7MHP | pdb_00007mhp

Ensemble refinement structure of SARS-CoV-2 main protease (Mpro) at 298 K at high humidity

• PDB DOI: https://doi.org/10.2210/pdb7MHP/pdb

• Classification: HYDROLASE
• Organism(s): Severe acute respiratory syndrome coronavirus 2
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2021-04-15 Released: 2021-05-12 
• Deposition Author(s): Ebrahim, A., Riley, B.T., Kumaran, D., Andi, B., Fuchs, M.R., McSweeney, S., Keedy, D.A.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), Department of Energy (DOE, United States)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.221 (Depositor), 0.265 (DCC) 
• R-Value Work: 
  0.159 (Depositor), 0.189 (DCC) 
• R-Value Observed: 
  0.163 (Depositor) 

Starting Model: experimental

Literature

The temperature-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

• PubMed: 36071812 
• DOI: https://doi.org/10.1107/S2052252522007497
• Primary Citation Related Structures: 
  7MHF, 7MHG, 7MHH, 7MHI, 7MHJ, 7MHK, 7MHL, 7MHM, 7MHN, 7MHO, 7MHP, 7MHQ


• 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.

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Organizational Affiliation: 
• Diamond Light Source, Harwell Science and Innovation Campus, Didcot, OX11 0DE, England, United Kingdom.
Structural Biology Initiative, CUNY Advanced Science Research Center, New York, NY 10031, USA.
Biology Department, Brookhaven National Laboratory, Upton, NY 11973, USA.
Center for BioMolecular Structure, NSLS-II, Brookhaven National Laboratory, Upton, NY 11973, USA.
National Virtual Biotechnology Laboratory (NVBL), US Department of Energy, Washington, DC, USA.
Department of Chemistry and Biochemistry, City College of New York, New York, NY 10031, USA.
PhD Programs in Biochemistry, Biology, and Chemistry, The Graduate Center-City University of New York, New York, NY 10016, USA.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 33.89 kDa 
• Atom Count: 2,402 
• Modeled Residue Count: 306 
• Deposited Residue Count: 306 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
3C-like proteinase	A	306	Severe acute respiratory syndrome coronavirus 2	Mutation(s): 0  Gene Names: rep, 1a-1b EC: 3.4.22.69
UniProt
Find proteins for P0DTD1 (Severe acute respiratory syndrome coronavirus 2) Explore P0DTD1  Go to UniProtKB:  P0DTD1

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	B [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free:  0.221 (Depositor), 0.265 (DCC) 
• R-Value Work:  0.159 (Depositor), 0.189 (DCC) 
• R-Value Observed: 0.163 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 114.88	α = 90
b = 54.736	β = 101.42
c = 45.24	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
xia2	data reduction
DIALS	data scaling
PHASER	phasing
PDB_EXTRACT	data extraction

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2021-05-12 
Deposition Author(s): Ebrahim, A., Riley, B.T., Kumaran, D., Andi, B., Fuchs, M.R., McSweeney, S., Keedy, D.A.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM133769
Department of Energy (DOE, United States)	United States	National Virtual Biotechnology Laboratory (NVBL)
Department of Energy (DOE, United States)	United States	Coronavirus CARES Act
Department of Energy (DOE, United States)	United States	BNL LDRD 20-042
Department of Energy (DOE, United States)	United States	DE-SC0012704
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	P30GM133893
Department of Energy (DOE, United States)	United States	KP1605010

Revision History  

• Version 1.0: 2021-05-12
  Type: Initial release
  
• Version 1.1: 2021-05-26
  Changes: Database references
• Version 2.0: 2022-04-06
  Type: Coordinate replacement
  Reason: Ligand identity
  Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Refinement description, Source and taxonomy, Structure summary
• Version 2.1: 2022-09-07
  Changes: Database references
• Version 2.2: 2023-10-18
  Changes: Data collection, Refinement description
• Version 2.3: 2026-04-15
  Changes: Database references, Structure summary