5D9A

Influenza C Virus RNA-dependent RNA Polymerase - Space group P212121


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 4.30 Å
  • R-Value Free: 0.368 
  • R-Value Work: 0.316 
  • R-Value Observed: 0.318 

wwPDB Validation   3D Report Full Report


This is version 1.5 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:  
    5D9A, 5D98

  • 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, PB2 and PA/P3 ...

    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:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Polymerase acidic proteinA, D, G, J709Influenza C virus (C/Johannesburg/1/66)Mutation(s): 0 
Gene Names: PAP3
EC: 3.1
UniProt
Find proteins for Q9IMP5 (Influenza C virus (strain C/Johannesburg/1/1966))
Explore Q9IMP5 
Go to UniProtKB:  Q9IMP5
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
RNA-directed RNA polymerase catalytic subunitB, E, H, K754Influenza C virus (C/Johannesburg/1/66)Mutation(s): 0 
Gene Names: PB1
EC: 2.7.7.48
UniProt
Find proteins for Q9IMP4 (Influenza C virus (strain C/Johannesburg/1/1966))
Explore Q9IMP4 
Go to UniProtKB:  Q9IMP4
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Polymerase basic protein 2C, F, I, L782Influenza C virus (C/Johannesburg/1/66)Mutation(s): 0 
Gene Names: PB2
UniProt
Find proteins for Q9IMP3 (Influenza C virus (strain C/Johannesburg/1/1966))
Explore Q9IMP3 
Go to UniProtKB:  Q9IMP3
Protein Feature View
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 4.30 Å
  • R-Value Free: 0.368 
  • R-Value Work: 0.316 
  • R-Value Observed: 0.318 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 107.28α = 90
b = 217.5β = 90
c = 597.75γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
xia2data reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

View Full Validation Report




Entry History & Funding Information

Deposition Data


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

Revision History  (Full details and data files)

  • Version 1.0: 2015-10-21
    Type: Initial release
  • Version 1.1: 2015-11-04
    Changes: Database references
  • Version 1.2: 2015-11-18
    Changes: Database references
  • Version 1.3: 2017-09-13
    Changes: Author supporting evidence
  • Version 1.4: 2019-02-20
    Changes: Advisory, Data collection, Derived calculations
  • Version 1.5: 2019-07-10
    Changes: Data collection