6KUJ

Structure of influenza D virus polymerase bound to cRNA promoter in class 1


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.40 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

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This is version 1.2 of the entry. See complete history


Literature

Structure of influenza D virus polymerase bound to cRNA promoter in Mode A conformation

Peng, Q.Liu, Y.Peng, R.Wang, M.Yang, W.Song, H.Chen, Y.Liu, S.Han, M.Zhang, X.Wang, P.Yan, J.Zhang, B.Qi, J.Deng, T.Gao, G.F.Shi, Y.

(2019) Nat Microbiol 

  • DOI: https://doi.org/10.1038/s41564-019-0487-5
  • Primary Citation of Related Structures:  
    6KUJ, 6KUK, 6KUP, 6KUR, 6KUT, 6KUV, 6KV5

  • PubMed Abstract: 

    The influenza virus polymerase uses capped RNA primers to initiate transcription, and a combination of terminal and internal de novo initiations for the two-step replication process by binding the conserved viral genomic RNA (vRNA) or complementary RNA (cRNA) promoter. Here, we determined the apo and promoter-bound influenza D polymerase structures using cryo-electron microscopy and found the polymerase has an evolutionarily conserved stable core structure with inherently flexible peripheral domains. Strikingly, two conformations (mode A and B) of the vRNA promoter were observed where the 3'-vRNA end can bind at two different sites, whereas the cRNA promoter only binds in the mode B conformation. Functional studies confirmed the critical role of the mode B conformation for vRNA synthesis via the intermediate cRNA but not for cRNA production, which is mainly regulated by the mode A conformation. Both conformations participate in the regulation of the transcription process. This work advances our understanding of the regulatory mechanisms for the synthesis of different RNA species by influenza virus polymerase and opens new opportunities for antiviral drug design.


  • Organizational Affiliation

    CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.


Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Polymerase 3710Influenza D virus (D/swine/Oklahoma/1334/2011)Mutation(s): 0 
Gene Names: P3
UniProt
Find proteins for K9LHJ4 (Influenza D virus)
Explore K9LHJ4 
Go to UniProtKB:  K9LHJ4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupK9LHJ4
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
RNA-directed RNA polymerase catalytic subunit753Influenza D virus (D/swine/Oklahoma/1334/2011)Mutation(s): 0 
Gene Names: PB1
EC: 2.7.7.48
UniProt
Find proteins for K9LH03 (Influenza D virus)
Explore K9LH03 
Go to UniProtKB:  K9LH03
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UniProt GroupK9LH03
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Polymerase PB2772Influenza D virus (D/swine/Oklahoma/1334/2011)Mutation(s): 0 
Gene Names: PB2
UniProt
Find proteins for K9LHF3 (Influenza D virus)
Explore K9LHF3 
Go to UniProtKB:  K9LHF3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupK9LHF3
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  • Reference Sequence

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Entity ID: 4
MoleculeChains LengthOrganismImage
3'-cRNA promoterD [auth R]14synthetic construct
Sequence Annotations
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  • Reference Sequence

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Entity ID: 5
MoleculeChains LengthOrganismImage
5'-cRNA promoterE [auth V]14synthetic construct
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.40 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION2.0

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Chinese Academy of SciencesChinaXDB08020100

Revision History  (Full details and data files)

  • Version 1.0: 2019-10-02
    Type: Initial release
  • Version 1.1: 2019-11-06
    Changes: Data collection, Other
  • Version 1.2: 2024-03-27
    Changes: Data collection, Database references