6OGZ

In situ structure of Rotavirus RNA-dependent RNA polymerase at transcript-elongated state

  • Classification: viral protein/rna/transferase
  • Organism(s): Rotavirus A
  • Mutation(s): No 

  • Deposited: 2019-04-03 Released: 2019-05-22 
  • Deposition Author(s): Ding, K., Chang, T., Shen, W., Roy, P., Zhou, Z.H.
  • Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID), National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), National Institutes of Health/National Institute of Dental and Craniofacial Research (NIH/NIDCR), National Institutes of Health/National Center for Research Resources (NIH/NCRR), National Institutes of Health/Office of the Director, National Science Foundation (NSF, United States)

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.60 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

In situ structures of rotavirus polymerase in action and mechanism of mRNA transcription and release.

Ding, K.Celma, C.C.Zhang, X.Chang, T.Shen, W.Atanasov, I.Roy, P.Zhou, Z.H.

(2019) Nat Commun 10: 2216-2216

  • DOI: 10.1038/s41467-019-10236-7
  • Primary Citation of Related Structures:  
    6OGY, 6OGZ

  • PubMed Abstract: 
  • Transcribing and replicating a double-stranded genome require protein modules to unwind, transcribe/replicate nucleic acid substrates, and release products. Here we present in situ cryo-electron microscopy structures of rotavirus dsRNA-dependent RNA ...

    Transcribing and replicating a double-stranded genome require protein modules to unwind, transcribe/replicate nucleic acid substrates, and release products. Here we present in situ cryo-electron microscopy structures of rotavirus dsRNA-dependent RNA polymerase (RdRp) in two states pertaining to transcription. In addition to the previously discovered universal "hand-shaped" polymerase core domain shared by DNA polymerases and telomerases, our results show the function of N- and C-terminal domains of RdRp: the former opens the genome duplex to isolate the template strand; the latter splits the emerging template-transcript hybrid, guides genome reannealing to form a transcription bubble, and opens a capsid shell protein (CSP) to release the transcript. These two "helicase" domains also extensively interact with CSP, which has a switchable N-terminal helix that, like cellular transcriptional factors, either inhibits or promotes RdRp activity. The in situ structures of RdRp, CSP, and RNA in action inform mechanisms of not only transcription, but also replication.


    Organizational Affiliation

    Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles, CA, 90095, USA. Hong.Zhou@ucla.edu.



Macromolecules

Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
RNA-dependent RNA polymerase of rotavirus AA1088Rotavirus AMutation(s): 0 
EC: 2.7.7.48
Find proteins for G0YZJ9 (Rotavirus A)
Explore G0YZJ9 
Go to UniProtKB:  G0YZJ9
Protein Feature View
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Inner capsid protein VP2E, F, G, H, I, J, K, L, M, N887Rotavirus AMutation(s): 0 
Find proteins for G0YZK0 (Rotavirus A)
Explore G0YZK0 
Go to UniProtKB:  G0YZK0
Protein Feature View
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence
  • Find similar nucleic acids by:  Sequence   |   Structure
  • Entity ID: 1
    MoleculeChainsLengthOrganismImage
    RNA (5'-R(P*UP*AP*UP*AP*UP*AP*UP*AP*UP*AP*UP*AP*UP*AP*UP*AP*UP*A)-3')B18Rotavirus A
    • Find similar nucleic acids by:  Sequence   |   Structure
    • Entity ID: 2
      MoleculeChainsLengthOrganismImage
      RNA (5'-R(P*AP*UP*AP*UP*AP*UP*AP*UP*AP*UP*AP*UP*AP*UP*AP*UP*A)-3')C17Rotavirus A
      Small Molecules
      Ligands 2 Unique
      IDChainsName / Formula / InChI Key2D Diagram3D Interactions
      GTP
      Query on GTP

      Download CCD File 
      A
      GUANOSINE-5'-TRIPHOSPHATE
      C10 H16 N5 O14 P3
      XKMLYUALXHKNFT-UUOKFMHZSA-N
       Ligand Interaction
      UTP
      Query on UTP

      Download CCD File 
      A
      URIDINE 5'-TRIPHOSPHATE
      C9 H15 N2 O15 P3
      PGAVKCOVUIYSFO-XVFCMESISA-N
       Ligand Interaction
      Experimental Data & Validation

      Experimental Data

      • Method: ELECTRON MICROSCOPY
      • Resolution: 3.60 Å
      • Aggregation State: PARTICLE 
      • Reconstruction Method: SINGLE PARTICLE 

      Structure Validation

      View Full Validation Report



      Entry History & Funding Information

      Deposition Data


      Funding OrganizationLocationGrant Number
      National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesAI094386
      National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM071940
      National Institutes of Health/National Institute of Dental and Craniofacial Research (NIH/NIDCR)United StatesDE025567
      National Institutes of Health/National Center for Research Resources (NIH/NCRR)United States1S10RR23057
      National Institutes of Health/Office of the DirectorUnited States1S10OD018111
      National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesU24GM116792
      National Science Foundation (NSF, United States)United StatesDBI-1338135
      National Science Foundation (NSF, United States)United StatesDMR-1548924

      Revision History 

      • Version 1.0: 2019-05-22
        Type: Initial release
      • Version 1.1: 2019-05-29
        Changes: Data collection, Database references
      • Version 1.2: 2019-11-27
        Changes: Author supporting evidence
      • Version 1.3: 2019-12-18
        Changes: Other