5MSG

Influenza B polymerase bound to vRNA promoter and capped RNA primer


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.8 Å
  • R-Value Free: 0.267 
  • R-Value Work: 0.235 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

An in vitro fluorescence based study of initiation of RNA synthesis by influenza B polymerase.

Reich, S.Guilligay, D.Cusack, S.

(2017) Nucleic Acids Res. 45: 3353-3368

  • DOI: 10.1093/nar/gkx043

  • PubMed Abstract: 
  • Influenza polymerase replicates, via a complementary RNA intermediate (cRNA), and transcribes the eight viral RNA (vRNA) genome segments. To initiate RNA synthesis it is bound to the conserved 5΄ and 3΄ extremities of the vRNA or cRNA (the 'promoter' ...

    Influenza polymerase replicates, via a complementary RNA intermediate (cRNA), and transcribes the eight viral RNA (vRNA) genome segments. To initiate RNA synthesis it is bound to the conserved 5΄ and 3΄ extremities of the vRNA or cRNA (the 'promoter'). 5΄-3΄ base-pairing in the distal promoter region is essential to position the template RNA at the polymerase active site, as shown by a new crystal structure with the 3΄ end threading through the template entry tunnel. We develop fluorescence polarization assays to quantify initiation of cap-primed (transcription) or unprimed (replication) RNA synthesis by recombinant influenza B polymerase bound to the vRNA or cRNA promoter. The rate-limiting step is formation of a primed initiation complex with minimally ApG required to stabilize the 3΄ end of the template within the active-site. Polymerase bound to the vRNA promoter initiates RNA synthesis terminally, while the cRNA promoter directs internal initiation at a significantly lower rate. Progression to elongation requires breaking the promoter 5΄-3΄ base-pairing region and favourable compensation by the emerging template-product base-pairs. The RNA synthesis assay is adaptable to high-throughput screening for polymerase inhibitors. In a pilot study, we find that initiation at the cRNA promoter is unusually susceptible to inhibition by 2΄F-2΄dNTPs.


    Organizational Affiliation

    Grenoble Outstation, European Molecular Biology Laboratory, Grenoble 38042, France.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Polymerase acidic protein
A
751Influenza B virus (B/Memphis/13/2003)Gene Names: PA
Find proteins for Q5V8Z9 (Influenza B virus (B/Memphis/13/2003))
Go to UniProtKB:  Q5V8Z9
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
RNA-directed RNA polymerase catalytic subunit
B
772Influenza B virus (B/Memphis/13/2003)Gene Names: PB1
EC: 2.7.7.48
Find proteins for Q5V8Y6 (Influenza B virus (B/Memphis/13/2003))
Go to UniProtKB:  Q5V8Y6
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Polymerase basic protein 2
C
798Influenza B virus (B/Memphis/13/2003)Gene Names: PB2
Find proteins for Q5V8X3 (Influenza B virus (B/Memphis/13/2003))
Go to UniProtKB:  Q5V8X3
Entity ID: 4
MoleculeChainsLengthOrganism
RNA (5'-D(*(GDM))-R(P*AP*AP*UP*C)-3')M14synthetic 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*U)-3')R18Influenza B virus
Entity ID: 6
MoleculeChainsLengthOrganism
RNA (5'-R(P*AP*GP*UP*AP*GP*UP*AP*AP*CP*AP*AP*GP*AP*G)-3')V14Influenza B virus
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PO4
Query on PO4

Download SDF File 
Download CCD File 
A, B
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
M7G
Query on M7G
M
NON-POLYMERC11 H19 N5 O11 P2

--

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.8 Å
  • R-Value Free: 0.267 
  • R-Value Work: 0.235 
  • Space Group: P 32 2 1
Unit Cell:
Length (Å)Angle (°)
a = 200.410α = 90.00
b = 200.410β = 90.00
c = 254.610γ = 120.00
Software Package:
Software NamePurpose
XDSdata reduction
PHASERphasing
XSCALEdata scaling
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationCountryGrant Number
ERCFrance322586

Revision History 

  • Version 1.0: 2017-02-08
    Type: Initial release
  • Version 1.1: 2017-05-03
    Type: Database references