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- PDB-8dh7: Cryo-EM structure of Saccharomyces cerevisiae Succinyl-CoA:acetat... -

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Basic information

Entry
Database: PDB / ID: 8dh7
TitleCryo-EM structure of Saccharomyces cerevisiae Succinyl-CoA:acetate CoA-transferase (Ach1p)
ComponentsAcetyl-CoA hydrolase
KeywordsTRANSFERASE / Ach1p / Succinyl-CoA / acetate CoA-transferase
Function / homology
Function and homology information


acetyl-CoA hydrolase / acetyl-CoA hydrolase activity / acetate CoA-transferase activity / acetate metabolic process / mitochondrion / cytosol
Similarity search - Function
Glutaconate Coenzyme A-transferase / Glutaconate Coenzyme A-transferase / 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 / NagB/RpiA transferase-like / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Acetyl-CoA hydrolase
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.99 Å
AuthorsGodoy, A.S. / Song, Y. / Cheruvara, H. / Quigley, A. / Oliva, G.
Funding support Brazil, 1items
OrganizationGrant numberCountry
Sao Paulo Research Foundation (FAPESP)2013/07600-3 Brazil
CitationJournal: To Be Published
Title: Cryo-EM structure of Saccharomyces cerevisiae cytochrome c oxidase (Complex IV) extracted in lipid nanodiscs
Authors: Godoy, A.S. / Song, Y. / Cheruvara, H. / Quigley, A. / Oliva, G.
History
DepositionJun 25, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 20, 2022Provider: repository / Type: Initial release
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Revision 1.0Jul 20, 2022Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
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Revision 1.0Jul 20, 2022Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
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Revision 1.1Feb 14, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Revision 1.2May 21, 2025Group: Data collection / Structure summary / Category: em_admin / em_software / pdbx_entry_details / Item: _em_admin.last_update / _em_software.name
Revision 1.1May 21, 2025Data content type: EM metadata / Data content type: EM metadata / EM metadata / Group: Data processing / Experimental summary / Data content type: EM metadata / EM metadata / Category: em_admin / em_software / Data content type: EM metadata / EM metadata / Item: _em_admin.last_update / _em_software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: Acetyl-CoA hydrolase
A: Acetyl-CoA hydrolase


Theoretical massNumber of molelcules
Total (without water)117,5842
Polymers117,5842
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein Acetyl-CoA hydrolase / Acetyl-CoA deacylase / Acetyl-CoA acylase


Mass: 58791.785 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P32316, acetyl-CoA hydrolase
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: Succinyl-CoA:acetate CoA-transferase / Type: COMPLEX / Entity ID: all / Source: NATURAL
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Buffer solutionpH: 7
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 3100 nm / Nominal defocus min: 1000 nm
Image recordingElectron dose: 0.989314222 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.19.2_4158: / Classification: refinement
EM softwareName: PHENIX / Category: model refinement
CTF correctionType: NONE
SymmetryPoint symmetry: C2 (2 fold cyclic)
3D reconstructionResolution: 2.99 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 82557 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0038470
ELECTRON MICROSCOPYf_angle_d0.52811494
ELECTRON MICROSCOPYf_dihedral_angle_d4.5731130
ELECTRON MICROSCOPYf_chiral_restr0.0451268
ELECTRON MICROSCOPYf_plane_restr0.0051514

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