6QCS

Influenza B polymerase pre-initiation complex

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.10 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.4 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:  
    6QCS, 6QCT, 6QCV, 6QCW, 6QCX

  • 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' extremities of the RNA ...

    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.



Macromolecules

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Polymerase acidic proteinA751Influenza B virusMutation(s): 0 
Gene Names: PA
EC: 3.1
UniProt
Find proteins for Q5V8Z9 (Influenza B virus)
Explore Q5V8Z9 
Go to UniProtKB:  Q5V8Z9
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UniProt GroupQ5V8Z9
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
RNA-directed RNA polymerase catalytic subunitB772Influenza B virusMutation(s): 0 
Gene Names: PB1
EC: 2.7.7.48
UniProt
Find proteins for Q5V8Y6 (Influenza B virus)
Explore Q5V8Y6 
Go to UniProtKB:  Q5V8Y6
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UniProt GroupQ5V8Y6
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Polymerase basic protein 2C798Influenza B virusMutation(s): 0 
Gene Names: PB2
UniProt
Find proteins for Q5V8X3 (Influenza B virus)
Explore Q5V8X3 
Go to UniProtKB:  Q5V8X3
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UniProt GroupQ5V8X3
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  • Reference Sequence

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Entity ID: 4
MoleculeChainsLengthOrganismImage
Capped RNAD [auth M]15Influenza B virus
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Entity ID: 5
MoleculeChainsLengthOrganismImage
5 endE [auth V]14Influenza B virus
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Entity ID: 6
MoleculeChainsLengthOrganismImage
3 endF [auth R]21Influenza B virus
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Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MG
Query on MG
Download Ideal Coordinates CCD File 
G [auth A],
H [auth B]		MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.10 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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View more in-depth experimental data
Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2019-06-05
    Type: Initial release
  • Version 1.1: 2019-06-12
    Changes: Data collection, Database references
  • Version 1.2: 2019-06-19
    Changes: Data collection, Database references
  • Version 1.3: 2019-12-18
    Changes: Other
  • Version 1.4: 2020-01-29
    Changes: Database references