Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

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

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

Macromolecule Content

• Total Structure Weight: 34.05 kDa 
• Atom Count: 2416 
• Modelled Residue Count: 306 
• Deposited Residue Count: 306 
• Unique protein chains: 1

7MHO

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

• PDB DOI: 10.2210/pdb7MHO/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: 1.88 Å
• R-Value Free: 0.208 
• R-Value Work: 0.150 
• R-Value Observed: 0.153 

Re-refinement Note

This entry reflects an alternative modeling of the original data in: 7MHI

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.

(2021) Biorxiv 

• PubMed: 33972941 
• DOI: 10.1101/2021.05.03.437411
• Primary Citation of 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 development of novel antiviral therapeutics. Previous X-ray crystal structures of M ^pro were obtained at cryogenic temperature or room temperature only. Here we report a series of high-resolution crystal structures of unliganded M ^pro across multiple temperatures from cryogenic to physiological, and another at high humidity. We interrogate these datasets with parsimonious multiconformer models, multi-copy ensemble models, and isomorphous difference density maps. Our analysis reveals a temperature-dependent conformational landscape for M ^pro , including a mobile water interleaved between the catalytic dyad, mercurial conformational heterogeneity in a key substrate-binding loop, and a far-reaching intramolecular network bridging the active site and dimer interface. Our results may inspire new strategies for antiviral drug development to counter-punch COVID-19 and combat future coronavirus pandemics.

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Organizational Affiliation: 

Department of Organic Chemistry, The Weizmann Institute of Science, Rehovot, Israel. [e-mail].

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 (PDB Primary Data), 3.4.19.12 (UniProt), 3.4.22 (UniProt), 2.7.7.48 (UniProt), 3.6.4.12 (UniProt), 3.6.4.13 (UniProt), 3.1.13 (UniProt), 3.1 (UniProt), 2.1.1 (UniProt)
UniProt
Find proteins for P0DTD1 (Severe acute respiratory syndrome coronavirus 2) Explore P0DTD1  Go to UniProtKB:  P0DTD1

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
DMS	B [auth A], C [auth A]	DIMETHYL SULFOXIDE C2 H6 O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N
ZN	D [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.88 Å
• R-Value Free: 0.208 
• R-Value Work: 0.150 
• R-Value Observed: 0.153 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 114.968	α = 90
b = 54.622	β = 101.67
c = 45.194	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

• Deposited Date: 2021-04-15 
• 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