6U1X

Structure of the Vesicular Stomatitis Virus L Protein in Complex with Its Phosphoprotein Cofactor (3.0 A resolution)


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.00 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Model: experimental
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This is version 1.1 of the entry. See complete history


Literature

Structure of the Vesicular Stomatitis Virus L Protein in Complex with Its Phosphoprotein Cofactor.

Jenni, S.Bloyet, L.M.Diaz-Avalos, R.Liang, B.Whelan, S.P.J.Grigorieff, N.Harrison, S.C.

(2020) Cell Rep 30: 53-60.e5

  • DOI: https://doi.org/10.1016/j.celrep.2019.12.024
  • Primary Citation of Related Structures:  
    6U1X

  • PubMed Abstract: 

    The large (L) proteins of non-segmented, negative-strand RNA viruses are multifunctional enzymes that produce capped, methylated, and polyadenylated mRNA and replicate the viral genome. A phosphoprotein (P), required for efficient RNA-dependent RNA polymerization from the viral ribonucleoprotein (RNP) template, regulates the function and conformation of the L protein. We report the structure of vesicular stomatitis virus L in complex with its P cofactor determined by electron cryomicroscopy at 3.0 Å resolution, enabling us to visualize bound segments of P. The contacts of three P segments with multiple L domains show how P induces a closed, compact, initiation-competent conformation. Binding of P to L positions its N-terminal domain adjacent to a putative RNA exit channel for efficient encapsidation of newly synthesized genomes with the nucleoprotein and orients its C-terminal domain to interact with an RNP template. The model shows that a conserved tryptophan in the priming loop can support the initiating 5' nucleotide.


  • Organizational Affiliation

    Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
RNA-directed RNA polymerase L2,109Vesicular stomatitis Indiana virus strain San JuanMutation(s): 0 
EC: 2.7.7.48 (PDB Primary Data), 2.1.1.56 (PDB Primary Data), 2.7.7.88 (PDB Primary Data), 2.1.1.296 (PDB Primary Data), 3.6.1 (UniProt), 2.1.1.375 (UniProt)
UniProt
Find proteins for P03523 (Vesicular stomatitis Indiana virus (strain San Juan))
Explore P03523 
Go to UniProtKB:  P03523
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP03523
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
PhosphoproteinB [auth P]265Vesicular stomatitis Indiana virus strain San JuanMutation(s): 0 
UniProt
Find proteins for P03520 (Vesicular stomatitis Indiana virus (strain San Juan))
Explore P03520 
Go to UniProtKB:  P03520
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP03520
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.00 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONFREALIGNX
MODEL REFINEMENTPHENIX1.16-3549

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)United StatesR37 AI059371

Revision History  (Full details and data files)

  • Version 1.0: 2020-01-22
    Type: Initial release
  • Version 1.1: 2024-03-20
    Changes: Data collection, Database references, Refinement description