D, E87Vesicular stomatitis Indiana virusMutation(s): 0 
Gene Names: nucleocapsid protein, P
Find proteins for P04880 (Vesicular stomatitis Indiana virus (strain Mudd-Summers))
Explore P04880 
Go to UniProtKB:  P04880
Protein Feature View
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  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Nucleoprotein K, L, M, N, O421Vesicular stomatitis Indiana virusMutation(s): 1 
Gene Names: N, phosphoprotein
Find proteins for Q77E03 (Vesicular stomatitis Indiana virus (strain 98COE North America))
Explore Q77E03 
Go to UniProtKB:  Q77E03
Protein Feature View
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  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE		A,B,C,D,EL-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.296 
  • R-Value Work: 0.263 
  • R-Value Observed: 0.264 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 170.602α = 90
b = 234.52β = 90
c = 95.05γ = 90
Software Package:
Software NamePurpose
SERGUIdata collection
COMOphasing
REFMACrefinement
HKL-2000data reduction
SCALEPACKdata scaling

Structure Validation

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View more in-depth experimental data

Entry History 

Deposition Data

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

Revision History  (Full details and data files)

  • Version 1.0: 2009-07-28
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Advisory, Version format compliance