4WRT

Crystal structure of Influenza B polymerase with bound vRNA promoter (form FluB2)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.211 
  • R-Value Work: 0.173 
  • R-Value Observed: 0.175 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Structural insight into cap-snatching and RNA synthesis by influenza polymerase.

Reich, S.Guilligay, D.Pflug, A.Malet, H.Berger, I.Crepin, T.Hart, D.Lunardi, T.Nanao, M.Ruigrok, R.W.Cusack, S.

(2014) Nature 516: 361-366

  • DOI: 10.1038/nature14009
  • Primary Citation of Related Structures:  
    4WRT, 4WSA, 4WSB

  • PubMed Abstract: 
  • Influenza virus polymerase uses a capped primer, derived by 'cap-snatching' from host pre-messenger RNA, to transcribe its RNA genome into mRNA and a stuttering mechanism to generate the poly(A) tail. By contrast, genome replication is unprimed and generates exact full-length copies of the template ...

    Influenza virus polymerase uses a capped primer, derived by 'cap-snatching' from host pre-messenger RNA, to transcribe its RNA genome into mRNA and a stuttering mechanism to generate the poly(A) tail. By contrast, genome replication is unprimed and generates exact full-length copies of the template. Here we use crystal structures of bat influenza A and human influenza B polymerases (FluA and FluB), bound to the viral RNA promoter, to give mechanistic insight into these distinct processes. In the FluA structure, a loop analogous to the priming loop of flavivirus polymerases suggests that influenza could initiate unprimed template replication by a similar mechanism. Comparing the FluA and FluB structures suggests that cap-snatching involves in situ rotation of the PB2 cap-binding domain to direct the capped primer first towards the endonuclease and then into the polymerase active site. The polymerase probably undergoes considerable conformational changes to convert the observed pre-initiation state into the active initiation and elongation states.


    Related Citations: 
    • Crystal structure of influenza A polymerase bound to the viral RNA promoter
      Pflug, A., Guilligay, D., Reich, S., Cusack, S.
      () To be published --: --

    Organizational Affiliation

    1] European Molecular Biology Laboratory, Grenoble Outstation, 71 Avenue des Martyrs, CS 90181, 38042 Grenoble Cedex 9, France [2] University Grenoble Alpes-Centre National de la Recherche Scientifique-EMBL Unit of Virus Host-Cell Interactions, 71 Avenue des Martyrs, CS 90181, 38042 Grenoble Cedex 9, France.



Macromolecules

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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
PAC [auth A]751Influenza B virus (B/Memphis/13/2003)Mutation(s): 0 
Gene Names: PA
EC: 3.1
UniProt
Find proteins for Q5V8Z9 (Influenza B virus)
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Go to UniProtKB:  Q5V8Z9
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UniProt GroupQ5V8Z9
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
RNA-directed RNA polymerase catalytic subunitD [auth B]772Influenza 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: 5
MoleculeChainsSequence LengthOrganismDetailsImage
PB2E [auth C]798Influenza 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: 1
MoleculeChainsLengthOrganismImage
Influenza virus polymerase vRNA promoter 3' endA [auth R]18Influenza B virus
Protein Feature View
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Entity ID: 2
MoleculeChainsLengthOrganismImage
Influenza virus polymerase vRNA promoter 5' endB [auth V]14Influenza B virus
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.211 
  • R-Value Work: 0.173 
  • R-Value Observed: 0.175 
  • Space Group: P 63 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 207.37α = 90
b = 207.37β = 90
c = 345.69γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-11-19
    Type: Initial release
  • Version 1.1: 2014-12-03
    Changes: Database references
  • Version 1.2: 2014-12-24
    Changes: Database references
  • Version 1.3: 2019-04-03
    Changes: Data collection, Source and taxonomy