6V85

Parainfluenza virus 5 L-P complex

  • Classification: VIRAL PROTEIN
  • Organism(s): Simian virus 5 (strain W3)
  • Expression System: Spodoptera frugiperda
  • Mutation(s): No 

  • Deposited: 2019-12-10 Released: 2020-02-19 
  • Deposition Author(s): Abdella, R., He, Y.
  • Funding Organization(s): Howard Hughes Medical Institute (HHMI), American Cancer Society, National Institutes of Health/National Cancer Institute (NIH/NCI), National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.38 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structure of a paramyxovirus polymerase complex reveals a unique methyltransferase-CTD conformation.

Abdella, R.Aggarwal, M.Okura, T.Lamb, R.A.He, Y.

(2020) Proc Natl Acad Sci U S A 117: 4931-4941

  • DOI: 10.1073/pnas.1919837117
  • Primary Citation of Related Structures:  
    6V85, 6V86, 6VAG

  • PubMed Abstract: 
  • Paramyxoviruses are enveloped, nonsegmented, negative-strand RNA viruses that cause a wide spectrum of human and animal diseases. The viral genome, packaged by the nucleoprotein (N), serves as a template for the polymerase complex, composed of the large protein (L) and the homo-tetrameric phosphoprotein (P) ...

    Paramyxoviruses are enveloped, nonsegmented, negative-strand RNA viruses that cause a wide spectrum of human and animal diseases. The viral genome, packaged by the nucleoprotein (N), serves as a template for the polymerase complex, composed of the large protein (L) and the homo-tetrameric phosphoprotein (P). The ∼250-kDa L possesses all enzymatic activities necessary for its function but requires P in vivo. Structural information is available for individual P domains from different paramyxoviruses, but how P interacts with L and how that affects the activity of L is largely unknown due to the lack of high-resolution structures of this complex in this viral family. In this study we determined the structure of the L-P complex from parainfluenza virus 5 (PIV5) at 4.3-Å resolution using cryoelectron microscopy, as well as the oligomerization domain (OD) of P at 1.4-Å resolution using X-ray crystallography. P-OD associates with the RNA-dependent RNA polymerase domain of L and protrudes away from it, while the X domain of one chain of P is bound near the L nucleotide entry site. The methyltransferase (MTase) domain and the C-terminal domain (CTD) of L adopt a unique conformation, positioning the MTase active site immediately above the poly-ribonucleotidyltransferase domain and near the likely exit site for the product RNA 5' end. Our study reveals a potential mechanism that mononegavirus polymerases may employ to switch between transcription and genome replication. This knowledge will assist in the design and development of antivirals against paramyxoviruses.


    Organizational Affiliation

    Robert H. Lurie Comprehensive Cancer Center of Northwestern University, Northwestern University, Chicago, IL 60611.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
RNA-directed RNA polymerase LA2,255Simian virus 5 (strain W3)Mutation(s): 0 
Gene Names: L
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 Q88434 (Parainfluenza virus 5 (strain W3))
Explore Q88434 
Go to UniProtKB:  Q88434
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ88434
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
PhosphoproteinC [auth B],
D [auth C],
E [auth D],
F [auth E],
B [auth F]
392Simian virus 5 (strain W3)Mutation(s): 0 
Gene Names: P/V
UniProt
Find proteins for P11208 (Parainfluenza virus 5 (strain W3))
Explore P11208 
Go to UniProtKB:  P11208
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP11208
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download Ideal Coordinates CCD File 
G [auth A],
H [auth A]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.38 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Howard Hughes Medical Institute (HHMI)United States--
American Cancer SocietyUnited StatesIRG-15-173-21
National Institutes of Health/National Cancer Institute (NIH/NCI)United StatesP01-CA092584
National Institutes of Health/National Cancer Institute (NIH/NCI)United StatesU54-CA193419
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesT32-GM008382

Revision History  (Full details and data files)

  • Version 1.0: 2020-02-19
    Type: Initial release
  • Version 1.1: 2020-03-04
    Changes: Database references
  • Version 1.2: 2020-03-18
    Changes: Database references