Crystal Structure of SARS-CoV-2 Main Protease (Mpro) at 298 K and High Humidity

Experimental Data Snapshot

  • Resolution: 2.00 Å
  • R-Value Free: 0.240 
  • R-Value Work: 0.195 
  • R-Value Observed: 0.197 

Starting Model: experimental
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This is version 2.3 of the entry. See complete history


The tem-per-ature-dependent conformational ensemble of SARS-CoV-2 main protease (M pro ).

Ebrahim, A.Riley, B.T.Kumaran, D.Andi, B.Fuchs, M.R.McSweeney, S.Keedy, D.A.

(2022) IUCrJ 9: 682-694

  • DOI: https://doi.org/10.1107/S2052252522007497
  • Primary Citation of Related Structures:  
    7MHF, 7MHG, 7MHH, 7MHI, 7MHJ, 7MHK, 7MHL, 7MHM

  • PubMed Abstract: 

    The COVID-19 pandemic, instigated by the SARS-CoV-2 coronavirus, continues to plague the globe. The SARS-CoV-2 main protease, or M pro , is a promising target for the development of novel antiviral therapeutics. Previous X-ray crystal structures of M pro were obtained at cryogenic tem-per-ature or room tem-per-ature only. Here we report a series of high-resolution crystal structures of unliganded M pro across multiple tem-per-atures from cryogenic to physiological, and another at high humidity. We inter-rogate these data sets with parsimonious multiconformer models, multi-copy ensemble models, and isomorphous difference density maps. Our analysis reveals a perturbation-dependent conformational landscape for M pro , including a mobile zinc ion inter-leaved between the catalytic dyad, mercurial conformational heterogeneity at various sites including a key substrate-binding loop, and a far-reaching intra-molecular network bridging the active site and dimer inter-face. Our results may inspire new strategies for antiviral drug development to aid preparation for future coronavirus pandemics.

  • Organizational Affiliation

    Diamond Light Source, Harwell Science and Innovation Campus, Didcot, OX11 0DE, England, United Kingdom.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
3C-like proteinase306Severe acute respiratory syndrome coronavirus 2Mutation(s): 0 
Gene Names: rep1a-1b
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
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on ZN

Download Ideal Coordinates CCD File 
B [auth A]ZINC ION
Experimental Data & Validation

Experimental Data

Unit Cell:
Length ( Å )Angle ( ˚ )
a = 114.88α = 90
b = 54.736β = 101.42
c = 45.24γ = 90
Software Package:
Software NamePurpose
xia2data reduction
DIALSdata scaling

Structure Validation

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Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United States133769
Department of Energy (DOE, United States)United StatesNational Virtual Biotechnology Laboratory (NVBL)
Department of Energy (DOE, United States)United StatesCoronavirus CARES Act
Department of Energy (DOE, United States)United StatesBNL LDRD 20-042
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesP30GM133893
Department of Energy (DOE, United States)United StatesKP1605010

Revision History  (Full details and data files)

  • Version 1.0: 2021-05-12
    Type: Initial release
  • Version 1.1: 2021-05-26
    Changes: Database references
  • Version 2.0: 2022-04-20
    Type: Coordinate replacement
    Reason: Ligand identity
    Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Other, Refinement description, Source and taxonomy, Structure summary
  • Version 2.1: 2022-09-07
    Changes: Database references
  • Version 2.2: 2022-09-21
    Changes: Database references
  • Version 2.3: 2023-10-18
    Changes: Data collection, Refinement description