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- EMDB-66124: Cryo-EM structure of TtCoAT-ADLP complex in NAD+-bound form -

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Basic information

Entry
Database: EMDB / ID: EMD-66124
TitleCryo-EM structure of TtCoAT-ADLP complex in NAD+-bound form
Map data
Sample
  • Complex: Complex of CoA transferase and alanine dehydrogenase-like protein in NAD+-bound form
    • Protein or peptide: alanine dehydrogenase
    • Protein or peptide: 4-hydroxybutyrate coenzyme A transferase
  • Ligand: NICOTINAMIDE-ADENINE-DINUCLEOTIDE
KeywordsCoA transferase / alanine dehydrogenase / NAD+ / regulatory protein / TRANSFERASE
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
4-hydroxybutyrate coenzyme A transferase / alanine dehydrogenase
Similarity search - Component
Biological speciesThermus thermophilus HB27 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.25 Å
AuthorsYoshida A / Miyata T / Namba K / Nishiyama M
Funding support Japan, 4 items
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, 2025-
Header (metadata) releaseSep 9, 2026-
Map releaseSep 9, 2026-
UpdateSep 9, 2026-
Current statusSep 9, 2026Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_66124.png

Downloads & links

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Map

FileDownload / File: emd_66124.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.97 Å/pix.
x 360 pix.
= 348.12 Å		0.97 Å/pix.
x 360 pix.
= 348.12 Å		0.97 Å/pix.
x 360 pix.
= 348.12 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.967 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.133
Minimum - Maximum-1.0779749 - 2.459603
Average (Standard dev.)0.00022093253 (±0.05181239)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 348.12 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_66124_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_66124_half_map_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_66124_half_map_2.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Complex of CoA transferase and alanine dehydrogenase-like protein...

EntireName: Complex of CoA transferase and alanine dehydrogenase-like protein in NAD+-bound form
Components
  • Complex: Complex of CoA transferase and alanine dehydrogenase-like protein in NAD+-bound form
    • Protein or peptide: alanine dehydrogenase
    • Protein or peptide: 4-hydroxybutyrate coenzyme A transferase
  • Ligand: NICOTINAMIDE-ADENINE-DINUCLEOTIDE

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Supramolecule #1: Complex of CoA transferase and alanine dehydrogenase-like protein...

SupramoleculeName: Complex of CoA transferase and alanine dehydrogenase-like protein in NAD+-bound form
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Thermus thermophilus HB27 (bacteria)
Molecular weightTheoretical: 401 kDa/nm

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Macromolecule #1: alanine dehydrogenase

MacromoleculeName: alanine dehydrogenase / type: protein_or_peptide / ID: 1 / Number of copies: 6 / Enantiomer: LEVO / EC number: alanine dehydrogenase
Source (natural)Organism: Thermus thermophilus HB27 (bacteria)
Molecular weightTheoretical: 37.886727 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MASWSHPQFE KGGMEFGVPK ERSGGEIPER RVPLTPQGVR ELVASGHRVY VERGAGEGAG FPDEAYEEAG ARLVGREEAF GRPQVVLKV ARPTLEEVGL MRKNAVLMAF LHLAVAESPL VEAMAQKGLT AIGYELVGEE GRRPVLKAMS EIAGRMAPQL A GRLLEAPQ ...String:
MASWSHPQFE KGGMEFGVPK ERSGGEIPER RVPLTPQGVR ELVASGHRVY VERGAGEGAG FPDEAYEEAG ARLVGREEAF GRPQVVLKV ARPTLEEVGL MRKNAVLMAF LHLAVAESPL VEAMAQKGLT AIGYELVGEE GRRPVLKAMS EIAGRMAPQL A GRLLEAPQ GPGILLSGLV GIPPADVVVL GAGVLGRAAA RAFLGAGASV HLLDRALPPL EEAAREAPGA ITALVTQDRL ER YVAFADV LVGAVAVPGE RTPLLLTRGL LARMRPGSVL LDFSIDQGGV SETSRPGVYQ EMGVTHFCLP NVPALVPRTA SHA LTATLL PYLLRIQEDP LALPGLRQGA YLLFGEKGGH LE

UniProtKB: alanine dehydrogenase

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Macromolecule #2: 4-hydroxybutyrate coenzyme A transferase

MacromoleculeName: 4-hydroxybutyrate coenzyme A transferase / type: protein_or_peptide / ID: 2 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Thermus thermophilus HB27 (bacteria)
Molecular weightTheoretical: 49.301562 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MSYRKKLTSP EDAVGLIRSG MRVFVSGNAA TPTPLLKALA ARKDELENVE LVHLLQMGED PFASLEMEGH FRRRSLFVGP ADREAVNQG RADYVPVMLH QVPWLFKRGI LPLDAAIVQV SPPDEHGFCS LGVEVIATKA AVETAPIVIA MVNPRMPRTL G DTFVHVSR ...String:
MSYRKKLTSP EDAVGLIRSG MRVFVSGNAA TPTPLLKALA ARKDELENVE LVHLLQMGED PFASLEMEGH FRRRSLFVGP ADREAVNQG RADYVPVMLH QVPWLFKRGI LPLDAAIVQV SPPDEHGFCS LGVEVIATKA AVETAPIVIA MVNPRMPRTL G DTFVHVSR FTAIVEVDWP LPELKREGFG EVERRIGEHV AGLIEDGATL QMGIGAIPDA VLASLEGRRD LGVHTEMISD GV LEAWEKG LITGAKKSLH PGKIVGTFVL GSERLYRFVH DNPLFELHPA DYVNDPFVIA QNRKMVAINS AIEVDLTGQV VAD SIGTRI YSGFGGQLDF IRGAARSEGG RPIIALPSTA KGQSRIVPFL KPGAGVVTTR ADVHYVVTEW GVAELFGRSL RERA KALIA IAHPDFREAL LQGAWERGLL PRGYPGVDLK GLEEKRGRPH HHHHH

UniProtKB: 4-hydroxybutyrate coenzyme A transferase

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Macromolecule #3: NICOTINAMIDE-ADENINE-DINUCLEOTIDE

MacromoleculeName: NICOTINAMIDE-ADENINE-DINUCLEOTIDE / type: ligand / ID: 3 / Number of copies: 6 / Formula: NAD
Molecular weightTheoretical: 663.425 Da
Chemical component information

ChemComp-NAD:
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / NAD*YM

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 8
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 200 / Support film - Material: CARBON / Support film - topology: HOLEY ARRAY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 20 sec.
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeJEOL CRYO ARM 300
Specialist opticsEnergy filter - Name: In-column Omega Filter / Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Digitization - Dimensions - Width: 5760 pixel / Digitization - Dimensions - Height: 4098 pixel / Number grids imaged: 1 / Number real images: 6675 / Average exposure time: 4.87 sec. / Average electron dose: 80.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.5 µm / Nominal magnification: 60000
Sample stageSpecimen holder model: JEOL CRYOSPECPORTER / Cooling holder cryogen: NITROGEN

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Image processing

Particle selectionNumber selected: 2281822
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C1 (asymmetric) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 2.25 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 632783
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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