9WNU | pdb_00009wnu

Cryo-EM structure of TtCoAT-ADLP complex in NAD+-bound form

• PDB DOI: https://doi.org/10.2210/pdb9WNU/pdb
• EM Map EMD-66124: EMDB EMDataResource

• Classification: TRANSFERASE
• Organism(s): Thermus thermophilus HB27
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2025-09-05 Released: 2026-09-09 
• Deposition Author(s): Yoshida, A., Miyata, T., Namba, K., Nishiyama, M.
• Funding Organization(s): Japan Society for the Promotion of Science (JSPS), Japan Agency for Medical Research and Development (AMED)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 2.25 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Catalytic regulation of CoA transferase by an NAD+-sensing accessory protein and protein acetylation

Yoshida, A., Yamamoto, H., Miyata, T., Tomita, T., Yoshida, M., Namba, K., Kosono, S., Kuzuyama, T., Nishiyama, M.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 12-mer - A6B4C1D1 

Local Symmetry: Dihedral - D3  (Explore in 3D)
Local Stoichiometry: Homo 6-mer - A6 Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - B2 Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - B2 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 527.11 kDa 
• Atom Count: 30,852 
• Modeled Residue Count: 4,148 
• Deposited Residue Count: 4,848 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
alanine dehydrogenase	A, B, C, D, E, F	358	Thermus thermophilus HB27	Mutation(s): 0  Gene Names: TT_C1082 EC: 1.4.1.1
UniProt
Find proteins for Q72IQ0 (Thermus thermophilus (strain ATCC BAA-163 / DSM 7039 / HB27)) Explore Q72IQ0  Go to UniProtKB:  Q72IQ0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
4-hydroxybutyrate coenzyme A transferase	G, H, I, J, K, L	450	Thermus thermophilus HB27	Mutation(s): 0  Gene Names: TT_C1083
UniProt
Find proteins for Q72IP9 (Thermus thermophilus (strain ATCC BAA-163 / DSM 7039 / HB27)) Explore Q72IP9  Go to UniProtKB:  Q72IP9

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAD (Subject of Investigation/LOI)	M [auth A], N [auth B], O [auth C], P [auth D], Q [auth E], R [auth F]	NICOTINAMIDE-ADENINE-DINUCLEOTIDE C21 H27 N7 O14 P2 BAWFJGJZGIEFAR-NNYOXOHSSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 2.25 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX
RECONSTRUCTION	cryoSPARC

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2026-09-09 
Deposition Author(s): Yoshida, A., Miyata, T., Namba, K., Nishiyama, M.

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Funding Organization	Location	Grant Number
Japan Society for the Promotion of Science (JSPS)	Japan	26870113
Japan Society for the Promotion of Science (JSPS)	Japan	17J40083
Japan Society for the Promotion of Science (JSPS)	Japan	20K05804
Japan Agency for Medical Research and Development (AMED)	Japan	JP23ama121003

Revision History  

• Version 1.0: 2026-09-09
  Type: Initial release