9FX6

Crystal structure of Cryo2RT SARS-CoV-2 main protease at 100K

• PDB DOI: https://doi.org/10.2210/pdb9FX6/pdb

• Classification: VIRAL PROTEIN
• Organism(s): Severe acute respiratory syndrome coronavirus 2
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2024-07-01 Released: 2024-07-31 
• Deposition Author(s): Huang, C.Y., Aumonier, S., Mac Sweeney, A., Olieric, V., Wang, M.
• Funding Organization(s): Swiss National Science Foundation, H2020 Marie Curie Actions of the European Commission

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.23 Å
• R-Value Free: 0.267 
• R-Value Work: 0.217 
• R-Value Observed: 0.219 

Starting Model: experimental

Literature

Cryo2RT: a high-throughput method for room-temperature macromolecular crystallography from frozen crystals Cryo2RT: a high-throughput method for room-temperature macromolecular crystallography from frozen crystals Cryo2RT: a high-throughput method for room-temperature macromolecular crystallography from frozen crystals Cryo2RT: a high-throughput method for room-temperature macromolecular crystallography from frozen crystals

Huang, C.Y., Aumonier, S., Olieric, V., Wang, M.

(2024) Acta Crystallogr D Biol Crystallogr 

• DOI: https://doi.org/10.1107/S2059798324006697

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: 68.26 kDa 
• Atom Count: 5,096 
• Modelled Residue Count: 602 
• 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): 0  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
SO4	E [auth A], H [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
DMS	C [auth A], D [auth A], F [auth B], G [auth B], J [auth B]	DIMETHYL SULFOXIDE C2 H6 O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N
MG	I [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.23 Å
• R-Value Free: 0.267 
• R-Value Work: 0.217 
• R-Value Observed: 0.219 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 68.118	α = 90
b = 99.267	β = 90
c = 103.67	γ = 90

Software Package:

Software Name	Purpose
BUSTER	refinement
XDS	data reduction
XSCALE	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-07-31 
Deposition Author(s): Huang, C.Y., Aumonier, S., Mac Sweeney, A., Olieric, V., Wang, M.

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Funding Organization	Location	Grant Number
Swiss National Science Foundation	Switzerland	182369
H2020 Marie Curie Actions of the European Commission	European Union	884104 PSI-FELLOW-III-3i

Revision History  

• Version 1.0: 2024-07-31
  Type: Initial release