6SZU

Bat Influenza A polymerase pre-termination complex with pyrophosphate using 44-mer vRNA template with mutated oligo(U) sequence


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.41 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

A Structure-Based Model for the Complete Transcription Cycle of Influenza Polymerase.

Wandzik, J.M.Kouba, T.Karuppasamy, M.Pflug, A.Drncova, P.Provaznik, J.Azevedo, N.Cusack, S.

(2020) Cell 181: 877

  • DOI: 10.1016/j.cell.2020.03.061
  • Primary Citation of Related Structures:  
    6TU5, 6TW1, 6T0N, 6T0S, 6T0R, 6T0U, 6T0W, 6T0V, 6T2C, 6SZV, 6SZU

  • PubMed Abstract: 
  • Influenza polymerase uses unique mechanisms to synthesize capped and polyadenylated mRNAs from the genomic viral RNA (vRNA) template, which is packaged inside ribonucleoprotein particles (vRNPs). Here, we visualize by cryoelectron microscopy the conformational dynamics of the polymerase during the complete transcription cycle from pre-initiation to termination, focusing on the template trajectory ...

    Influenza polymerase uses unique mechanisms to synthesize capped and polyadenylated mRNAs from the genomic viral RNA (vRNA) template, which is packaged inside ribonucleoprotein particles (vRNPs). Here, we visualize by cryoelectron microscopy the conformational dynamics of the polymerase during the complete transcription cycle from pre-initiation to termination, focusing on the template trajectory. After exiting the active site cavity, the template 3' extremity rebinds into a specific site on the polymerase surface. Here, it remains sequestered during all subsequent transcription steps, forcing the template to loop out as it further translocates. At termination, the strained connection between the bound template 5' end and the active site results in polyadenylation by stuttering at uridine 17. Upon product dissociation, further conformational changes release the trapped template, allowing recycling back into the pre-initiation state. Influenza polymerase thus performs transcription while tightly binding to and protecting both template ends, allowing efficient production of multiple mRNAs from a single vRNP.


    Organizational Affiliation

    European Molecular Biology Laboratory, 71 Avenue des Martyrs, CS 90181, 38042 Grenoble Cedex 9, France. Electronic address: cusack@embl.fr.



Macromolecules

Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Polymerase acidic proteinA738Influenza 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
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
RNA-directed RNA polymerase catalytic subunitB776Influenza 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
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Polymerase basic protein 2C809Influenza 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
Protein Feature View
Expand
  • Reference Sequence
Find similar nucleic acids by:  (by identity cutoff)  |  Structure
Entity ID: 4
MoleculeChainsLengthOrganismImage
vRNAD [auth V]44Influenza B virus
Protein Feature View
Expand
  • Reference Sequence
  • Find similar nucleic acids by:  Sequence   |   Structure
  • Entity ID: 5
    MoleculeChainsLengthOrganismImage
    mRNAE [auth M]10Influenza B virus
    Protein Feature View
    Expand
    • Reference Sequence
    Small Molecules
    Ligands 3 Unique
    IDChainsName / Formula / InChI Key2D Diagram3D Interactions
    M4H (Subject of Investigation/LOI)
    Query on M4H

    Download Ideal Coordinates CCD File 
    F [auth A]5-oxidanyl-4-oxidanylidene-1-[(1-pyrrolo[2,3-b]pyridin-1-ylcyclopentyl)methyl]pyridine-3-carboxylic acid
    C19 H19 N3 O4
    OTPKNUJKFUZRDR-UHFFFAOYSA-N
     Ligand Interaction
    POP
    Query on POP

    Download Ideal Coordinates CCD File 
    K [auth B]PYROPHOSPHATE 2-
    H2 O7 P2
    XPPKVPWEQAFLFU-UHFFFAOYSA-L
     Ligand Interaction
    MG
    Query on MG

    Download Ideal Coordinates CCD File 
    G [auth A], H [auth A], I [auth B], J [auth B], L [auth V], MMAGNESIUM ION
    Mg
    JLVVSXFLKOJNIY-UHFFFAOYSA-N
     Ligand Interaction
    Experimental Data & Validation

    Experimental Data

    • Method: ELECTRON MICROSCOPY
    • Resolution: 2.41 Å
    • Aggregation State: PARTICLE 
    • Reconstruction Method: SINGLE PARTICLE 

    Structure Validation

    View Full Validation Report




    Entry History & Funding Information

    Deposition Data


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

    Revision History  (Full details and data files)

    • Version 1.0: 2020-04-15
      Type: Initial release
    • Version 1.1: 2020-04-29
      Changes: Database references
    • Version 1.2: 2020-05-27
      Changes: Database references