9VYL | pdb_00009vyl

Crystal structure of BdThsB1 with NAD

PDB DOI: https://doi.org/10.2210/pdb9VYL/pdb

Classification: IMMUNE SYSTEM
Organism(s): Cytobacillus dafuensis
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2025-07-21 Released: 2026-01-28
Deposition Author(s): Hong, S., Choe, J.
Funding Organization(s): National Research Foundation (NRF, Korea)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.54 Å
R-Value Free:
0.183 (Depositor), 0.183 (DCC)
R-Value Work:
0.147 (Depositor), 0.147 (DCC)

Starting Model: in silico
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Crystal structure of Bacillus dafuensis Thoeris B1 protein in complex with NAD.

Hong, S., Choe, J.

(2025) Biochem Biophys Res Commun 793: 153001-153001

PubMed: 41270486 Search on PubMed
DOI: https://doi.org/10.1016/j.bbrc.2025.153001
Primary Citation of Related Structures:
9VYL

PubMed Abstract:
The Type 1 Thoeris defense system is an NAD ⁺-based innate immune mechanism that protects bacterial populations against viral infection by triggering NAD ⁺ depletion-induced cell death. Central to this system is the TIR domain-containing protein Ths B, which uses NAD ⁺ to synthesize a cyclic ADPR (cADPR) signal upon sensing viral antigens. However, the structural basis of NAD ⁺ binding by Ths B remains poorly understood. Here, we report the 1.54 Å resolution X-ray crystal structure of the Thoeris B1 protein from Bacillus dafuensis (Bd) in complex with NAD ⁺. The structure reveals a canonical TIR fold comprising a five-stranded parallel β-sheet flanked by five α-helices, along with an unpredicted CCCH-type zinc finger domain formed by two flexible loops and a hydrophobic cavity. NAD ⁺ binds in a distinctive C-shaped conformation, engaging residues near the conserved catalytic core. These findings suggest a pre-activation binding of NAD ⁺ prior to antigen detection, providing structural clues into the specificity and catalytic mechanism of cADPR production. Our study uncovers unique structural features of bacterial TIR domains and expands our understanding of the molecular basis of Thoeris-mediated antiviral immunity.

Organizational Affiliation

Department of Life Science, University of Seoul, Seoul, 02504, Republic of Korea.

