4WSB

Bat Influenza A polymerase with bound vRNA promoter


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.65 Å
  • R-Value Free: 0.267 
  • R-Value Work: 0.215 

wwPDB Validation 3D Report Full Report


This is version 1.4 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:  

  • 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 g ...

    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.


    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

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Polymerase PA
A
738Influenza A virusMutation(s): 0 
Gene Names: PA
Find proteins for H6QM92 (Influenza A virus)
Go to UniProtKB:  H6QM92
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
RNA-directed RNA polymerase catalytic subunit
B
776Influenza A virusMutation(s): 0 
Gene Names: PB1
EC: 2.7.7.48
Find proteins for H6QM91 (Influenza A virus)
Go to UniProtKB:  H6QM91
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Polymerase PB2
C
787Influenza A virusMutation(s): 0 
Gene Names: PB2
Find proteins for H6QM90 (Influenza A virus)
Go to UniProtKB:  H6QM90
Entity ID: 4
MoleculeChainsLengthOrganism
Influenza A polymerase vRNA promoter 3' endR18unidentified influenza virus
Entity ID: 5
MoleculeChainsLengthOrganism
Influenza A polymerase vRNA promoter 5' endV16unidentified influenza virus
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PO4
Query on PO4

Download SDF File 
Download CCD File 
A, B, C
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
ZN
Query on ZN

Download SDF File 
Download CCD File 
A
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.65 Å
  • R-Value Free: 0.267 
  • R-Value Work: 0.215 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 268.190α = 90.00
b = 149.320β = 98.00
c = 88.620γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
XDSdata reduction
PHENIXrefinement
XSCALEdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-11-19
    Type: Initial release
  • Version 1.1: 2014-12-03
    Type: Database references
  • Version 1.2: 2014-12-24
    Type: Database references
  • Version 1.3: 2018-10-10
    Type: Data collection, Database references, Source and taxonomy, Structure summary
  • Version 1.4: 2019-04-03
    Type: Data collection, Source and taxonomy, Structure summary