7WKU | pdb_00007wku

Structure of PDCoV Mpro in complex with an inhibitor

PDB DOI: https://doi.org/10.2210/pdb7WKU/pdb

Classification: VIRAL PROTEIN
Organism(s): Porcine deltacoronavirus, synthetic construct
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2022-01-11 Released: 2022-05-25
Deposition Author(s): Wang, F.H., Yang, H.T.
Funding Organization(s): National Natural Science Foundation of China (NSFC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.60 Å
R-Value Free:
0.241 (Depositor), 0.241 (DCC)
R-Value Work:
0.191 (Depositor), 0.194 (DCC)
R-Value Observed:
0.193 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 2.2 of the entry. See complete history.

Literature

The Structure of the Porcine Deltacoronavirus Main Protease Reveals a Conserved Target for the Design of Antivirals.

Wang, F., Chen, C., Wang, Z., Han, X., Shi, P., Zhou, K., Liu, X., Xiao, Y., Cai, Y., Huang, J., Zhang, L., Yang, H.

(2022) Viruses 14

PubMed: 35336895 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.3390/v14030486
Primary Citation Related Structures:
7WKU

PubMed Abstract:
The existing zoonotic coronaviruses (CoVs) and viral genetic variants are important microbiological pathogens that cause severe disease in humans and animals. Currently, no effective broad-spectrum antiviral drugs against existing and emerging CoVs are available. The CoV main protease (M ^pro) plays an essential role in viral replication, making it an ideal target for drug development. However, the structure of the Deltacoronavirus M ^pro is still unavailable. Porcine deltacoronavirus (PDCoV) is a novel CoV that belongs to the genus Deltacoronavirus and causes atrophic enteritis, severe diarrhea, vomiting and dehydration in pigs. Here, we determined the structure of PDCoV M ^pro complexed with a Michael acceptor inhibitor. Structural comparison showed that the backbone of PDCoV M ^pro is similar to those of alpha-, beta- and gamma-CoV M ^pros. The substrate-binding pocket of M ^pro is well conserved in the subfamily Coronavirinae . In addition, we also observed that M ^pros from the same genus adopted a similar conformation. Furthermore, the structure of PDCoV M ^pro in complex with a Michael acceptor inhibitor revealed the mechanism of its inhibition of PDCoV M ^pro. Our results provide a basis for the development of broad-spectrum antivirals against PDCoV and other CoVs.

Organizational Affiliation

School of Life Sciences, Tianjin University, Tianjin 300072, China.

Macromolecule Content

Total Structure Weight: 212.1 kDa
Atom Count: 14,877
Modeled Residue Count: 1,834
Deposited Residue Count: 1,884
Unique protein chains: 2

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Peptidase C30	A, B, C, D, E A, B, C, D, E, F	308	Porcine deltacoronavirus	Mutation(s): 0 Gene Names: ORF1ab
UniProt
Find proteins for A0A140ESF0 (Porcine deltacoronavirus) Explore A0A140ESF0 Go to UniProtKB: A0A140ESF0
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A140ESF0
Sequence Annotations Expand
Reference Sequence

Find similar proteins by: Sequence | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
N-[(5-METHYLISOXAZOL-3-YL)CARBONYL]ALANYL-L-VALYL-N~1~-((1R,2Z)-4-(BENZYLOXY)-4-OXO-1-{[(3R)-2-OXOPYRROLIDIN-3-YL]METHYL}BUT-2-ENYL)-L-LEUCINAMIDE	G [auth H] H [auth I] I [auth J] J [auth K] K [auth L] G [auth H], H [auth I], I [auth J], J [auth K], K [auth L], L [auth M]	6	synthetic construct	Mutation(s): 0

Biologically Interesting Molecules (External Reference)

1 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_002214 Query on PRD_002214	G [auth H] H [auth I] I [auth J] J [auth K] K [auth L] G [auth H], H [auth I], I [auth J], J [auth K], K [auth L], L [auth M]	N-[(5-METHYLISOXAZOL-3-YL)CARBONYL]ALANYL-L-VALYL-N~1~-((1R,2Z)-4-(BENZYLOXY)-4-OXO-1-{[(3R)-2-OXOPYRROLIDIN-3-YL]METHYL}BUT-2-ENYL)-L-LEUCINAMIDE	Peptide-like / Inhibitor		Interactions Focus chain G [auth H] Focus chain H [auth I] Focus chain I [auth J] Focus chain J [auth K] Focus chain K [auth L] Focus chain L [auth M] Interactions & Density Focus chain G [auth H] Focus chain H [auth I] Focus chain I [auth J] Focus chain J [auth K] Focus chain K [auth L] Focus chain L [auth M]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.60 Å
R-Value Free: 0.241 (Depositor), 0.241 (DCC)
R-Value Work: 0.191 (Depositor), 0.194 (DCC)
R-Value Observed: 0.193 (Depositor)

Space Group: P 6₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 122.292	α = 90
b = 122.292	β = 90
c = 289.754	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data scaling
PDB_EXTRACT	data extraction
PHENIX	model building
PHENIX	phasing

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2022-05-25

Deposition Author(s):

Wang, F.H.

Yang, H.T.

Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	81772204

Revision History (Full details and data files)

Version 1.0: 2022-05-25
Type: Initial release
Version 2.0: 2023-11-15
Changes: Atomic model, Data collection, Derived calculations
Version 2.1: 2023-11-29
Changes: Refinement description
Version 2.2: 2024-10-16
Changes: Structure summary