7UML | pdb_00007uml

Structure of vesicular stomatitis virus (local reconstruction, 3.5 A resolution)

• PDB DOI: https://doi.org/10.2210/pdb7UML/pdb
• NAKB: 7UML
• EM Map EMD-26603: EMDB EMDataResource

• Classification: VIRAL PROTEIN/RNA
• Organism(s): Vesicular stomatitis Indiana virus
• Expression System: Mesocricetus auratus
• Mutation(s): Yes 


• Deposited: 2022-04-07 Released: 2022-04-20 
• Deposition Author(s): Jenni, S., Horwitz, J.A., Bloyet, L.-M., Whelan, S.P.J., Harrison, S.C.
• Funding Organization(s): National Institutes of Health/National Library of Medicine (NIH/NLM)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.50 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Visualizing molecular interactions that determine assembly of a bullet-shaped vesicular stomatitis virus particle.

Jenni, S., Horwitz, J.A., Bloyet, L.M., Whelan, S.P.J., Harrison, S.C.

(2022) Nat Commun 13: 4802-4802

• PubMed: 35970826 
• DOI: https://doi.org/10.1038/s41467-022-32223-1
• Primary Citation Related Structures: 
  7UMK, 7UML


• PubMed Abstract: 
  

  Vesicular stomatitis virus (VSV) is a negative-strand RNA virus with a non-segmented genome, closely related to rabies virus. Both have characteristic bullet-like shapes. We report the structure of intact, infectious VSV particles determined by cryogenic electron microscopy. By compensating for polymorphism among viral particles with computational classification, we obtained a reconstruction of the shaft ("trunk") at 3.5 Å resolution, with lower resolution for the rounded tip. The ribonucleoprotein (RNP), genomic RNA complexed with nucleoprotein (N), curls into a dome-like structure with about eight gradually expanding turns before transitioning into the regular helical trunk. Two layers of matrix (M) protein link the RNP with the membrane. Radial inter-layer subunit contacts are fixed within single RNA-N-M1-M2 modules, but flexible lateral and axial interactions allow assembly of polymorphic virions. Together with published structures of recombinant N in various states, our results suggest a mechanism for membrane-coupled self-assembly of VSV and its relatives.

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Organizational Affiliation: 
• Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, 02115, USA. [e-mail].
Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, 02115, USA.
Department of Microbiology, Harvard Medical School, Boston, MA, 02115, USA.
Molecular Pharmacology and Virology Group, PureTech Health LLC, Boston, MA, 02210, USA.
Department of Molecular Microbiology, Washington University in St. Louis, St. Louis, MO, 63110, USA.
Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, 02115, USA. [e-mail].
Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, 02115, USA. [e-mail].
Laboratory of Molecular Medicine, Boston Children's Hospital, Boston, MA, 02115, USA. [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 6-mer - A2B1C1D1E1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 224.64 kDa 
• Atom Count: 6,750 
• Modeled Residue Count: 825 
• Deposited Residue Count: 1,966 
• Unique protein chains: 2
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Nucleoprotein	A, D, E	422	Vesicular stomatitis Indiana virus	Mutation(s): 0
UniProt
Find proteins for P03521 (Vesicular stomatitis Indiana virus (strain San Juan)) Explore P03521  Go to UniProtKB:  P03521

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Matrix protein	B, C, F	229	Vesicular stomatitis Indiana virus	Mutation(s): 1
UniProt
Find proteins for P03519 (Vesicular stomatitis Indiana virus (strain San Juan)) Explore P03519  Go to UniProtKB:  P03519

Entity ID: 3
Molecule	Chains	Length	Organism	Image
RNA (5'-R(P*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*U)-3')	G [auth R]	13	Vesicular stomatitis Indiana virus

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.50 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2022-04-20 
Deposition Author(s): Jenni, S., Horwitz, J.A., Bloyet, L.-M., Whelan, S.P.J., Harrison, S.C.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Library of Medicine (NIH/NLM)	United States	AI1059371
National Institutes of Health/National Library of Medicine (NIH/NLM)	United States	CA13202

Revision History  

• Version 1.0: 2022-04-20
  Type: Initial release
  
• Version 1.1: 2022-08-31
  Changes: Database references
• Version 1.2: 2024-02-14
  Changes: Data collection, Database references