9LEW | pdb_00009lew

The crystal structure of DinJ-YafQ complex from Vibrio cholerae

PDB DOI: https://doi.org/10.2210/pdb9LEW/pdb

Classification: TOXIN
Organism(s): Vibrio cholerae O1 biovar El Tor str. N16961
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2025-01-07 Released: 2025-07-30
Deposition Author(s): Mun, S.A., Ha, J.H., Jang, T.H., Hong, E., Bae, J., Son, J.
Funding Organization(s): National Research Foundation (NRF, Korea)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free:
0.231 (Depositor), 0.229 (DCC)
R-Value Work:
0.201 (Depositor), 0.201 (DCC)
R-Value Observed:
0.202 (Depositor)

Starting Model: in silico
View more details

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Novel oligomerization state of DinJ-YafQ complex from Vibrio cholerae-Structural and biochemical insights.

Mun, S.A., Yeon, G.B., Park, Y.H., Yoon, H., Ha, J.H., Jang, T.H., Hong, E., Bae, J., Son, J.

(2025) Int J Biol Macromol 320: 145865-145865

PubMed: 40639525 Search on PubMed
DOI: https://doi.org/10.1016/j.ijbiomac.2025.145865
Primary Citation Related Structures:
9LEW

PubMed Abstract:
Toxin-antitoxin (TA) systems are widely distributed in archaeal and bacterial genomes and are crucial for maintaining the physiological functions required for cellular homeostasis. The DinJ-YafQ TA system belongs to the well-known RelBE family of Type II TA systems. Vibrio cholerae, the causative agent of cholera, infects humans through the consumption of contaminated, unpurified drinking water. Its genome contains a cassette of 19 TA system-related genes located on chromosome II, six of which are classified under the RelBE family. Herein, we determined the crystal structure of the V. cholerae DinJ (VcDinJ, antitoxin)-YafQ (VcYafQ, toxin) complex at 2.3 Å resolution. The unique orientation of the VcDinJ RHH ₂ motifs relative to the YafQ molecules promotes the formation of a highly oligomerized hetero-hexadecamer (16-mer) in a concentration-dependent manner. According to biochemical experiments, the VcDinJ-YafQ complex directly binds to the promoter region of its operon, suggesting its role as a transcriptional repressor. An autoregulatory mechanism in which DNA binding induces conformational changes is suggested based on structural modeling through DNA superposition. This finding supports the concentration-dependent and DNA-associated oligomerization of the VcDinJ-YafQ complex.

Organizational Affiliation

New Drug Development Center, Daegu-Gyeongbuk Medical Innovation Foundation (DGMIF), 360-4 Dongnae-dong, Dong-gu, Daegu 41061, Republic of Korea.

Macromolecule Content

Total Structure Weight: 87.68 kDa
Atom Count: 5,862
Modeled Residue Count: 712
Deposited Residue Count: 776
Unique protein chains: 2

Macromolecules

Find similar proteins by:

| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-damage-inducible protein J	A, C, E, G	94	Vibrio cholerae O1 biovar El Tor str. N16961	Mutation(s): 0 Gene Names: VC_A0324
UniProt
Find proteins for Q9KML3 (Vibrio cholerae serotype O1 (strain ATCC 39315 / El Tor Inaba N16961)) Explore Q9KML3 Go to UniProtKB: Q9KML3
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9KML3
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Type II toxin-antitoxin system YafQ family toxin	B, D, F, H	100	Vibrio cholerae O1 biovar El Tor str. N16961	Mutation(s): 1 Gene Names: VC_A0323
UniProt
Find proteins for Q9KML4 (Vibrio cholerae serotype O1 (strain ATCC 39315 / El Tor Inaba N16961)) Explore Q9KML4 Go to UniProtKB: Q9KML4
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9KML4
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 I [auth B] MOL2 format, chain I [auth B] mmCIF format, chain I [auth B]	I [auth B]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain I [auth B] Interactions & Density Focus chain I [auth B]
ACT (Subject of Investigation/LOI) Query on ACT Download:Ideal Coordinates CCD File SDF format, chain J [auth C] SDF format, chain K [auth C] SDF format, chain L [auth D] SDF format, chain M [auth D] SDF format, chain N [auth D] SDF format, chain O [auth E] SDF format, chain P [auth H] SDF format, chain Q [auth H] MOL2 format, chain J [auth C] MOL2 format, chain K [auth C] MOL2 format, chain L [auth D] MOL2 format, chain M [auth D] MOL2 format, chain N [auth D] MOL2 format, chain O [auth E] MOL2 format, chain P [auth H] MOL2 format, chain Q [auth H] mmCIF format, chain J [auth C] mmCIF format, chain K [auth C] mmCIF format, chain L [auth D] mmCIF format, chain M [auth D] mmCIF format, chain N [auth D] mmCIF format, chain O [auth E] mmCIF format, chain P [auth H] mmCIF format, chain Q [auth H]	J [auth C] K [auth C] L [auth D] M [auth D] N [auth D] J [auth C], K [auth C], L [auth D], M [auth D], N [auth D], O [auth E], P [auth H], Q [auth H]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain J [auth C] Focus chain K [auth C] Focus chain L [auth D] Focus chain M [auth D] Focus chain N [auth D] Focus chain O [auth E] Focus chain P [auth H] Focus chain Q [auth H] Interactions & Density Focus chain J [auth C] Focus chain K [auth C] Focus chain L [auth D] Focus chain M [auth D] Focus chain N [auth D] Focus chain O [auth E] Focus chain P [auth H] Focus chain Q [auth H]