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- EMDB-76137: SpACSA with AMPCPP, conformation 1 -

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Basic information

Entry
Database: EMDB / ID: EMD-76137
TitleSpACSA with AMPCPP, conformation 1
Map data
Sample
  • Complex: SpACSA with AMPCPP
    • Protein or peptide: Acetyl-coenzyme A synthetase
  • Ligand: DIPHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER
Keywordsacetyl-CoA synthetase / complex / LIGASE
Function / homology
Function and homology information


Ethanol oxidation / acetate-CoA ligase / acetyl-CoA synthetase activity / acetyl-CoA biosynthetic process / AMP binding / mitochondrial matrix / nucleus / cytosol / cytoplasm
Similarity search - Function
Acetate-CoA ligase / Acetyl-coenzyme A synthetase, N-terminal domain / Acetyl-coenzyme A synthetase N-terminus / ANL, N-terminal domain / AMP-binding enzyme C-terminal domain / AMP-binding enzyme, C-terminal domain / AMP-binding, conserved site / Putative AMP-binding domain signature. / AMP-dependent synthetase/ligase / AMP-binding enzyme / AMP-binding enzyme, C-terminal domain superfamily
Similarity search - Domain/homology
Probable acetyl-coenzyme A synthetase
Similarity search - Component
Biological speciesSchizosaccharomyces pombe (fission yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.3 Å
AuthorsLi M / Zhou M / Marmorstein R
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) United States
CitationJournal: Structure / Year: 2026
Title: Ligand-dependent interdomain rearrangements drive catalysis by acetyl-CoA synthetases.
Authors: Meng Li / Mingyang Zhou / Ronen Marmorstein /
Abstract: Acetyl-coenzyme A synthetases convert ATP, acetate, and coenzyme A (CoA) into acetyl-CoA, a central metabolite that fuels lipid biosynthesis and regulates protein and RNA acetylation. ACS enzymes ...Acetyl-coenzyme A synthetases convert ATP, acetate, and coenzyme A (CoA) into acetyl-CoA, a central metabolite that fuels lipid biosynthesis and regulates protein and RNA acetylation. ACS enzymes contain N- and C-terminal domains that coordinate a two-step ping-pong mechanism involving sequential adenylation and thioester formation at the interdomain interface. How domain motions coordinate these chemical steps remains unclear. Here, we report single-particle cryo-electron microscopy structures of Schizosaccharomyces pombe ACSA captured in apo, pre-adenylation, intermediate, and product states. These structures reveal ligand-dependent reorganization of the C-terminal domain: apo and pre-adenylation forms display increased conformational heterogeneity, whereas intermediate- and product-bound states adopt ordered conformations compatible with catalysis. Structure-guided mutagenesis and in vitro activity assays, together with sequence conservation, support the functional importance and evolutionary conservation of the observed conformational transitions across ACS homologs. These findings establish a ligand-coupled interdomain rearrangement mechanism underlying catalysis by ACS enzymes and a structural framework for inhibitor development.
History
DepositionMar 16, 2026-
Header (metadata) releaseJul 22, 2026-
Map releaseJul 22, 2026-
UpdateAug 19, 2026-
Current statusAug 19, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_76137.png

Downloads & links

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Map

FileDownload / File: emd_76137.map.gz / Format: CCP4 / Size: 144.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
0.86 Å/pix.
x 336 pix.
= 288.96 Å		0.86 Å/pix.
x 336 pix.
= 288.96 Å		0.86 Å/pix.
x 336 pix.
= 288.96 Å

Surface

Projections

Slices (1/3)

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Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.86 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.07
Minimum - Maximum-0.26318803 - 0.52763766
Average (Standard dev.)-0.00020268948 (±0.012615556)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions336336336
Spacing336336336
CellA=B=C: 288.96 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_76137_half_map_1.map
Projections & Slices
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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_76137_half_map_2.map
Projections & Slices
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Histogram

Histogram (log scale)

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Sample components

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Entire : SpACSA with AMPCPP

EntireName: SpACSA with AMPCPP
Components
  • Complex: SpACSA with AMPCPP
    • Protein or peptide: Acetyl-coenzyme A synthetase
  • Ligand: DIPHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER

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Supramolecule #1: SpACSA with AMPCPP

SupramoleculeName: SpACSA with AMPCPP / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1 / Details: AMPCPP is a non-hydrolysable analogue of ATP.
Source (natural)Organism: Schizosaccharomyces pombe (fission yeast)

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Macromolecule #1: Acetyl-coenzyme A synthetase

MacromoleculeName: Acetyl-coenzyme A synthetase / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO / EC number: acetate-CoA ligase
Source (natural)Organism: Schizosaccharomyces pombe (fission yeast)
Molecular weightTheoretical: 74.966695 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MHHHHHHENL YFQSMTKNPV DHTLIIEPPV RLHGDPTVPK PNIASLDEYK RMYEESINDP STFWGNMARD MMTWDKQFST VVQGSIDKA DSAWFADGAI SPCYNLVDRH AIARPDAVAL IYEADEPNQG RYITYRELLA SVSQCAGALQ SMGVGMGDRV A IYMPMIPE ...String:
MHHHHHHENL YFQSMTKNPV DHTLIIEPPV RLHGDPTVPK PNIASLDEYK RMYEESINDP STFWGNMARD MMTWDKQFST VVQGSIDKA DSAWFADGAI SPCYNLVDRH AIARPDAVAL IYEADEPNQG RYITYRELLA SVSQCAGALQ SMGVGMGDRV A IYMPMIPE TIIAMLAIVR LGAIHSVIFA GFSAESVADR VNDSECKVII TADESHRGGK RIPLKGVVNK ALTECPTIKK VL VFQRSAE PTASMVEGRD VWWHDIIPKF PRYCPPAVVN PEHPLFLLYT SGSTGKPKGV VHCTGGYLLG AAATCKYVFD LHP TDRMGC AGDVGWITGH TYIVYGPLML GAATLVFEST PAYPDYSRYW SVVERHRLTQ WYIAPTAIRL LQRAGNEFVK HDRS SLRVL GSVGEPIAPE SFMWYYEVVG EKRCAVADTY WQTETGSHIV TSLGPVTPMK PGSATLPFFG IDAVIIDPLT GKIIE GNDV EGVLAIRSPW PSAARTVWRG HDRYIDTYLK PYPGFYFTGD GATRDKDGYI WIRGRVDDVV NISGHRLSTA EIEAAL LSH DAVAESAVVG VHDELTGQAV NAFILLKPGY EATVELEKEL IMAVRSTIGP FASPRKLIFS DLPKTRSGKI MRRILRK IL AGEVDQIGDL STLADPKVVE HIIHAVHYAH QKKP

UniProtKB: Probable acetyl-coenzyme A synthetase

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Macromolecule #2: DIPHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER

MacromoleculeName: DIPHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER / type: ligand / ID: 2 / Number of copies: 1 / Formula: APC
Molecular weightTheoretical: 505.208 Da
Chemical component information

ChemComp-APC:
DIPHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER / AMP-CPP, energy-carrying molecule analogue*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: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 46.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.5 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Details: Initial models for domains with higher resolution were generated using ModelAngelo. For domains with lower resolution, the initial models were based on a previously determined structure ...Details: Initial models for domains with higher resolution were generated using ModelAngelo. For domains with lower resolution, the initial models were based on a previously determined structure obtained with a different ligand (deposition ID: D_1000305711).
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 98143
Initial angle assignmentType: RANDOM ASSIGNMENT
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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