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
  • Structures With Same Primary Citation

  • 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: Sequence  |  Structure

Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
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
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  • Reference Sequence

Find similar proteins by: Sequence  |  Structure

Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
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
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  • Reference Sequence
  • Find similar nucleic acids by: Sequence   |   Structure
Entity ID: 1
MoleculeChainsLengthOrganism
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
MoleculeChainsLengthOrganism
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