8G6R

Porcine epidemic diarrhea virus core polymerase complex


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.30 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

An alphacoronavirus polymerase structure reveals conserved co-factor functions.

Anderson, T.K.Hoferle, P.J.Lee, K.W.Coon, J.J.Kirchdoerfer, R.N.

(2023) bioRxiv 

  • DOI: https://doi.org/10.1101/2023.03.15.532841
  • Primary Citation of Related Structures:  
    8G6R, 8URB

  • PubMed Abstract: 

    Coronaviruses are a diverse subfamily of viruses containing pathogens of humans and animals. This subfamily of viruses replicates their RNA genomes using a core polymerase complex composed of viral non-structural proteins: nsp7, nsp8 and nsp12. Most of our understanding of coronavirus molecular biology comes from the betacoronaviruses like SARS-CoV and SARS-CoV-2, the latter of which is the causative agent of COVID-19. In contrast, members of the alphacoronavirus genus are relatively understudied despite their importance in human and animal health. Here we have used cryo-electron microscopy to determine the structure of the alphacoronavirus porcine epidemic diarrhea virus (PEDV) core polymerase complex bound to RNA. Our structure shows an unexpected nsp8 stoichiometry in comparison to other published coronavirus polymerase structures. Biochemical analysis shows that the N-terminal extension of one nsp8 is not required for in vitro RNA synthesis for alpha and betacoronaviruses as previously hypothesized. Our work shows the importance of studying diverse coronaviruses to reveal aspects of coronavirus replication while also identifying areas of conservation to be targeted by antiviral drugs.


  • Organizational Affiliation

    Biochemistry Department, University of Wisconsin-Madison, Madison, WI 53706.


Macromolecules

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
nsp12921Porcine epidemic diarrhea virusMutation(s): 0 
UniProt
Find proteins for A0A0U2C263 (Porcine epidemic diarrhea virus)
Explore A0A0U2C263 
Go to UniProtKB:  A0A0U2C263
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A0U2C263
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
nsp8114Porcine epidemic diarrhea virusMutation(s): 0 
Gene Names: ORF1a1b
UniProt
Find proteins for A0A1Z2R8Q6 (Porcine epidemic diarrhea virus)
Explore A0A1Z2R8Q6 
Go to UniProtKB:  A0A1Z2R8Q6
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A1Z2R8Q6
Sequence Annotations
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
nsp762Porcine epidemic diarrhea virusMutation(s): 0 
Gene Names: ORF1
UniProt
Find proteins for A0A0M4AW09 (Porcine epidemic diarrhea virus)
Explore A0A0M4AW09 
Go to UniProtKB:  A0A0M4AW09
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A0M4AW09
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  • Reference Sequence

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Entity ID: 4
MoleculeChains LengthOrganismImage
RNA (5'-R(P*AP*AP*GP*AP*AP*GP*CP*UP*AP*UP*UP*AP*AP*AP*AP*UP*CP*AP*CP*A)-3')D [auth I]20synthetic construct
Sequence Annotations
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  • Reference Sequence

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Entity ID: 5
MoleculeChains LengthOrganismImage
RNA (5'-R(P*GP*GP*UP*UP*GP*UP*GP*AP*UP*UP*UP*UP*AP*AP*UP*AP*GP*CP*UP*U)-3')E [auth J]20synthetic construct
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.30 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONcryoSPARC3.3.1

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesAI123498
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesAI158463
United States Department of Agriculture (USDA)United StatesWIS03099

Revision History  (Full details and data files)

  • Version 1.0: 2023-03-29
    Type: Initial release
  • Version 1.1: 2023-04-12
    Changes: Database references
  • Version 1.2: 2023-10-04
    Changes: Data collection, Data processing