8URB

Porcine epidemic diarrhea virus complete core polymerase complex


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.40 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.0 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

    Biomolecular Chemistry Department, University of Wisconsin-Madison, Madison, WI 53706.


Macromolecules

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
nsp12957Porcine epidemic diarrhea virusMutation(s): 0 
Gene Names: 1bORF1a
UniProt
Find proteins for U6BRU0 (Porcine epidemic diarrhea virus)
Explore U6BRU0 
Go to UniProtKB:  U6BRU0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupU6BRU0
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
nsp8
B, D
195Porcine epidemic diarrhea virusMutation(s): 0 
Gene Names: 1bORF1a
UniProt
Find proteins for U6BRU0 (Porcine epidemic diarrhea virus)
Explore U6BRU0 
Go to UniProtKB:  U6BRU0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupU6BRU0
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
nsp783Porcine epidemic diarrhea virusMutation(s): 0 
Gene Names: 1bORF1a
UniProt
Find proteins for U6BRU0 (Porcine epidemic diarrhea virus)
Explore U6BRU0 
Go to UniProtKB:  U6BRU0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupU6BRU0
Sequence Annotations
Expand
  • Reference Sequence
Find similar nucleic acids by:  (by identity cutoff)  |  3D Structure
Entity ID: 4
MoleculeChains LengthOrganismImage
RNA (33-MER)E [auth I]33synthetic construct
Sequence Annotations
Expand
  • Reference Sequence
Find similar nucleic acids by:  (by identity cutoff)  |  3D Structure
Entity ID: 5
MoleculeChains LengthOrganismImage
RNA (55-MER)F [auth J]55synthetic construct
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ZN (Subject of Investigation/LOI)
Query on ZN

Download Ideal Coordinates CCD File 
G [auth A],
H [auth A]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.40 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONcryoSPARC4.1.0
MODEL REFINEMENTPHENIX1.20.1_4487:
MODEL REFINEMENTISOLDE

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 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: 2023-11-15
    Type: Initial release