6QCX

Crystal structure of influenza B polymerase initiation state with capped 15-mer RNA primer


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.08 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.202 
  • R-Value Observed: 0.204 

Starting Model: experimental
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This is version 2.0 of the entry. See complete history


Literature

Structural snapshots of actively transcribing influenza polymerase.

Kouba, T.Drncova, P.Cusack, S.

(2019) Nat Struct Mol Biol 26: 460-470

  • DOI: https://doi.org/10.1038/s41594-019-0232-z
  • Primary Citation of Related Structures:  
    6QCS, 6QCT, 6QCV, 6QCW, 6QCX

  • PubMed Abstract: 

    Influenza virus RNA-dependent RNA polymerase uses unique mechanisms to transcribe its single-stranded genomic viral RNA (vRNA) into messenger RNA. The polymerase is initially bound to a promoter comprising the partially base-paired 3' and 5' extremities of the RNA. A short, capped primer, 'cap-snatched' from a nascent host polymerase II transcript, is directed towards the polymerase active site to initiate RNA synthesis. Here we present structural snapshots, as determined by X-ray crystallography and cryo-electron microscopy, of actively initiating influenza polymerase as it transitions towards processive elongation. Unexpected conformational changes unblock the active site cavity to allow establishment of a nine-base-pair template-product RNA duplex before the strands separate into distinct exit channels. Concomitantly, as the template translocates, the promoter base pairs are broken and the template entry region is remodeled. These structures reveal details of the influenza polymerase active site that will help optimize nucleoside analogs or other compounds that directly inhibit viral RNA synthesis.


  • Organizational Affiliation

    European Molecular Biology Laboratory, Grenoble, France.


Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Polymerase acidic protein751Influenza B virus (B/Memphis/13/2003)Mutation(s): 0 
Gene Names: PA
EC: 3.1
UniProt
Find proteins for Q5V8Z9 (Influenza B virus)
Explore Q5V8Z9 
Go to UniProtKB:  Q5V8Z9
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UniProt GroupQ5V8Z9
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
RNA-directed RNA polymerase catalytic subunit772Influenza B virus (B/Memphis/13/2003)Mutation(s): 0 
Gene Names: PB1
EC: 2.7.7.48
UniProt
Find proteins for Q5V8Y6 (Influenza B virus)
Explore Q5V8Y6 
Go to UniProtKB:  Q5V8Y6
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UniProt GroupQ5V8Y6
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Polymerase basic protein 2798Influenza B virus (B/Memphis/13/2003)Mutation(s): 0 
Gene Names: PB2
UniProt
Find proteins for Q5V8X3 (Influenza B virus)
Explore Q5V8X3 
Go to UniProtKB:  Q5V8X3
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UniProt GroupQ5V8X3
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  • Reference Sequence

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Entity ID: 4
MoleculeChains LengthOrganismImage
RNA (5'-D(*(GDM))-R(P*GP*AP*AP*UP*GP*CP*UP*AP*UP*AP*AP*UP*AP*GP*C)-3')D [auth M]16synthetic construct
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Entity ID: 5
MoleculeChains LengthOrganismImage
RNA (5'-R(*UP*AP*UP*AP*CP*CP*UP*CP*UP*GP*CP*UP*UP*CP*UP*GP*CP*UP*AP*UP*U)-3')E [auth R]21synthetic construct
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Entity ID: 6
MoleculeChains LengthOrganismImage
RNA (5'-R(P*AP*GP*UP*AP*GP*UP*AP*AP*CP*AP*AP*GP*AP*G)-3')F [auth V]14synthetic construct
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.08 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.202 
  • R-Value Observed: 0.204 
  • Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 200.407α = 90
b = 200.407β = 90
c = 256.372γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
autoPROCdata scaling
PHASERphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
European CommissionEuropean Union322586
French National Research AgencyFranceANR-18-CE11-0028

Revision History  (Full details and data files)

  • Version 1.0: 2019-06-05
    Type: Initial release
  • Version 1.1: 2019-06-12
    Changes: Data collection, Database references
  • Version 1.2: 2019-06-19
    Changes: Data collection, Database references
  • Version 1.3: 2024-01-24
    Changes: Data collection, Database references, Derived calculations, Refinement description
  • Version 2.0: 2024-02-28
    Changes: Atomic model, Author supporting evidence, Data collection, Derived calculations, Non-polymer description, Polymer sequence, Structure summary