5FML

Crystal structure of the endonuclease from the PA subunit of influenza B virus bound to the PB2 subunit NLS peptide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.276 
  • R-Value Work: 0.224 

wwPDB Validation 3D Report Full Report


This is version 1.1 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

  • 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.


    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.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
PB2 SUBUNIT OF INFLUENZA B POLYMERASE
A
29Influenza B virusMutation(s): 0 
Gene Names: PB2
Find proteins for Q5V8X3 (Influenza B virus)
Go to UniProtKB:  Q5V8X3
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
PA SUBUNIT OF INFLUENZA B POLYMERASE
B
202Influenza B virusMutation(s): 0 
Gene Names: PA
EC: 3.1.-.-
Find proteins for Q5V8Z9 (Influenza B virus)
Go to UniProtKB:  Q5V8Z9
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL

Download SDF File 
Download CCD File 
B
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

Download SDF File 
Download CCD File 
B
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.276 
  • R-Value Work: 0.224 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 35.380α = 90.00
b = 80.850β = 97.15
c = 37.910γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
PHASERphasing
XDSdata reduction
XSCALEdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2016-01-13
    Type: Initial release
  • Version 1.1: 2016-01-20
    Type: Database references