9A1T | pdb_00009a1t

SARS-CoV-2 nsp7-8 polyprotein

• PDB DOI: https://doi.org/10.2210/pdb9A1T/pdb

• Organism(s): Severe acute respiratory syndrome coronavirus 2
• Mutation(s): No 


• Deposited: 2022-05-20 Released: 2022-12-16 
• Deposition Author(s): Ruchi Yadav, Valentine V. Courouble, Sanjay K. Dey, Francesc X. Ruiz, Patrick R. Griffin, Eddy Arnold

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Integrative Structure Snapshot

• Multi-Scale: No 
• Multi-State: No 
• Ordered-State: No 
• Deposited Models: 10 
• Representative Model: 1 

Literature

Biochemical and structural insights into SARS-CoV-2 polyprotein processing by Mpro

Ruchi Yadav, Valentine V. Courouble, Sanjay K. Dey, Jerry Joe E.K. Harrison, Jennifer Timm, Jesse B. Hopkins, Ryan L. Slack, Stefan G. Sarafianos, Francesc X. Ruiz, Patrick R. Griffin, Eddy Arnold

(2022) Sci Adv 8: eadd2191

• PubMed: 36490335 
• DOI: https://doi.org/10.1126/sciadv.add2191
• Primary Citation of Related Structures:  
  9A1T, 9A1U


• PubMed Abstract: 
  

  SARS-CoV-2, a human coronavirus, is the causative agent of the COVID-19 pandemic. Its genome is translated into two large polyproteins subsequently cleaved by viral papain-like protease and main protease (Mpro). Polyprotein processing is essential yet incompletely understood. We studied Mpro-mediated processing of the nsp7-11 polyprotein, whose mature products include cofactors of the viral replicase, and identified the order of cleavages. Integrative modeling based on mass spectrometry (including hydrogen-deuterium exchange and cross-linking) and x-ray scattering yielded a nsp7-11 structural ensemble, demonstrating shared secondary structural elements with individual nsps. The pattern of cross-links and HDX footprint of the C145A Mpro and nsp7-11 complex demonstrate preferential binding of the enzyme active site to the polyprotein junction sites and additional transient contacts to help orient the enzyme on its substrate for cleavage. Last, proteolysis assays were used to characterize the effect of inhibitors/binders on Mpro processing/inhibition using the nsp7-11 polyprotein as substrate.

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Organizational Affiliation: 
• Center for Advanced Biotechnology and Medicine (CABM), Rutgers University, Piscataway, NJ, USA.
Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ, USA.
Department of Molecular Medicine, The Scripps Research Institute, Jupiter, FL, USA.
Skaggs Graduate School of Chemical and Biological Sciences, The Scripps Research Institute, Jupiter, FL, USA.
Department of Chemistry, University of Ghana, Legon, Ghana.
BioCAT, Department of Physics, Illinois Institute of Technology, Chicago, IL, USA.
Division of Laboratory of Biochemical Pharmacology and Division of Infectious Diseases, Department of Pediatrics, Emory University School of Medicine, Atlanta, GA, USA.
Children's Healthcare of Atlanta, Atlanta, GA, USA.
Department of Integrative Structural and Computational Biology, The Scripps Research Institute, Jupiter, FL, USA.
Department of Molecular Medicine, UF Scripps Biomedical Research, University of Florida, Jupiter, FL, USA.

Assembly  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Macromolecule Content 

• Total Structure Weight: 36.37 kDa 
• Atom Count: 2,180 
• Modeled Residue Count: 283 
• Deposited Residue Count: 283 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
SARS-CoV-2 nsp7-8 polyprotein	A	283	N/A	Mutation(s): 0
UniProt
Find proteins for P0DTC1 (Severe acute respiratory syndrome coronavirus 2) Explore P0DTC1  Go to UniProtKB:  P0DTC1

Experimental Data & Validation

Integrative Structure Snapshot

• Multi-Scale: No 
• Multi-State: No 
• Ordered-State: No 
• Deposited Models: 10 
• Representative Model: 1 

Structure Validation

View Full Validation Report

View Summary Validation Report

Entry History 

Deposition Data

• Released Date: 2022-12-16 
Deposition Author(s): Ruchi Yadav, Valentine V. Courouble, Sanjay K. Dey, Francesc X. Ruiz, Patrick R. Griffin, Eddy Arnold

Revision History  

• Version 1.0: 2022-12-16
  Type: Initial release