5EPI

CRYSTAL STRUCTURE OF INFLUENZA B POLYMERASE WITH BOUND 5' CRNA EXHIBITS A NOVEL DOMAIN ARRANGEMENT


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 4.1 Å
  • R-Value Free: 0.287 
  • R-Value Work: 0.257 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Influenza Polymerase Can Adopt an Alternative Configuration Involving a Radical Repacking of PB2 Domains.

Thierry, E.Guilligay, D.Kosinski, J.Bock, T.Gaudon, S.Round, A.Pflug, A.Hengrung, N.El Omari, K.Baudin, F.Hart, D.J.Beck, M.Cusack, S.

(2016) Mol.Cell 61: 125-137

  • DOI: 10.1016/j.molcel.2015.11.016
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Influenza virus polymerase transcribes or replicates the segmented RNA genome (vRNA) into respectively viral mRNA or full-length copies and initiates RNA synthesis by binding the conserved 3' and 5' vRNA ends (the promoter). In recent structures of p ...

    Influenza virus polymerase transcribes or replicates the segmented RNA genome (vRNA) into respectively viral mRNA or full-length copies and initiates RNA synthesis by binding the conserved 3' and 5' vRNA ends (the promoter). In recent structures of promoter-bound polymerase, the cap-binding and endonuclease domains are configured for cap snatching, which generates capped transcription primers. Here, we present a FluB polymerase structure with a bound complementary cRNA 5' end that exhibits a major rearrangement of the subdomains within the C-terminal two-thirds of PB2 (PB2-C). Notably, the PB2 nuclear localization signal (NLS)-containing domain translocates ∼90 Å to bind to the endonuclease domain. FluA PB2-C alone and RNA-free FluC polymerase are similarly arranged. Biophysical and cap-dependent endonuclease assays show that in solution the polymerase explores different conformational distributions depending on which RNA is bound. The inherent flexibility of the polymerase allows it to adopt alternative conformations that are likely important during polymerase maturation into active progeny RNPs.


    Related Citations: 
    • Crystal Structure Of Influenza A Polymerase Bound To The Viral RNA Promoter
      Reich, S.,Guilligay, D.,Pflug, A.,Cusack, S.
      () TO BE PUBLISHED --: --


    Organizational Affiliation

    European Molecular Biology Laboratory Grenoble Outstation and Unit of Virus Host-Cell Interactions, University Grenoble Alpes-CNRS-EMBL, 71 Avenue des Martyrs, CS 90181, 38042 Grenoble Cedex 9, France. Electronic address: cusack@embl.fr.,Structural and Computational Biology Unit, European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany.,European Molecular Biology Laboratory Grenoble Outstation and Unit of Virus Host-Cell Interactions, University Grenoble Alpes-CNRS-EMBL, 71 Avenue des Martyrs, CS 90181, 38042 Grenoble Cedex 9, France.,European Molecular Biology Laboratory Grenoble Outstation and Unit of Virus Host-Cell Interactions, University Grenoble Alpes-CNRS-EMBL, 71 Avenue des Martyrs, CS 90181, 38042 Grenoble Cedex 9, France; Structural and Computational Biology Unit, European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany.,Division of Structural Biology, Henry Wellcome Building for Genomic Medicine, University of Oxford, Oxford OX3 7BN, UK.,Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, UK; Division of Structural Biology, Henry Wellcome Building for Genomic Medicine, University of Oxford, Oxford OX3 7BN, UK.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Polymerase acidic protein
A, E, I, M, Q, U
751Influenza B virusMutation(s): 0 
Gene Names: PA
EC: 3.1.-.-
Find proteins for Q5V8Z9 (Influenza B virus)
Go to UniProtKB:  Q5V8Z9
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
RNA-directed RNA polymerase catalytic subunit
B, F, J, N, R, V
772Influenza B virusMutation(s): 0 
Gene Names: PB1
EC: 2.7.7.48
Find proteins for Q5V8Y6 (Influenza B virus)
Go to UniProtKB:  Q5V8Y6
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Polymerase basic protein 2
C, G, K, O, S, W
798Influenza B virusMutation(s): 0 
Gene Names: PB2
Find proteins for Q5V8X3 (Influenza B virus)
Go to UniProtKB:  Q5V8X3
Entity ID: 4
MoleculeChainsLengthOrganism
CRNA 5' ENDD,H,L,P,T,X12Influenza B virus (B/Memphis/13/2003)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 4.1 Å
  • R-Value Free: 0.287 
  • R-Value Work: 0.257 
  • Space Group: P 1
Unit Cell:
Length (Å)Angle (°)
a = 193.730α = 117.71
b = 209.980β = 92.81
c = 210.600γ = 113.68
Software Package:
Software NamePurpose
XDSdata reduction
PHENIXrefinement
PHASERphasing
XSCALEdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
European Research CouncilFrance322586

Revision History 

  • Version 1.0: 2016-01-13
    Type: Initial release
  • Version 1.1: 2016-01-20
    Type: Database references
  • Version 1.2: 2019-04-03
    Type: Author supporting evidence, Data collection, Derived calculations, Source and taxonomy