6KUR

Structure of influenza D virus polymerase bound to vRNA promoter in Mode B conformation (Class B1)

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.70 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

Structural insight into RNA synthesis by influenza D polymerase.

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 4: 1750-1759

  • 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 ...

    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.

    Related Citations: 
    • 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 --: --
    Organizational Affiliation: 

    Chongqing Key Laboratory of Neurodegenerative Diseases, Chongqing General Hospital, University of Chinese Academy of Sciences, Chongqing, China. shiyi@im.ac.cn.



Macromolecules

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Entity ID: 1
MoleculeChainsSequence 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
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UniProt GroupK9LHJ4
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Entity ID: 2
MoleculeChainsSequence 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
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Entity ID: 3
MoleculeChainsSequence 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
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UniProt GroupK9LHF3
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Entity ID: 4
MoleculeChainsLengthOrganismImage
3'-vRNAD [auth R]14synthetic construct
Protein Feature View
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Entity ID: 5
MoleculeChainsLengthOrganismImage
5'-vRNAE [auth V]15synthetic construct
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Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.70 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

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: 2021-04-14
    Changes: Database references