8EKE

Cryo-EM structure of SARS CoV-2 Mpro WT protease


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.36 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

SARS-CoV-2 polyprotein substrate regulates the stepwise M pro cleavage reaction.

Narwal, M.Armache, J.P.Edwards, T.J.Murakami, K.S.

(2023) J Biol Chem 299: 104697-104697

  • DOI: https://doi.org/10.1016/j.jbc.2023.104697
  • Primary Citation of Related Structures:  
    8EIR, 8EKE

  • PubMed Abstract: 

    The processing of the Coronavirus polyproteins pp1a and pp1ab by the main protease M pro to produce mature proteins is a crucial event in virus replication and a promising target for antiviral drug development. M pro cleaves polyproteins in a defined order, but how M pro and/or the polyproteins determine the order of cleavage remains enigmatic due to a lack of structural information about polyprotein-bound M pro . Here, we present the cryo-EM structures of SARS-CoV-2 M pro in an apo form and in complex with the nsp7-10 region of the pp1a polyprotein. The complex structure shows that M pro interacts with only the recognition site residues between nsp9 and nsp10, without any association with the rest of the polyprotein. Comparison between the apo form and polyprotein-bound structures of M pro highlights the flexible nature of the active site region of M pro , which allows it to accommodate ten recognition sites found in the polyprotein. These observations suggest that the role of M pro in selecting a preferred cleavage site is limited and underscores the roles of the structure, conformation, and/or dynamics of the polyproteins in determining the sequence of polyprotein cleavage by M pro .


  • Organizational Affiliation

    Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, Pennsylvania, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
3C-like proteinase nsp5
A, B
306Severe acute respiratory syndrome coronavirus 2Mutation(s): 1 
Gene Names: rep1a-1b
EC: 3.4.22.69
UniProt
Find proteins for P0DTD1 (Severe acute respiratory syndrome coronavirus 2)
Explore P0DTD1 
Go to UniProtKB:  P0DTD1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0DTD1
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.36 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 Cancer Institute (NIH/NCI)United StatesR35 GM131860

Revision History  (Full details and data files)

  • Version 1.0: 2023-04-26
    Type: Initial release
  • Version 1.1: 2023-05-24
    Changes: Database references
  • Version 1.2: 2024-06-19
    Changes: Data collection