Crystal Structure of a vesicular stomatitis virus nucleocapsid-polyC complex

Experimental Data Snapshot

  • Resolution: 3.09 Å
  • R-Value Free: 0.290 
  • R-Value Work: 0.250 
  • R-Value Observed: 0.252 

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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: https://doi.org/10.1128/JVI.01927-10
  • Primary Citation of Related Structures:  
    3PTO, 3PTX, 3PU0, 3PU1, 3PU4

  • 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 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.


Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
A, B, C, D, E
421Vesicular stomatitis Indiana virusMutation(s): 0 
Gene Names: N
Find proteins for P03521 (Vesicular stomatitis Indiana virus (strain San Juan))
Explore P03521 
Go to UniProtKB:  P03521
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP03521
Sequence Annotations
  • Reference Sequence
Find similar nucleic acids by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains LengthOrganismImage
RNA (45-MER)F [auth R]45synthetic construct
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on IUM

Download Ideal Coordinates CCD File 
G [auth A]
H [auth A]
I [auth A]
J [auth B]
K [auth B]
G [auth A],
H [auth A],
I [auth A],
J [auth B],
K [auth B],
L [auth B],
M [auth B],
N [auth C],
O [auth C],
P [auth D],
Q [auth D],
R [auth D],
S [auth E],
T [auth E],
U [auth E],
V [auth R],
W [auth R],
X [auth R],
Y [auth R],
Z [auth R]
O2 U
Experimental Data & Validation

Experimental Data

  • Resolution: 3.09 Å
  • R-Value Free: 0.290 
  • R-Value Work: 0.250 
  • R-Value Observed: 0.252 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 164.652α = 90
b = 235.554β = 90
c = 75.857γ = 90
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2011-01-12
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2018-04-04
    Changes: Data collection
  • Version 1.3: 2018-04-11
    Changes: Data collection, Source and taxonomy
  • Version 1.4: 2024-02-21
    Changes: Data collection, Database references, Derived calculations