6OGY

In situ structure of Rotavirus RNA-dependent RNA polymerase at duplex-open state

  • Classification: viral protein/transferase/rna
  • Organism(s): Rotavirus A

  • 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; National Institutes of Health/National Institute of General Medical Sciences; National Institutes of Health/National Institute of Dental and Craniofacial Research; National Institutes of Health/National Center for Research Resources; National Institutes of Health/Office of the Director; National Science Foundation (United States) 

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.4 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

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:  

  • 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 Pathogen Molecular Biology, London School of Hygiene and Tropical Medicine, London, WC1E 7HT, UK.,California NanoSystems Institute, University of California, Los Angeles, CA, 90095, USA.,Department of Bioengineering, University of California, Los Angeles, CA, 90095, USA.,Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles, CA, 90095, USA.,Department of Bioengineering, University of California, Los Angeles, CA, 90095, USA. Hong.Zhou@ucla.edu.,California NanoSystems Institute, University of California, Los Angeles, CA, 90095, USA. Hong.Zhou@ucla.edu.,Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles, CA, 90095, USA. Hong.Zhou@ucla.edu.,Department of Pathogen Molecular Biology, London School of Hygiene and Tropical Medicine, London, WC1E 7HT, UK. Polly.Roy@lshtm.ac.uk.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
RNA-dependent RNA polymerase of rotavirus A
A
1088Rotavirus AMutation(s): 0 
EC: 2.7.7.48
Find proteins for G0YZJ9 (Rotavirus A)
Go to UniProtKB:  G0YZJ9
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Inner capsid protein VP2
C, D, E, F, G, H, I, J, K, L
887Rotavirus AMutation(s): 0 
Find proteins for G0YZK0 (Rotavirus A)
Go to UniProtKB:  G0YZK0
Entity ID: 3
MoleculeChainsLengthOrganism
DNA/RNA (5'-D(*(GTG))-R(P*GP*C)-3')M3Rotavirus A
Entity ID: 4
MoleculeChainsLengthOrganism
RNA (5'-R(P*AP*GP*CP*C)-3')N4Rotavirus A
Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
GTG
Query on GTG
M
NON-POLYMERC21 H30 N10 O18 P3

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Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.4 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
National Institutes of Health/National Institute Of Allergy and Infectious DiseasesUnited StatesAI094386
National Institutes of Health/National Institute of General Medical SciencesUnited StatesGM071940
National Institutes of Health/National Institute of Dental and Craniofacial ResearchUnited StatesDE025567
National Institutes of Health/National Center for Research ResourcesUnited States1S10RR23057
National Institutes of Health/Office of the DirectorUnited States1S10OD018111
National Institutes of Health/National Institute of General Medical SciencesUnited StatesU24GM116792
National Science Foundation (United States)United StatesDBI-1338135
National Science Foundation (United States)United StatesDMR-1548924

Revision History 

  • Version 1.0: 2019-05-22
    Type: Initial release
  • Version 1.1: 2019-05-29
    Type: Data collection, Database references