5M3H

Bat influenza A/H17N10 polymerase bound to four heptad repeats of serine 5 phosphorylated Pol II CTD


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.245 
  • R-Value Work: 0.210 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Structural basis of an essential interaction between influenza polymerase and Pol II CTD.

Lukarska, M.Fournier, G.Pflug, A.Resa-Infante, P.Reich, S.Naffakh, N.Cusack, S.

(2017) Nature 541: 117-121

  • DOI: 10.1038/nature20594
  • Primary Citation of Related Structures:  5M3J

  • PubMed Abstract: 
  • The heterotrimeric influenza polymerase (FluPol), comprising subunits PA, PB1 and PB2, binds to the conserved 5' and 3' termini (the 'promoter') of each of the eight single-stranded viral RNA (vRNA) genome segments and performs both transcription and ...

    The heterotrimeric influenza polymerase (FluPol), comprising subunits PA, PB1 and PB2, binds to the conserved 5' and 3' termini (the 'promoter') of each of the eight single-stranded viral RNA (vRNA) genome segments and performs both transcription and replication of vRNA in the infected cell nucleus. To transcribe viral mRNAs, FluPol associates with cellular RNA polymerase II (Pol II), which enables it to take 5'-capped primers from nascent Pol II transcripts. Here we present a co-crystal structure of bat influenza A polymerase bound to a Pol II C-terminal domain (CTD) peptide mimic, which shows two distinct phosphoserine-5 (SeP5)-binding sites in the polymerase PA subunit, accommodating four CTD heptad repeats overall. Mutagenesis of the SeP5-contacting basic residues (PA K289, R454, K635 and R638) weakens CTD repeat binding in vitro without affecting the intrinsic cap-primed (transcription) or unprimed (replication) RNA synthesis activity of recombinant polymerase, whereas in cell-based minigenome assays the same mutations substantially reduce overall polymerase activity. Only recombinant viruses with a single mutation in one of the SeP5-binding sites can be rescued, but these viruses are severely attenuated and genetically unstable. Several previously described mutants that modulate virulence can be rationalized by our results, including a second site mutation (PA(C453R)) that enables the highly attenuated mutant virus (PA(R638A)) to revert to near wild-type infectivity. We conclude that direct binding of FluPol to the SeP5 Pol II CTD is fine-tuned to allow efficient viral transcription and propose that the CTD-binding site on FluPol could be targeted for antiviral drug development.


    Organizational Affiliation

    European Molecular Biology Laboratory, Grenoble Outstation, 71 Avenue des Martyrs, CS 90181, 38042 Grenoble Cedex 9, France.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Polymerase acidic protein
A
728Influenza A virus (A/little yellow-shouldered bat/Guatemala/060/2010(H17N10))Gene Names: PA
Find proteins for H6QM92 (Influenza A virus (A/little yellow-shouldered bat/Guatemala/060/2010(H17N10)))
Go to UniProtKB:  H6QM92
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
RNA-directed RNA polymerase catalytic subunit
B
776Influenza A virus (A/little yellow-shouldered bat/Guatemala/060/2010(H17N10))Gene Names: PB1
EC: 2.7.7.48
Find proteins for H6QM91 (Influenza A virus (A/little yellow-shouldered bat/Guatemala/060/2010(H17N10)))
Go to UniProtKB:  H6QM91
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Polymerase basic protein 2
C
797Influenza A virus (A/little yellow-shouldered bat/Guatemala/060/2010(H17N10))Gene Names: PB2
Find proteins for H6QM90 (Influenza A virus (A/little yellow-shouldered bat/Guatemala/060/2010(H17N10)))
Go to UniProtKB:  H6QM90
Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
TYR-SER-PRO-THR-SEP-PRO
X, Y
28Homo sapiensGene Names: POLR2A (POLR2)
EC: 2.7.7.6, 2.7.7.48
Find proteins for P24928 (Homo sapiens)
Go to Gene View: POLR2A
Go to UniProtKB:  P24928
Entity ID: 4
MoleculeChainsLengthOrganism
RNA (5'-R(*UP*AP*UP*AP*CP*CP*UP*CP*UP*GP*CP*UP*U)-3')R18Influenza A virus
Entity ID: 5
MoleculeChainsLengthOrganism
RNA 5'-pAGUAGUAACAAGAGGGV16Influenza A 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
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
SEP
Query on SEP
X, Y
L-PEPTIDE LINKINGC3 H8 N O6 PSER
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.245 
  • R-Value Work: 0.210 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 269.490α = 90.00
b = 147.520β = 97.22
c = 88.480γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationCountryGrant Number
ERCFrance322586

Revision History 

  • Version 1.0: 2016-12-21
    Type: Initial release
  • Version 1.1: 2017-01-11
    Type: Database references
  • Version 1.2: 2017-01-18
    Type: Database references
  • Version 1.3: 2017-12-27
    Type: Source and taxonomy, Structure summary