8EY2

Cryo-EM structure of SARS-CoV-2 Main protease C145S in complex with N-terminal peptide

PDB DOI: https://doi.org/10.2210/pdb8EY2/pdb
EM Map EMD-28666: EMDB EMDataResource

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

Deposited: 2022-10-26 Released: 2022-12-07
Deposition Author(s): Noske, G.D., Song, Y., Fernandes, R.S., Oliva, G., Godoy, A.S.
Funding Organization(s): Sao Paulo Research Foundation (FAPESP)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.50 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

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

Re-refinement Note

This entry reflects an alternative modeling of the original data in: 7S82

Literature

An in-solution snapshot of SARS-COV-2 main protease maturation process and inhibition

Noske, G.D., Song, Y., Fernandes, R.S., Chalk, R., Elmassoudi, H., Koekemoer, L., Owen, C.D., El-Baba, T.J., Robinson, C.V., Oliva, G., Godoy, A.S.

(2023) Nat Commun 14: 1545

DOI: https://doi.org/10.1038/s41467-023-37035-5

Macromolecule Content

Total Structure Weight: 138.27 kDa
Atom Count: 4,908
Modelled Residue Count: 634
Deposited Residue Count: 1,256
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	A, B [auth C], C [auth D], D [auth B]	314	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: ELECTRON MICROSCOPY
Resolution: 3.50 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX
RECONSTRUCTION	cryoSPARC

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2022-12-07

Deposition Author(s):

Fernandes, R.S.

Funding Organization	Location	Grant Number
Sao Paulo Research Foundation (FAPESP)	Brazil	2013/07600-3

Revision History (Full details and data files)

Version 1.0: 2022-12-07
Type: Initial release
Version 1.1: 2023-03-29
Changes: Database references

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.