6EVK

Crystal structure of bat influenza A/H17N10 polymerase with viral RNA promoter and cap analogue m7GTP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free: 0.273 
  • R-Value Work: 0.234 
  • R-Value Observed: 0.236 

Starting Model: experimental
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This is version 1.2 of the entry. See complete history


Literature

Capped RNA primer binding to influenza polymerase and implications for the mechanism of cap-binding inhibitors.

Pflug, A.Gaudon, S.Resa-Infante, P.Lethier, M.Reich, S.Schulze, W.M.Cusack, S.

(2018) Nucleic Acids Res 46: 956-971

  • DOI: https://doi.org/10.1093/nar/gkx1210
  • Primary Citation of Related Structures:  
    6EUV, 6EUW, 6EUX, 6EUY, 6EVJ, 6EVK

  • PubMed Abstract: 

    Influenza polymerase uses short capped primers snatched from nascent Pol II transcripts to initiate transcription of viral mRNAs. Here we describe crystal structures of influenza A and B polymerase bound to a capped primer in a configuration consistent with transcription initiation ('priming state') and show by functional assays that conserved residues from both the PB2 midlink and cap-binding domains are important for positioning the capped RNA. In particular, mutation of PB2 Arg264, which interacts with the triphosphate linkage in the cap, significantly and specifically decreases cap-dependent transcription. We also compare the configuration of the midlink and cap-binding domains in the priming state with their very different relative arrangement (called the 'apo' state) in structures where the potent cap-binding inhibitor VX-787, or a close analogue, is bound. In the 'apo' state the inhibitor makes additional interactions to the midlink domain that increases its affinity beyond that to the cap-binding domain alone. The comparison suggests that the mechanism of resistance of certain mutations that allow virus to escape from VX-787, notably PB2 N510T, can only be rationalized if VX-787 has a dual mode of action, direct inhibition of capped RNA binding as well as stabilization of the transcriptionally inactive 'apo' state.


  • Organizational Affiliation

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


Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Polymerase acidic protein738Influenza A virus (A/little yellow-shouldered bat/Guatemala/060/2010(H17N10))Mutation(s): 0 
Gene Names: PA
UniProt
Find proteins for H6QM92 (Influenza A virus)
Explore H6QM92 
Go to UniProtKB:  H6QM92
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupH6QM92
Sequence Annotations
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
RNA-directed RNA polymerase catalytic subunit776Influenza A virus (A/little yellow-shouldered bat/Guatemala/060/2010(H17N10))Mutation(s): 0 
Gene Names: PB1
EC: 2.7.7.48
UniProt
Find proteins for H6QM91 (Influenza A virus)
Explore H6QM91 
Go to UniProtKB:  H6QM91
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UniProt GroupH6QM91
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Polymerase basic protein 2809Influenza A virus (A/little yellow-shouldered bat/Guatemala/060/2010(H17N10))Mutation(s): 0 
Gene Names: PB2
UniProt
Find proteins for H6QM90 (Influenza A virus)
Explore H6QM90 
Go to UniProtKB:  H6QM90
Entity Groups  
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UniProt GroupH6QM90
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Entity ID: 4
MoleculeChains LengthOrganismImage
RNA (5'-R(*UP*AP*UP*AP*CP*CP*UP*CP*UP*GP*CP*UP*U)-3')D [auth R]18Influenza A virus
Sequence Annotations
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Entity ID: 5
MoleculeChains LengthOrganismImage
RNA (5'-R(P*AP*GP*UP*AP*GP*UP*AP*AP*CP*AP*AP*GP*AP*GP*GP*G)-3')E [auth V]16Influenza A virus
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
MGP (Subject of Investigation/LOI)
Query on MGP

Download Ideal Coordinates CCD File 
Q [auth C]7-METHYL-GUANOSINE-5'-TRIPHOSPHATE
C11 H19 N5 O14 P3
DKVRNHPCAOHRSI-KQYNXXCUSA-O
PO4
Query on PO4

Download Ideal Coordinates CCD File 
G [auth A]
H [auth A]
I [auth A]
J [auth A]
K [auth B]
G [auth A],
H [auth A],
I [auth A],
J [auth A],
K [auth B],
L [auth B],
M [auth B],
N [auth B],
O [auth B],
P [auth B],
R [auth C],
S [auth C]
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
ZN
Query on ZN

Download Ideal Coordinates CCD File 
F [auth A]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free: 0.273 
  • R-Value Work: 0.234 
  • R-Value Observed: 0.236 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 269.34α = 90
b = 148.7β = 98.17
c = 88.51γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
European Research CouncilFrance322586

Revision History  (Full details and data files)

  • Version 1.0: 2017-12-13
    Type: Initial release
  • Version 1.1: 2018-02-07
    Changes: Author supporting evidence, Database references, Source and taxonomy
  • Version 1.2: 2024-01-17
    Changes: Data collection, Database references, Refinement description