6U1X | pdb_00006u1x

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

• PDB DOI: https://doi.org/10.2210/pdb6U1X/pdb
• EM Map EMD-20614: EMDB EMDataResource

• Classification: VIRAL PROTEIN
• Organism(s): Vesicular stomatitis Indiana virus strain San Juan
• Expression System: Spodoptera frugiperda, Escherichia coli
• Mutation(s): No 


• Deposited: 2019-08-17 Released: 2020-01-22 
• Deposition Author(s): Jenni, S., Bloyet, L.M., Dias-Avalos, R., Liang, B., Wheelman, S.P.J., Grigorieff, N., Harrison, S.C.
• Funding Organization(s): National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)

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Experimental Data Snapshot

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

Starting Model: experimental

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

• PubMed: 31914397 
• DOI: https://doi.org/10.1016/j.celrep.2019.12.024
• Primary Citation 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.

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Organizational Affiliation: 
• Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA.
Department of Microbiology, Harvard Medical School, Boston, MA 02115, USA.
Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA 20147, USA.
Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA; Department of Microbiology, Harvard Medical School, Boston, MA 02115, USA.
Department of Microbiology, Harvard Medical School, Boston, MA 02115, USA; Department of Molecular Microbiology, Washington University in St. Louis, St. Louis, MO 63110, USA.
Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA 20147, USA; RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, MA 01605, USA.
Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA; Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA. Electronic address: [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: microscopy

Macromolecule Content 

• Total Structure Weight: 271.39 kDa 
• Atom Count: 16,761 
• Modeled Residue Count: 2,087 
• Deposited Residue Count: 2,374 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
RNA-directed RNA polymerase L	A	2,109	Vesicular stomatitis Indiana virus strain San Juan	Mutation(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)
UniProt
Find proteins for P03523 (Vesicular stomatitis Indiana virus (strain San Juan)) Explore P03523  Go to UniProtKB:  P03523

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Phosphoprotein	B [auth P]	265	Vesicular stomatitis Indiana virus strain San Juan	Mutation(s): 0
UniProt
Find proteins for P03520 (Vesicular stomatitis Indiana virus (strain San Juan)) Explore P03520  Go to UniProtKB:  P03520

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN (Subject of Investigation/LOI)	C [auth A], D [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

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

EM Software:

Task	Software Package	Version
RECONSTRUCTION	FREALIGN	X
MODEL REFINEMENT	PHENIX	1.16-3549

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2020-01-22 
Deposition Author(s): Jenni, S., Bloyet, L.M., Dias-Avalos, R., Liang, B., Wheelman, S.P.J., Grigorieff, N., Harrison, S.C.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)	United States	R37 AI059371

Revision History  

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