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- EMDB-76136: SpACSA with AMP and acetyl-CoA -

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Basic information

Entry
Database: EMDB / ID: EMD-76136
TitleSpACSA with AMP and acetyl-CoA
Map data
Sample
  • Complex: SpACSA with acetyl-CoA and AMP
    • Protein or peptide: Acetyl-coenzyme A synthetase
  • Ligand: ADENOSINE MONOPHOSPHATE
  • Ligand: ACETYL COENZYME *A
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 / mitochondrion / ATP binding / 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: 3.2 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: Acta Crystallogr D Struct Biol / Year: 2019
Title: Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix.
Authors: Dorothee Liebschner / Pavel V Afonine / Matthew L Baker / Gábor Bunkóczi / Vincent B Chen / Tristan I Croll / Bradley Hintze / Li Wei Hung / Swati Jain / Airlie J McCoy / Nigel W Moriarty ...Authors: Dorothee Liebschner / Pavel V Afonine / Matthew L Baker / Gábor Bunkóczi / Vincent B Chen / Tristan I Croll / Bradley Hintze / Li Wei Hung / Swati Jain / Airlie J McCoy / Nigel W Moriarty / Robert D Oeffner / Billy K Poon / Michael G Prisant / Randy J Read / Jane S Richardson / David C Richardson / Massimo D Sammito / Oleg V Sobolev / Duncan H Stockwell / Thomas C Terwilliger / Alexandre G Urzhumtsev / Lizbeth L Videau / Christopher J Williams / Paul D Adams /
Abstract: Diffraction (X-ray, neutron and electron) and electron cryo-microscopy are powerful methods to determine three-dimensional macromolecular structures, which are required to understand biological ...Diffraction (X-ray, neutron and electron) and electron cryo-microscopy are powerful methods to determine three-dimensional macromolecular structures, which are required to understand biological processes and to develop new therapeutics against diseases. The overall structure-solution workflow is similar for these techniques, but nuances exist because the properties of the reduced experimental data are different. Software tools for structure determination should therefore be tailored for each method. Phenix is a comprehensive software package for macromolecular structure determination that handles data from any of these techniques. Tasks performed with Phenix include data-quality assessment, map improvement, model building, the validation/rebuilding/refinement cycle and deposition. Each tool caters to the type of experimental data. The design of Phenix emphasizes the automation of procedures, where possible, to minimize repetitive and time-consuming manual tasks, while default parameters are chosen to encourage best practice. A graphical user interface provides access to many command-line features of Phenix and streamlines the transition between programs, project tracking and re-running of previous tasks.
History
DepositionMar 16, 2026-
Header (metadata) releaseJul 22, 2026-
Map releaseJul 22, 2026-
UpdateJul 22, 2026-
Current statusJul 22, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_76136.png

Downloads & links

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Map

FileDownload / File: emd_76136.map.gz / Format: CCP4 / Size: 144.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.86 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)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.86 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.12
Minimum - Maximum-0.3088899 - 0.5982128
Average (Standard dev.)-0.00007307632 (±0.014278399)
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_76136_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_76136_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : SpACSA with acetyl-CoA and AMP

EntireName: SpACSA with acetyl-CoA and AMP
Components
  • Complex: SpACSA with acetyl-CoA and AMP
    • Protein or peptide: Acetyl-coenzyme A synthetase
  • Ligand: ADENOSINE MONOPHOSPHATE
  • Ligand: ACETYL COENZYME *A

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Supramolecule #1: SpACSA with acetyl-CoA and AMP

SupramoleculeName: SpACSA with acetyl-CoA and AMP / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
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: ADENOSINE MONOPHOSPHATE

MacromoleculeName: ADENOSINE MONOPHOSPHATE / type: ligand / ID: 2 / Number of copies: 1 / Formula: AMP
Molecular weightTheoretical: 347.221 Da
Chemical component information

ChemComp-AMP:
ADENOSINE MONOPHOSPHATE / AMP*YM

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Macromolecule #3: ACETYL COENZYME *A

MacromoleculeName: ACETYL COENZYME *A / type: ligand / ID: 3 / Number of copies: 1 / Formula: ACO
Molecular weightTheoretical: 809.571 Da
Chemical component information

ChemComp-ACO:
ACETYL COENZYME *A

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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: 45.0 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 correctionDetails: Initial model built de novo using ModelAngelo from the cryo-EM density map
Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 350438
Initial angle assignmentType: RANDOM ASSIGNMENT
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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