3HHZ

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.50 Å
  • R-Value Free: 0.323 
  • R-Value Work: 0.254 
  • R-Value Observed: 0.258 

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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 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
PhosphoproteinA, B, C, D, E87Vesicular stomatitis Indiana virusMutation(s): 0 
Gene Names: nucleocapsid proteinP
UniProt
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
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
NucleoproteinF [auth K], G [auth L], H [auth M], I [auth N], J [auth O]421Vesicular stomatitis Indiana virusMutation(s): 0 
Gene Names: Nphosphoprotein
UniProt
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
Find similar nucleic acids by:  (by identity cutoff)  |  Structure
Entity ID: 3
MoleculeChainsLengthOrganismImage
RNA (45-MER)K [auth R]45Escherichia coli
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.50 Å
  • R-Value Free: 0.323 
  • R-Value Work: 0.254 
  • R-Value Observed: 0.258 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 166.568α = 90
b = 235.248β = 90
c = 96.138γ = 90
Software Package:
Software NamePurpose
Blu-Icedata collection
COMOphasing
REFMACrefinement
HKL-2000data reduction
SCALEPACKdata scaling

Structure Validation

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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
  • Version 1.2: 2017-11-01
    Changes: Refinement description