8J9Y | pdb_00008j9y

cryo-EM structure of viral topoisomerase in conformation 1

PDB DOI: https://doi.org/10.2210/pdb8J9Y/pdb
EM Map EMD-36119: EMDB EMDataResource

Classification: VIRAL PROTEIN
Organism(s): African swine fever virus LIS57
Expression System: Komagataella pastoris
Mutation(s): No

Deposited: 2023-05-05 Released: 2023-08-16
Deposition Author(s): Deng, Z.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.16 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

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

Literature

Cryo-EM structures of African swine fever virus topoisomerase.

Zhao, Y., Kuang, W., An, Q., Li, J., Wang, Y., Deng, Z.

(2023) mBio 14: e0122823-e0122823

PubMed: 37610250 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1128/mbio.01228-23
Primary Citation Related Structures:
8J9Y, 8J9Z

PubMed Abstract:
African swine fever virus (ASFV) is a highly contagious virus that causes lethal hemorrhagic diseases known as African swine fever (ASF) with a case fatality rate of 100%. There is an urgent need to develop anti-ASFV drugs. We determine the first high-resolution structures of viral topoisomerase ASFV P1192R in both the closed and open C-gate forms. P1192R shows a similar overall architecture with eukaryotic and prokaryotic type II topoisomerases, which have been successful targets of many antimicrobials and anticancer drugs, with the most similarity to yeast topo II. P1192R also exhibits differences in the details of active site configuration, which are important to enzyme activity. These two structures offer useful structural information for antiviral drug design and provide structural evidence to support that eukaryotic type IIA topoisomerase likely originated from horizontal gene transfer from the virus.

Organizational Affiliation

Wuhan Institute of Virology, Center for Antiviral Research, Chinese Academy of Sciences , Wuhan, Hubei, China.

Macromolecule Content

Total Structure Weight: 271.38 kDa
Atom Count: 12,154
Modeled Residue Count: 1,494
Deposited Residue Count: 2,384
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA topoisomerase 2	A [auth B], B [auth A]	1,192	African swine fever virus LIS57	Mutation(s): 0 Gene Names: P1192R CDS EC: 5.6.2.2
UniProt
Find proteins for A0A2X0THW2 (African swine fever virus) Explore A0A2X0THW2 Go to UniProtKB: A0A2X0THW2
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A2X0THW2
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 3.16 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX	1.20.1_4487:

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2023-08-16

Deposition Author(s):

Funding Organization	Location	Grant Number
Not funded		--

Revision History (Full details and data files)

Version 1.0: 2023-08-16
Type: Initial release
Version 1.1: 2023-09-06
Changes: Database references
Version 1.2: 2023-11-29
Changes: Database references

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), 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 R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.