9FX7

Crystal structure of Cryo2RT SARS-CoV-2 main protease at 294K

PDB DOI: https://doi.org/10.2210/pdb9FX7/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

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.28 Å
R-Value Free: 0.244
R-Value Work: 0.203
R-Value Observed: 0.205

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 1.2 of the entry. See complete history.

Literature

Cryo2RT: a high-throughput method for room-temperature macromolecular crystallography from cryo-cooled crystals.

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

(2024) Acta Crystallogr D Struct Biol 80: 620-628

PubMed: 39052318 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1107/S2059798324006697
Primary Citation of Related Structures:
7H56, 7H57, 7H58, 7H59, 7H5A, 7H5B, 7H5C, 7H5D, 7H5E, 7H5F, 7H5G, 7H5H, 7H5I, 7H5J, 7H5K, 7H5L, 7H5M, 7H5N, 7H5O, 7H5P, 7H5Q, 7H5R, 7H5S, 7H5T, 7H5U, 7H5V, 7H5W, 7H5X, 7H5Y, 7H5Z, 9FX4, 9FX5, 9FX6, 9FX7

PubMed Abstract:
Advances in structural biology have relied heavily on synchrotron cryo-crystallography and cryogenic electron microscopy to elucidate biological processes and for drug discovery. However, disparities between cryogenic and room-temperature (RT) crystal structures pose challenges. Here, Cryo2RT, a high-throughput RT data-collection method from cryo-cooled crystals that leverages the cryo-crystallography workflow, is introduced. Tested on endothiapepsin crystals with four soaked fragments, thaumatin and SARS-CoV-2 3CL ^pro, Cryo2RT reveals unique ligand-binding poses, offers a comparable throughput to cryo-crystallography and eases the exploration of structural dynamics at various temperatures.

Organizational Affiliation

Swiss Light Source, Center for Photon Science, Paul Scherrer Institute, Forschungsstrasse 111, 5232 Villigen PSI, Switzerland.

Macromolecule Content

Total Structure Weight: 68.28 kDa
Atom Count: 4,946
Modelled Residue Count: 605
Deposited Residue Count: 612
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

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 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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P0DTD1
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain J [auth B] SDF format, chain E [auth A] MOL2 format, chain J [auth B] MOL2 format, chain E [auth A] mmCIF format, chain J [auth B] mmCIF format, chain E [auth A]	E [auth A], J [auth B]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain E [auth A] Focus chain J [auth B] Interactions & Density Focus chain E [auth A] Focus chain J [auth B]
DMS Query on DMS Download Ideal Coordinates CCD File SDF format, chain H [auth B] SDF format, chain C [auth A] SDF format, chain D [auth A] SDF format, chain G [auth A] SDF format, chain I [auth B] MOL2 format, chain H [auth B] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain G [auth A] MOL2 format, chain I [auth B] mmCIF format, chain H [auth B] mmCIF format, chain C [auth A] mmCIF format, chain D [auth A] mmCIF format, chain G [auth A] mmCIF format, chain I [auth B]	C [auth A], D [auth A], G [auth A], H [auth B], I [auth B]	DIMETHYL SULFOXIDE C₂ H₆ O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain G [auth A] Focus chain H [auth B] Focus chain I [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain G [auth A] Focus chain H [auth B] Focus chain I [auth B]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain K [auth B] MOL2 format, chain F [auth A] MOL2 format, chain K [auth B] mmCIF format, chain F [auth A] mmCIF format, chain K [auth B]	F [auth A], K [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain K [auth B] Interactions & Density Focus chain F [auth A] Focus chain K [auth B]