6PNS

In situ structure of BTV RNA-dependent RNA polymerase in BTV virion

  • Classification: VIRAL PROTEIN TRANSFERASE
  • Organism(s): Bluetongue virus 1

  • Deposited: 2019-07-03 Released: 2019-08-07 
  • Deposition Author(s): He, Y., Shivakoti, S., Ding, K., Cui, Y., Roy, P., Zhou, Z.H.
  • Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID); Wellcome Trust; National Institutes of Health/Office of the Director; National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS); National Science Foundation (NSF, United States) 

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.7 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

In situ structures of RNA-dependent RNA polymerase inside bluetongue virus before and after uncoating.

He, Y.Shivakoti, S.Ding, K.Cui, Y.Roy, P.Zhou, Z.H.

(2019) Proc.Natl.Acad.Sci.USA 116: 16535-16540

  • DOI: 10.1073/pnas.1905849116
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Bluetongue virus (BTV), a major threat to livestock, is a multilayered, nonturreted member of the <i>Reoviridae </i>, a family of segmented dsRNA viruses characterized by endogenous RNA transcription through an RNA-dependent RNA polymerase (RdRp). T ...

    Bluetongue virus (BTV), a major threat to livestock, is a multilayered, nonturreted member of the Reoviridae , a family of segmented dsRNA viruses characterized by endogenous RNA transcription through an RNA-dependent RNA polymerase (RdRp). To date, the structure of BTV RdRp has been unknown, limiting our mechanistic understanding of BTV transcription and hindering rational drug design effort targeting this essential enzyme. Here, we report the in situ structures of BTV RdRp VP1 in both the triple-layered virion and double-layered core, as determined by cryo-electron microscopy (cryoEM) and subparticle reconstruction. BTV RdRp has 2 unique motifs not found in other viral RdRps: a fingernail, attached to the conserved fingers subdomain, and a bundle of 3 helices: 1 from the palm subdomain and 2 from the N-terminal domain. BTV RdRp VP1 is anchored to the inner surface of the capsid shell via 5 asymmetrically arranged N termini of the inner capsid shell protein VP3A around the 5-fold axis. The structural changes of RdRp VP1 and associated capsid shell proteins between BTV virions and cores suggest that the detachment of the outer capsid proteins VP2 and VP5 during viral entry induces both global movements of the inner capsid shell and local conformational changes of the N-terminal latch helix (residues 34 to 51) of 1 inner capsid shell protein VP3A, priming RdRp VP1 within the capsid for transcription. Understanding this mechanism in BTV also provides general insights into RdRp activation and regulation during viral entry of other multilayered, nonturreted dsRNA viruses.


    Organizational Affiliation

    Department of Microbiology, Immunology & Molecular Genetics, University of California, Los Angeles, CA 90095.,Department of Microbiology, Immunology & Molecular Genetics, University of California, Los Angeles, CA 90095; Hong.Zhou@UCLA.edu.,California NanoSystems Institute, University of California, Los Angeles, CA 90095.,Department of Pathogen Molecular Biology, London School of Hygiene and Tropical Medicine, WC1E 7HT London, United Kingdom.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
RNA-directed RNA polymerase
A
1302Bluetongue virus 1Mutation(s): 0 
EC: 2.7.7.48
Find proteins for W0G557 (Bluetongue virus 1)
Go to UniProtKB:  W0G557
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Inner core structural protein VP3
B, C, D, E, F, G, H, I, J, K
901Bluetongue virus 1Mutation(s): 0 
Gene Names: VP3
Find proteins for Q1AE73 (Bluetongue virus 1)
Go to UniProtKB:  Q1AE73
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.7 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
Software Package:
Software NamePurpose
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesAI094386
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesAI045000
Wellcome TrustUnited Kingdom100218
National Institutes of Health/Office of the DirectorUnited States1S10OD018111
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United States1U24GM116792
National Science Foundation (NSF, United States)United StatesDBI-1338135
National Science Foundation (NSF, United States)United StatesDMR-1548924

Revision History 

  • Version 1.0: 2019-08-07
    Type: Initial release
  • Version 1.1: 2019-08-28
    Type: Data collection, Database references
  • Version 1.2: 2019-11-27
    Type: Author supporting evidence