5D98

Influenza C Virus RNA-dependent RNA Polymerase - Space group P43212


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.9 Å
  • R-Value Free: 0.326 
  • R-Value Work: 0.286 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Crystal structure of the RNA-dependent RNA polymerase from influenza C virus.

Hengrung, N.El Omari, K.Serna Martin, I.Vreede, F.T.Cusack, S.Rambo, R.P.Vonrhein, C.Bricogne, G.Stuart, D.I.Grimes, J.M.Fodor, E.

(2015) Nature 527: 114-117

  • DOI: 10.1038/nature15525
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Negative-sense RNA viruses, such as influenza, encode large, multidomain RNA-dependent RNA polymerases that can both transcribe and replicate the viral RNA genome. In influenza virus, the polymerase (FluPol) is composed of three polypeptides: PB1, PB ...

    Negative-sense RNA viruses, such as influenza, encode large, multidomain RNA-dependent RNA polymerases that can both transcribe and replicate the viral RNA genome. In influenza virus, the polymerase (FluPol) is composed of three polypeptides: PB1, PB2 and PA/P3. PB1 houses the polymerase active site, whereas PB2 and PA/P3 contain, respectively, cap-binding and endonuclease domains required for transcription initiation by cap-snatching. Replication occurs through de novo initiation and involves a complementary RNA intermediate. Currently available structures of the influenza A and B virus polymerases include promoter RNA (the 5' and 3' termini of viral genome segments), showing FluPol in transcription pre-initiation states. Here we report the structure of apo-FluPol from an influenza C virus, solved by X-ray crystallography to 3.9 Å, revealing a new 'closed' conformation. The apo-FluPol forms a compact particle with PB1 at its centre, capped on one face by PB2 and clamped between the two globular domains of P3. Notably, this structure is radically different from those of promoter-bound FluPols. The endonuclease domain of P3 and the domains within the carboxy-terminal two-thirds of PB2 are completely rearranged. The cap-binding site is occluded by PB2, resulting in a conformation that is incompatible with transcription initiation. Thus, our structure captures FluPol in a closed, transcription pre-activation state. This reveals the conformation of newly made apo-FluPol in an infected cell, but may also apply to FluPol in the context of a non-transcribing ribonucleoprotein complex. Comparison of the apo-FluPol structure with those of promoter-bound FluPols allows us to propose a mechanism for FluPol activation. Our study demonstrates the remarkable flexibility of influenza virus RNA polymerase, and aids our understanding of the mechanisms controlling transcription and genome replication.


    Organizational Affiliation

    Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, UK.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Polymerase acidic protein
A, D
709Influenza C virus (strain C/Johannesburg/1/1966)Mutation(s): 0 
Gene Names: PA (P3)
EC: 3.1.-.-
Find proteins for Q9IMP5 (Influenza C virus (strain C/Johannesburg/1/1966))
Go to UniProtKB:  Q9IMP5
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
RNA-directed RNA polymerase catalytic subunit
B, E
754Influenza C virus (strain C/Johannesburg/1/1966)Mutation(s): 0 
Gene Names: PB1
EC: 2.7.7.48
Find proteins for Q9IMP4 (Influenza C virus (strain C/Johannesburg/1/1966))
Go to UniProtKB:  Q9IMP4
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Polymerase basic protein 2
C, F
782Influenza C virus (strain C/Johannesburg/1/1966)Mutation(s): 0 
Gene Names: PB2
Find proteins for Q9IMP3 (Influenza C virus (strain C/Johannesburg/1/1966))
Go to UniProtKB:  Q9IMP3
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MG
Query on MG

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.9 Å
  • R-Value Free: 0.326 
  • R-Value Work: 0.286 
  • Space Group: P 43 21 2
Unit Cell:
Length (Å)Angle (°)
a = 185.660α = 90.00
b = 185.660β = 90.00
c = 598.220γ = 90.00
Software Package:
Software NamePurpose
SHELXphasing
REFMACrefinement
xia2data reduction
Aimlessdata scaling
PHENIXphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Wellcome TrustUnited Kingdom092931/Z/10/Z
Medical Research Council (United Kingdom)United KingdomMR/K000241/1
Medical Research Council (United Kingdom)United KingdomG1000099
Medical Research Council (United Kingdom)United KingdomG1100138
Wellcome TrustUnited Kingdom075491/Z/04

Revision History 

  • Version 1.0: 2015-10-21
    Type: Initial release
  • Version 1.1: 2015-11-18
    Type: Database references
  • Version 1.2: 2017-09-13
    Type: Author supporting evidence