Macromolecule Content

Total Structure Weight: 118.4 kDa
Atom Count: 8,622
Modeled Residue Count: 892
Deposited Residue Count: 972
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative cyclic ADP-D-ribose synthase TIR1	A, B, C, D	243	Cytobacillus dafuensis	Mutation(s): 0 Gene Names: thsB1, FSZ17_06165 EC: 3.2.2
UniProt
Find proteins for A0A5B8Z670 (Cytobacillus dafuensis) Explore A0A5B8Z670 Go to UniProtKB: A0A5B8Z670
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A5B8Z670
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAD (Subject of Investigation/LOI) Query on NAD Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain IA [auth D] SDF format, chain O [auth B] SDF format, chain Y [auth C] MOL2 format, chain E [auth A] MOL2 format, chain IA [auth D] MOL2 format, chain O [auth B] MOL2 format, chain Y [auth C] mmCIF format, chain E [auth A] mmCIF format, chain IA [auth D] mmCIF format, chain O [auth B] mmCIF format, chain Y [auth C]	E [auth A], IA [auth D], O [auth B], Y [auth C]	NICOTINAMIDE-ADENINE-DINUCLEOTIDE C₂₁ H₂₇ N₇ O₁₄ P₂ BAWFJGJZGIEFAR-NNYOXOHSSA-N		Interactions Focus chain E [auth A] Focus chain IA [auth D] Focus chain O [auth B] Focus chain Y [auth C] Interactions & Density Focus chain E [auth A] Focus chain IA [auth D] Focus chain O [auth B] Focus chain Y [auth C]
SPD (Subject of Investigation/LOI) Query on SPD Download Ideal Coordinates CCD File SDF format, chain AA [auth C] SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain JA [auth D] SDF format, chain KA [auth D] SDF format, chain P [auth B] SDF format, chain Q [auth B] SDF format, chain Z [auth C] MOL2 format, chain AA [auth C] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain JA [auth D] MOL2 format, chain KA [auth D] MOL2 format, chain P [auth B] MOL2 format, chain Q [auth B] MOL2 format, chain Z [auth C] mmCIF format, chain AA [auth C] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain JA [auth D] mmCIF format, chain KA [auth D] mmCIF format, chain P [auth B] mmCIF format, chain Q [auth B] mmCIF format, chain Z [auth C]	AA [auth C] F [auth A] G [auth A] JA [auth D] KA [auth D] AA [auth C], F [auth A], G [auth A], JA [auth D], KA [auth D], P [auth B], Q [auth B], Z [auth C]	SPERMIDINE C₇ H₁₉ N₃ ATHGHQPFGPMSJY-UHFFFAOYSA-N		Interactions Focus chain AA [auth C] Focus chain F [auth A] Focus chain G [auth A] Focus chain JA [auth D] Focus chain KA [auth D] Focus chain P [auth B] Focus chain Q [auth B] Focus chain Z [auth C] Interactions & Density Focus chain AA [auth C] Focus chain F [auth A] Focus chain G [auth A] Focus chain JA [auth D] Focus chain KA [auth D] Focus chain P [auth B] Focus chain Q [auth B] Focus chain Z [auth C]
ZN (Subject of Investigation/LOI) Query on ZN Download Ideal Coordinates CCD File SDF format, chain BA [auth C] SDF format, chain LA [auth D] SDF format, chain R [auth B] SDF format, chain H [auth A] MOL2 format, chain BA [auth C] MOL2 format, chain LA [auth D] MOL2 format, chain R [auth B] MOL2 format, chain H [auth A] mmCIF format, chain BA [auth C] mmCIF format, chain LA [auth D] mmCIF format, chain R [auth B] mmCIF format, chain H [auth A]	BA [auth C], H [auth A], LA [auth D], R [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain BA [auth C] Focus chain H [auth A] Focus chain LA [auth D] Focus chain R [auth B] Interactions & Density Focus chain BA [auth C] Focus chain H [auth A] Focus chain LA [auth D] Focus chain R [auth B]
NA (Subject of Investigation/LOI) Query on NA Download Ideal Coordinates CCD File SDF format, chain CA [auth C] SDF format, chain DA [auth C] SDF format, chain FA [auth C] SDF format, chain J [auth A] SDF format, chain K [auth A] SDF format, chain M [auth A] SDF format, chain MA [auth D] SDF format, chain N [auth A] SDF format, chain OA [auth D] SDF format, chain S [auth B] SDF format, chain T [auth B] SDF format, chain V [auth B] SDF format, chain W [auth B] SDF format, chain X [auth B] SDF format, chain U [auth B] SDF format, chain RA [auth D] SDF format, chain QA [auth D] SDF format, chain PA [auth D] SDF format, chain NA [auth D] SDF format, chain L [auth A] SDF format, chain I [auth A] SDF format, chain HA [auth C] SDF format, chain GA [auth C] SDF format, chain EA [auth C] MOL2 format, chain CA [auth C] MOL2 format, chain DA [auth C] MOL2 format, chain FA [auth C] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] MOL2 format, chain M [auth A] MOL2 format, chain MA [auth D] MOL2 format, chain N [auth A] MOL2 format, chain OA [auth D] MOL2 format, chain S [auth B] MOL2 format, chain T [auth B] MOL2 format, chain V [auth B] MOL2 format, chain W [auth B] MOL2 format, chain X [auth B] MOL2 format, chain U [auth B] MOL2 format, chain RA [auth D] MOL2 format, chain QA [auth D] MOL2 format, chain PA [auth D] MOL2 format, chain NA [auth D] MOL2 format, chain L [auth A] MOL2 format, chain I [auth A] MOL2 format, chain HA [auth C] MOL2 format, chain GA [auth C] MOL2 format, chain EA [auth C] mmCIF format, chain CA [auth C] mmCIF format, chain DA [auth C] mmCIF format, chain FA [auth C] mmCIF format, chain J [auth A] mmCIF format, chain K [auth A] mmCIF format, chain M [auth A] mmCIF format, chain MA [auth D] mmCIF format, chain N [auth A] mmCIF format, chain OA [auth D] mmCIF format, chain S [auth B] mmCIF format, chain T [auth B] mmCIF format, chain V [auth B] mmCIF format, chain W [auth B] mmCIF format, chain X [auth B] mmCIF format, chain U [auth B] mmCIF format, chain RA [auth D] mmCIF format, chain QA [auth D] mmCIF format, chain PA [auth D] mmCIF format, chain NA [auth D] mmCIF format, chain L [auth A] mmCIF format, chain I [auth A] mmCIF format, chain HA [auth C] mmCIF format, chain GA [auth C] mmCIF format, chain EA [auth C]	CA [auth C] DA [auth C] EA [auth C] FA [auth C] GA [auth C] CA [auth C], DA [auth C], EA [auth C], FA [auth C], GA [auth C], HA [auth C], I [auth A], J [auth A], K [auth A], L [auth A], M [auth A], MA [auth D], N [auth A], NA [auth D], OA [auth D], PA [auth D], QA [auth D], RA [auth D], S [auth B], T [auth B], U [auth B], V [auth B], W [auth B], X [auth B]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain CA [auth C] Focus chain DA [auth C] Focus chain EA [auth C] Focus chain FA [auth C] Focus chain GA [auth C] Focus chain HA [auth C] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain MA [auth D] Focus chain N [auth A] Focus chain NA [auth D] Focus chain OA [auth D] Focus chain PA [auth D] Focus chain QA [auth D] Focus chain RA [auth D] Focus chain S [auth B] Focus chain T [auth B] Focus chain U [auth B] Focus chain V [auth B] Focus chain W [auth B] Focus chain X [auth B] Interactions & Density Focus chain CA [auth C] Focus chain DA [auth C] Focus chain EA [auth C] Focus chain FA [auth C] Focus chain GA [auth C] Focus chain HA [auth C] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain MA [auth D] Focus chain N [auth A] Focus chain NA [auth D] Focus chain OA [auth D] Focus chain PA [auth D] Focus chain QA [auth D] Focus chain RA [auth D] Focus chain S [auth B] Focus chain T [auth B] Focus chain U [auth B] Focus chain V [auth B] Focus chain W [auth B] Focus chain X [auth B]