9JS5 | pdb_00009js5

Crystal structure of the ASFV-derived histone-like protein pA104R

PDB DOI: https://doi.org/10.2210/pdb9JS5/pdb

Classification: DNA BINDING PROTEIN
Organism(s): African swine fever virus
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2024-09-30 Released: 2025-04-30
Deposition Author(s): Li, Q., Shao, H., Yi, D., Cen, S.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free:
0.239 (Depositor), 0.244 (DCC)
R-Value Work:
0.198 (Depositor), 0.206 (DCC)
R-Value Observed:
0.200 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 1.0 of the entry. See complete history.

Literature

Thonningianin A disrupts pA104R-DNA binding and inhibits African swine fever virus replication.

Li, Q.J., Shao, H.H., Zheng, L.L., Liu, Q., Huo, C.C., Yi, D.R., Feng, T., Cen, S.

(2025) Emerg Microbes Infect 14: 2482697-2482697

PubMed: 40138179 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1080/22221751.2025.2482697
Primary Citation of Related Structures:
9JS5

PubMed Abstract:
African swine fever is a highly lethal disease caused by the African swine fever virus (ASFV), posing a significant threat to the global pig industry, wherease no approved treatments are currently available. The ASFV DNA-binding protein, pA104R, plays a critical role in viral genome packaging and replication, making it a key target for drug discovery. Through structure-based virtual screening, we identified a polyphenolic compound, thonningianin A, which disrupts the pA104R-DNA binding and significantly inhibits ASFV replication. Mechanistic study revealed that thonningianin A binds to the DNA-binding region of pA104R, forming strong hydrogen bonds with H100 and occupying the vital DNA-binding residues K92, R94, and K97. In addition, we resolved the high-resolution (1.8 Å) structure of pA104R (PDB ID 9JS5), providing valuable insights for future drug screening. Together, these results demonstrate that thonningianin A holds great potential for the development of anti-ASFV drug, as a herb extract with favourable pharmacokinetic properties and safety.

Organizational Affiliation

Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, People's Republic of China.

Macromolecule Content

Total Structure Weight: 23.96 kDa
Atom Count: 1,738
Modeled Residue Count: 198
Deposited Residue Count: 208
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Viral histone-like protein	A, B	104	African swine fever virus	Mutation(s): 0 Gene Names: A104R, A104R CDS, BA71V-A104R, AFSV47Ss_0056, ASFV-Georgia_4-058, ASFVARMWT4_00043
UniProt
Find proteins for P68742 (African swine fever virus (strain Badajoz 1971 Vero-adapted)) Explore P68742 Go to UniProtKB: P68742
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P68742
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain H [auth B] SDF format, chain I [auth B] SDF format, chain J [auth B] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain H [auth B] MOL2 format, chain I [auth B] MOL2 format, chain J [auth B] mmCIF format, chain D [auth A] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain H [auth B] mmCIF format, chain I [auth B] mmCIF format, chain J [auth B]	D [auth A] E [auth A] F [auth A] H [auth B] I [auth B] D [auth A], E [auth A], F [auth A], H [auth B], I [auth B], J [auth B]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain H [auth B] Focus chain I [auth B] Focus chain J [auth B] Interactions & Density Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain H [auth B] Focus chain I [auth B] Focus chain J [auth B]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain G [auth B] MOL2 format, chain C [auth A] MOL2 format, chain G [auth B] mmCIF format, chain C [auth A] mmCIF format, chain G [auth B]	C [auth A], G [auth B]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain G [auth B] Interactions & Density Focus chain C [auth A] Focus chain G [auth B]