8DKL

Polymorphism in SARS-CoV-2 Nsp5 main protease reveals differences in cleavage of viral and host substrates

PDB DOI: https://doi.org/10.2210/pdb8DKL/pdb

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

Deposited: 2022-07-05 Released: 2023-05-03
Deposition Author(s): Lu, J., Khan, M.B., Young, H.S., Lemieux, M.J.
Funding Organization(s): Canadian Institutes of Health Research (CIHR), Natural Sciences and Engineering Research Council (NSERC, Canada)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free: 0.241
R-Value Work: 0.200
R-Value Observed: 0.202

wwPDB Validation 3D Report Full Report

This is version 1.1 of the entry. See complete history.

Literature

SARS-CoV-2 Mpro Protease Variants of Concern Display Altered Viral Substrate and Cell Host Target Galectin-8 Processing but Retain Sensitivity toward Antivirals

Chen, S.A., Arutyunova, E., Lu, J., Khan, M.B., Rut, W., Zmudzinski, M., Shahbaz, S., Iyyathurai, J., Moussa, E.W., Turner, Z., Bai, B., Lamer, T., Nieman, J.A., Vederas, J.C., Julien, O., Drag, M., Elahi, S., Young, H.S., Lemieux, M.J.

(2023) ACS Cent Sci 9: 696-708

DOI: https://doi.org/10.1021/acscentsci.3c00054

Macromolecule Content

Total Structure Weight: 67.72 kDa
Atom Count: 5,062
Modelled Residue Count: 612
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): 1 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

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free: 0.241
R-Value Work: 0.200
R-Value Observed: 0.202
Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 44.96	α = 90
b = 53.8	β = 101.355
c = 114.76	γ = 90

Software Package:

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

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2023-05-03

Deposition Author(s):

Funding Organization	Location	Grant Number
Canadian Institutes of Health Research (CIHR)	Canada	VR3-172655
Natural Sciences and Engineering Research Council (NSERC, Canada)	Canada	549297-2019

Revision History (Full details and data files)

Version 1.0: 2023-05-03
Type: Initial release
Version 1.1: 2023-10-25
Changes: Data collection, Refinement description

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM133198.