6QCV

Crystal structure of influenza B polymerase initiation state with capped 14-mer RNA primer and CTP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.24 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.209 

wwPDB Validation 3D Report Full Report


This is version 1.2 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: 10.1038/s41594-019-0232-z
  • Primary Citation of Related Structures:  

  • 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' extremit ...

    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. cusack@embl.fr.,European Molecular Biology Laboratory, Grenoble, France.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Polymerase acidic protein
A
751Influenza B virusMutation(s): 0 
Gene Names: PA
EC: 3.1.-.-
Find proteins for Q5V8Z9 (Influenza B virus)
Go to UniProtKB:  Q5V8Z9
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
RNA-directed RNA polymerase catalytic subunit
B
772Influenza B virusMutation(s): 0 
Gene Names: PB1
EC: 2.7.7.48
Find proteins for Q5V8Y6 (Influenza B virus)
Go to UniProtKB:  Q5V8Y6
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Polymerase basic protein 2
C
798Influenza B virusMutation(s): 0 
Gene Names: PB2
Find proteins for Q5V8X3 (Influenza B virus)
Go to UniProtKB:  Q5V8X3
Entity ID: 4
MoleculeChainsLengthOrganism
RNA (5'-D(*(GDM))-R(P*GP*AP*AP*UP*GP*CP*UP*AP*UP*AP*AP*UP*AP*G)-3')M15synthetic construct
Entity ID: 5
MoleculeChainsLengthOrganism
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')R21synthetic construct
Entity ID: 6
MoleculeChainsLengthOrganism
RNA (5'-R(P*AP*GP*UP*AP*GP*UP*AP*AP*CP*AP*AP*GP*AP*G)-3')V14synthetic construct
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PO4
Query on PO4

Download SDF File 
Download CCD File 
A
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
MG
Query on MG

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Download CCD File 
B
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
CTP
Query on CTP

Download SDF File 
Download CCD File 
B
CYTIDINE-5'-TRIPHOSPHATE
C9 H16 N3 O14 P3
PCDQPRRSZKQHHS-XVFCMESISA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
8NK
Query on 8NK
M
NON-POLYMERC11 H18 N5 O11 P2

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Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.24 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.209 
  • Space Group: P 32 2 1
Unit Cell:
Length (Å)Angle (°)
a = 200.191α = 90.00
b = 200.191β = 90.00
c = 256.208γ = 120.00
Software Package:
Software NamePurpose
XDSdata reduction
REFMACrefinement
PHASERphasing
AutoPROCdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
European CommissionFrance322586
French National Research AgencyFranceANR-18-CE11-0028

Revision History 

  • Version 1.0: 2019-06-05
    Type: Initial release
  • Version 1.1: 2019-06-12
    Type: Data collection, Database references
  • Version 1.2: 2019-06-19
    Type: Data collection, Database references