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- PDB-9wnu: Cryo-EM structure of TtCoAT-ADLP complex in NAD+-bound form -

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Basic information

Entry
Database: PDB / ID: 9wnu
TitleCryo-EM structure of TtCoAT-ADLP complex in NAD+-bound form
Components
  • 4-hydroxybutyrate coenzyme A transferase
  • alanine dehydrogenase
KeywordsTRANSFERASE / CoA transferase / alanine dehydrogenase / NAD+ / regulatory protein
Function / homology
Function and homology information


alanine dehydrogenase / L-alanine dehydrogenase (NAD+) activity / L-alanine catabolic process / acetate CoA-transferase activity / acetate metabolic process / plasma membrane
Similarity search - Function
Alanine dehydrogenase / Acetyl-CoA hydrolase/transferase, N-terminal / Acetyl-CoA hydrolase/transferase C-terminal domain / Acetyl-CoA hydrolase/transferase, C-terminal domain superfamily / Acetyl-CoA hydrolase/transferase / Acetyl-CoA hydrolase/transferase N-terminal domain / Acetyl-CoA hydrolase/transferase C-terminal domain / Alanine dehydrogenase/PNT, C-terminal domain / Alanine dehydrogenase/pyridine nucleotide transhydrogenase, N-terminal / Alanine dehydrogenase/PNT, N-terminal domain ...Alanine dehydrogenase / Acetyl-CoA hydrolase/transferase, N-terminal / Acetyl-CoA hydrolase/transferase C-terminal domain / Acetyl-CoA hydrolase/transferase, C-terminal domain superfamily / Acetyl-CoA hydrolase/transferase / Acetyl-CoA hydrolase/transferase N-terminal domain / Acetyl-CoA hydrolase/transferase C-terminal domain / Alanine dehydrogenase/PNT, C-terminal domain / Alanine dehydrogenase/pyridine nucleotide transhydrogenase, N-terminal / Alanine dehydrogenase/PNT, N-terminal domain / Alanine dehydrogenase/PNT, C-terminal domain / Alanine dehydrogenase/PNT, N-terminal domain / Alanine dehydrogenase/pyridine nucleotide transhydrogenase, NAD(H)-binding domain / NagB/RpiA transferase-like / NAD(P)-binding domain superfamily
Similarity search - Domain/homology
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / 4-hydroxybutyrate coenzyme A transferase / alanine dehydrogenase
Similarity search - Component
Biological speciesThermus thermophilus HB27 (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.25 Å
AuthorsYoshida, A. / Miyata, T. / Namba, K. / Nishiyama, M.
Funding support Japan, 4items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)26870113 Japan
Japan Society for the Promotion of Science (JSPS)17J40083 Japan
Japan Society for the Promotion of Science (JSPS)20K05804 Japan
Japan Agency for Medical Research and Development (AMED)JP23ama121003 Japan
CitationJournal: To Be Published
Title: Catalytic regulation of CoA transferase by an NAD+-sensing accessory protein and protein acetylation
Authors: Yoshida, A. / Yamamoto, H. / Miyata, T. / Tomita, T. / Yoshida, M. / Namba, K. / Kosono, S. / Kuzuyama, T. / Nishiyama, M.
History
DepositionSep 5, 2025Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 9, 2026Provider: repository / Type: Initial release
Revision 1.0Sep 9, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Sep 9, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Sep 9, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Sep 9, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Sep 9, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Sep 9, 2026Data content type: Mask / Part number: 1 / Data content type: Mask / Provider: repository / Type: Initial release
Revision 1.0Sep 9, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: alanine dehydrogenase
B: alanine dehydrogenase
C: alanine dehydrogenase
D: alanine dehydrogenase
E: alanine dehydrogenase
F: alanine dehydrogenase
G: 4-hydroxybutyrate coenzyme A transferase
H: 4-hydroxybutyrate coenzyme A transferase
I: 4-hydroxybutyrate coenzyme A transferase
J: 4-hydroxybutyrate coenzyme A transferase
K: 4-hydroxybutyrate coenzyme A transferase
L: 4-hydroxybutyrate coenzyme A transferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)527,11018
Polymers523,13012
Non-polymers3,9816
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein
alanine dehydrogenase / Alanine dehydrogenase-like protein


Mass: 37886.727 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus HB27 (bacteria) / Gene: TT_C1082 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q72IQ0, alanine dehydrogenase
#2: Protein
4-hydroxybutyrate coenzyme A transferase


Mass: 49301.562 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus HB27 (bacteria) / Gene: TT_C1083 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q72IP9
#3: Chemical
ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: NAD*YM
Has ligand of interestY
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Complex of CoA transferase and alanine dehydrogenase-like protein in NAD+-bound form
Type: COMPLEX / Entity ID: #1-#2 / Source: RECOMBINANT
Molecular weightValue: 401 kDa/nm / Experimental value: YES
Source (natural)Organism: Thermus thermophilus HB27 (bacteria)
Source (recombinant)Organism: Escherichia coli BL21(DE3) (bacteria)
Buffer solutionpH: 8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 200 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K

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Electron microscopy imaging

MicroscopyModel: JEOL CRYO ARM 300
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 60000 X / Nominal defocus max: 2000 nm / Nominal defocus min: 500 nm / Cs: 2.7 mm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: JEOL CRYOSPECPORTER
Image recordingAverage exposure time: 4.87 sec. / Electron dose: 80 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) / Num. of grids imaged: 1 / Num. of real images: 6675
EM imaging opticsEnergyfilter name: In-column Omega Filter / Energyfilter slit width: 20 eV
Image scansWidth: 5760 / Height: 4098

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Processing

EM software
IDNameCategory
1Warpparticle selection
2PHENIXmodel refinement
13cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 2281822
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 2.25 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 632783 / Algorithm: FOURIER SPACE / Num. of class averages: 1 / Symmetry type: POINT
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 62.7 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.002331492
ELECTRON MICROSCOPYf_angle_d0.492842877
ELECTRON MICROSCOPYf_chiral_restr0.04444969
ELECTRON MICROSCOPYf_plane_restr0.00475598
ELECTRON MICROSCOPYf_dihedral_angle_d4.64044516

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