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- PDB-8rwj: cryoEM structure of Acs1 filament determined by FilamentID -

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Basic information

Entry
Database: PDB / ID: 8rwj
TitlecryoEM structure of Acs1 filament determined by FilamentID
ComponentsAcetyl-coenzyme A synthetase
KeywordsCYTOSOLIC PROTEIN / metabolic enzyme / filament / cryoEM
Function / homology
Function and homology information


acetate-CoA ligase / acetate-CoA ligase activity / acetyl-CoA biosynthetic process from acetate / AMP binding / mitochondrion / ATP binding / cytosol
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, C-terminal domain superfamily / AMP-binding enzyme
Similarity search - Domain/homology
Chem-6R9 / Acetyl-coenzyme A synthetase
Similarity search - Component
Biological speciesSaccharomyces cerevisiae SK1 (yeast)
MethodELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 3.5 Å
AuthorsHugener, J. / Xu, J. / Wettstein, R. / Ioannidi, L. / Velikov, D. / Wollweber, F. / Henggeler, A. / Matos, J. / Pilhofer, M.
Funding support Switzerland, European Union, 2items
OrganizationGrant numberCountry
Swiss National Science Foundation176108 Switzerland
European Research Council (ERC)101002629European Union
CitationJournal: Cell / Year: 2024
Title: FilamentID reveals the composition and function of metabolic enzyme polymers during gametogenesis.
Authors: Jannik Hugener / Jingwei Xu / Rahel Wettstein / Lydia Ioannidi / Daniel Velikov / Florian Wollweber / Adrian Henggeler / Joao Matos / Martin Pilhofer /
Abstract: Gamete formation and subsequent offspring development often involve extended phases of suspended cellular development or even dormancy. How cells adapt to recover and resume growth remains poorly ...Gamete formation and subsequent offspring development often involve extended phases of suspended cellular development or even dormancy. How cells adapt to recover and resume growth remains poorly understood. Here, we visualized budding yeast cells undergoing meiosis by cryo-electron tomography (cryoET) and discovered elaborate filamentous assemblies decorating the nucleus, cytoplasm, and mitochondria. To determine filament composition, we developed a "filament identification" (FilamentID) workflow that combines multiscale cryoET/cryo-electron microscopy (cryoEM) analyses of partially lysed cells or organelles. FilamentID identified the mitochondrial filaments as being composed of the conserved aldehyde dehydrogenase Ald4 and the nucleoplasmic/cytoplasmic filaments as consisting of acetyl-coenzyme A (CoA) synthetase Acs1. Structural characterization further revealed the mechanism underlying polymerization and enabled us to genetically perturb filament formation. Acs1 polymerization facilitates the recovery of chronologically aged spores and, more generally, the cell cycle re-entry of starved cells. FilamentID is broadly applicable to characterize filaments of unknown identity in diverse cellular contexts.
History
DepositionFeb 5, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 26, 2024Provider: repository / Type: Initial release
Revision 1.1Jul 3, 2024Group: Data collection / Database references / Category: citation / em_admin
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.pdbx_database_id_PubMed / _citation.title / _em_admin.last_update

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
D: Acetyl-coenzyme A synthetase
I: Acetyl-coenzyme A synthetase
A: Acetyl-coenzyme A synthetase
B: Acetyl-coenzyme A synthetase
C: Acetyl-coenzyme A synthetase
E: Acetyl-coenzyme A synthetase
F: Acetyl-coenzyme A synthetase
G: Acetyl-coenzyme A synthetase
H: Acetyl-coenzyme A synthetase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)716,93818
Polymers713,4359
Non-polymers3,5039
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein
Acetyl-coenzyme A synthetase


Mass: 79270.570 Da / Num. of mol.: 9 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae SK1 (yeast) / References: UniProt: N1P7N2, acetate-CoA ligase
#2: Chemical
ChemComp-6R9 / [[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] ethanoate


Mass: 389.258 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C12H16N5O8P / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: FILAMENT / 3D reconstruction method: helical reconstruction

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Sample preparation

ComponentName: Acetyl-CoA synthetase 1 filament from spread meiotic yeast spheroplasts
Type: COMPLEX / Entity ID: #1 / Source: NATURAL
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast) / Strain: SK1
Buffer solutionpH: 6.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE-PROPANE

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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: 2800 nm / Nominal defocus min: 1200 nm
Image recordingElectron dose: 60 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

EM software
IDNameVersionCategory
2PHENIX1.14_3260:model refinement
13RELION3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Helical symmertyAngular rotation/subunit: 13.03 ° / Axial rise/subunit: 53.61 Å / Axial symmetry: C3
3D reconstructionResolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 17169 / Symmetry type: HELICAL

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