9GHN | pdb_00009ghn

Structure of SARS-CoV-2 Main Protease (Mpro) with mutation of Q256A

• PDB DOI: https://doi.org/10.2210/pdb9GHN/pdb

• Classification: HYDROLASE
• Organism(s): Severe acute respiratory syndrome coronavirus 2
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2024-08-15 Released: 2025-09-03 
• Deposition Author(s): Creon, A., Scheer, T.E.S., Lane, T.J., Rahmani Mashhour, A., Guenther, S., Reinke, P.Y.A., Meents, A., Chapman, H.N.
• Funding Organization(s): Helmholtz Association

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.40 Å
• R-Value Free: 
  0.218 (Depositor), 0.195 (DCC) 
• R-Value Work: 
  0.193 (Depositor) 
• R-Value Observed: 
  0.193 (Depositor) 

Starting Model: experimental

Literature

Statistical crystallography reveals an allosteric network in SARS-CoV-2 M pro.

Creon, A., Scheer, T.E.S., Reinke, P., Rahmani Mashhour, A., Gunther, S., Niebling, S., Schamoni-Kast, K., Uetrecht, C., Meents, A., Chapman, H.N., Sprenger, J., Lane, T.J.

(2026) Commun Biol 9

• PubMed: 42069849 
• DOI: https://doi.org/10.1038/s42003-026-10127-w
• Primary Citation Related Structures: 
  9GHN, 9GHO, 9GI6


• PubMed Abstract: 
  

  To interpret and transmit biological signals, proteins use correlated motions. Experimental determination of these dynamics and the structural distributions they generate remains a key challenge. Here, using 1146 crystal structures of the main protease (M ^pro ) from SARS-CoV-2, we were able to infer a model of the enzyme's structural fluctuations. M ^pro is regulated by concentration, becoming enzymatically active after forming a homodimer. To understand the structural changes that enable dimerization to activate catalysis, we employed our model, predicting which regions of the dimerization domain are structurally correlated with the active site. Mutations at these positions, expected to disrupt catalysis, resulted in a dramatic reduction in activity in one case, a mild effect in the second, and none in the third. Additional crystallography and biophysical experiments provide a mechanistic explanation for these results. Our work suggests that a statistical crystallography, in which numerous crystallographic datasets are analyzed, can reveal the structural fluctuations of protein native states and help uncover their biological function.

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Organizational Affiliation: 
• Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, Hamburg, Germany.
Centre for Structural Systems Biology CSSB, Hamburg, Germany.
European Molecular Biology Laboratory Hamburg, Hamburg, Germany.
Centre for Structural Systems Biology CSSB, Deutsches Elektronen-Synchrotron DESY, Leibniz Institute of Virology (LIV), University of Lübeck, Hamburg, Germany.
Institute of Chemistry and Metabolomics, University of Lübeck, Lübeck, Germany.
The Hamburg Centre for Ultrafast Imaging, Hamburg, Germany.
Department of Physics, University of Hamburg, Hamburg, Germany.
Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, Hamburg, Germany. [e-mail].
The Hamburg Centre for Ultrafast Imaging, Hamburg, Germany. [e-mail].

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)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 67.84 kDa 
• Atom Count: 5,537 
• Modeled Residue Count: 612 
• Deposited Residue Count: 612 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
3C-like proteinase nsp5	A, B	306	Severe acute respiratory syndrome coronavirus 2	Mutation(s): 1  EC: 3.4.22.69
UniProt
Find proteins for P0DTC1 (Severe acute respiratory syndrome coronavirus 2) Explore P0DTC1  Go to UniProtKB:  P0DTC1

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EDO	C [auth A], F [auth B], G [auth B]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
CL	D [auth A], H [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
NA	E [auth A], I [auth B]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.40 Å
• R-Value Free:  0.218 (Depositor), 0.195 (DCC) 
• R-Value Work:  0.193 (Depositor) 
• R-Value Observed: 0.193 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 78.538	α = 90
b = 88.438	β = 90
c = 100.766	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PHENIX	refinement
DIALS	data reduction
DIALS	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2025-09-03 
Deposition Author(s): Creon, A., Scheer, T.E.S., Lane, T.J., Rahmani Mashhour, A., Guenther, S., Reinke, P.Y.A., Meents, A., Chapman, H.N.

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Funding Organization	Location	Grant Number
Helmholtz Association	Germany	--

Revision History  

• Version 1.0: 2025-09-03
  Type: Initial release
  
• Version 1.1: 2026-09-23
  Changes: Database references