6ABD

Structure of influenza D virus polymerase bound to vRNA promoter in Mode A conformation(Class A2)


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.3 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report


This is version 1.1 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 --: --

  • DOI: 10.1038/s41564-019-0487-5
  • Primary Citation of Related Structures:  

  • 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 R ...

    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.,Savaid Medical School, University of Chinese Academy of Sciences, Beijing, China. shiyi@im.ac.cn.,Shenzhen Key Laboratory of Pathogen and Immunity, Shenzhen Third People's Hospital, Shenzhen, China. shiyi@im.ac.cn.,MOH Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China.,Savaid Medical School, University of Chinese Academy of Sciences, Beijing, China. gaof@im.ac.cn.,Chongqing Key Laboratory of Neurodegenerative Diseases, Chongqing General Hospital, University of Chinese Academy of Sciences, Chongqing, China. shiyi@im.ac.cn.,CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China. shiyi@im.ac.cn.,CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.,CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China. gaof@im.ac.cn.,CAS Center for Influenza Research and Early-warning, CAS-TWAS Center of Excellence for Emerging Infectious Disease, Chinese Academy of Sciences, Beijing, China.,Shenzhen Key Laboratory of Pathogen and Immunity, Shenzhen Third People's Hospital, Shenzhen, China. gaof@im.ac.cn.,National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China. gaof@im.ac.cn.,Research Network of Immunity and Health, Beijing Institute of Life Sciences, Chinese Academy of Sciences, Beijing, China. gaof@im.ac.cn.,National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China.,Department of Biology, Southern University of Science and Technology, Shenzhen, China.,CAS Center for Influenza Research and Early-warning, CAS-TWAS Center of Excellence for Emerging Infectious Disease, Chinese Academy of Sciences, Beijing, China. gaof@im.ac.cn.,CAS Center for Influenza Research and Early-warning, CAS-TWAS Center of Excellence for Emerging Infectious Disease, Chinese Academy of Sciences, Beijing, China. shiyi@im.ac.cn.,Institute of Physical Science and Information Technology, Anhui University, Hefei, China.,Savaid Medical School, University of Chinese Academy of Sciences, Beijing, China.,Shenzhen Key Laboratory of Pathogen and Immunity, Shenzhen Third People's Hospital, Shenzhen, China.,Research Network of Immunity and Health, Beijing Institute of Life Sciences, Chinese Academy of Sciences, Beijing, China.,College of Basic Medicine, Jilin University, Changchun, China. shiyi@im.ac.cn.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Polymerase 3
A
710Influenza D virusMutation(s): 0 
Gene Names: P3
Find proteins for K9LHJ4 (Influenza D virus)
Go to UniProtKB:  K9LHJ4
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
RNA-directed RNA polymerase catalytic subunit
B
753Influenza D virusMutation(s): 0 
Gene Names: PB1
EC: 2.7.7.48
Find proteins for K9LH03 (Influenza D virus)
Go to UniProtKB:  K9LH03
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Polymerase PB2
C
772Influenza D virusMutation(s): 0 
Gene Names: PB2
Find proteins for K9LHF3 (Influenza D virus)
Go to UniProtKB:  K9LHF3
Entity ID: 4
MoleculeChainsLengthOrganism
RNA (5'-R(P*CP*UP*CP*CP*UP*GP*CP*UP*UP*AP*UP*GP*CP*U)-3')R14synthetic construct
Entity ID: 5
MoleculeChainsLengthOrganism
RNA (5'-R(P*AP*GP*CP*AP*GP*UP*AP*GP*CP*AP*AP*GP*GP*AP*G)-3')V15synthetic construct
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.3 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
Software Package:
Software NamePurpose
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Chinese Academy of SciencesChinaXDB08020100

Revision History 

  • Version 1.0: 2019-06-12
    Type: Initial release
  • Version 1.1: 2019-07-10
    Type: Data collection, Database references