[English] 日本語
Yorodumi
- EMDB-19548: cryoEM structure of Acs1 filament determined by FilamentID -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-19548
TitlecryoEM structure of Acs1 filament determined by FilamentID
Map data
Sample
  • Complex: Acetyl-CoA synthetase 1 filament from spread meiotic yeast spheroplasts
    • Protein or peptide: Acetyl-coenzyme A synthetase
  • Ligand: [[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] ethanoate
Keywordsmetabolic enzyme / filament / cryoEM / CYTOSOLIC PROTEIN
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
Acetyl-coenzyme A synthetase
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast) / Saccharomyces cerevisiae SK1 (yeast)
Methodhelical 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, 2 items
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, 2024-
Header (metadata) releaseJun 26, 2024-
Map releaseJun 26, 2024-
UpdateJul 3, 2024-
Current statusJul 3, 2024Processing site: PDBe / Status: Released

-
Structure visualization

Supplemental images

emd_19548.png

Downloads & links

-
Map

FileDownload / File: emd_19548.map.gz / Format: CCP4 / Size: 52.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1.07 Å
Density
Contour LevelBy AUTHOR: 0.012
Minimum - Maximum-0.04811491 - 0.08490145
Average (Standard dev.)0.00039581815 (±0.0041219834)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions240240240
Spacing240240240
CellA=B=C: 256.80002 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Mask #1

Fileemd_19548_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Additional map: cryoEM map further improved by deepEMhancer

Fileemd_19548_additional_1.map
AnnotationcryoEM map further improved by deepEMhancer
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #2

Fileemd_19548_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_19548_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Acetyl-CoA synthetase 1 filament from spread meiotic yeast sphero...

EntireName: Acetyl-CoA synthetase 1 filament from spread meiotic yeast spheroplasts
Components
  • Complex: Acetyl-CoA synthetase 1 filament from spread meiotic yeast spheroplasts
    • Protein or peptide: Acetyl-coenzyme A synthetase
  • Ligand: [[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] ethanoate

-
Supramolecule #1: Acetyl-CoA synthetase 1 filament from spread meiotic yeast sphero...

SupramoleculeName: Acetyl-CoA synthetase 1 filament from spread meiotic yeast spheroplasts
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast) / Strain: SK1

-
Macromolecule #1: Acetyl-coenzyme A synthetase

MacromoleculeName: Acetyl-coenzyme A synthetase / type: protein_or_peptide / ID: 1 / Number of copies: 9 / Enantiomer: LEVO / EC number: acetate-CoA ligase
Source (natural)Organism: Saccharomyces cerevisiae SK1 (yeast)
Molecular weightTheoretical: 79.27057 KDa
SequenceString: MSPSAVQSSK LEEQSSEIDK LKAKMSQSAS TAQQKKEHEY EHLTSVKIVP QRPISDRLQP AIATHYSPHL DGLQDYQRLH KESIEDPAK FFGSKATQFL NWSKPFDKVF IPDSKTGRPS FQNNAWFLNG QLNACYNCVD RHALKTPNKK AIIFEGDEPG Q GYSITYKE ...String:
MSPSAVQSSK LEEQSSEIDK LKAKMSQSAS TAQQKKEHEY EHLTSVKIVP QRPISDRLQP AIATHYSPHL DGLQDYQRLH KESIEDPAK FFGSKATQFL NWSKPFDKVF IPDSKTGRPS FQNNAWFLNG QLNACYNCVD RHALKTPNKK AIIFEGDEPG Q GYSITYKE LLEEVCQVAQ VLTYSMGVRK GDTVAVYMPM VPEAIITLLA ISRIGAIHSV VFAGFSSNSL RDRINDGDSK VV ITTDESN RGGKVIETKR IVDDALRETP GVRHVLVYRK TNNPSVAFHA PRDLDWATEK KKYKTYYPCT PVDSEDPLFL LYT SGSTGA PKGVQHSTAG YLLGALLTMR YTFDTHQEDV FFTAGDIGWI TGHTYVVYGP LLYGCATLVF EGTPAYPNYS RYWD IIDEH KVTQFYVAPT ALRLLKRAGD SYIENHSLKS LRCLGSVGEP IAAEVWEWYS EKIGKNEIPI VDTYWQTESG SHLVT PLAG GVTPMKPGSA SFPFFGIDAV VLDPNTGEEL NTSHAEGVLA VKAAWPSFAR TIWKNHDRYL DTYLNPYPGY YFTGDG AAK DKDGYIWILG RVDDVVNVSG HRLSTAEIEA AIIEDPIVAE CAVVGFNDDL TGQAVAAFVV LKNKSNWSTA TDDELQD IK KHLVFTVRKD IGPFAAPKLI ILVDDLPKTR SGKIMRRILR KILAGESDQL GDVSTLSNPG IVRHLIDSVK L

UniProtKB: Acetyl-coenzyme A synthetase

-
Macromolecule #2: [[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidany...

MacromoleculeName: [[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] ethanoate
type: ligand / ID: 2 / Number of copies: 9 / Formula: 6R9
Molecular weightTheoretical: 389.258 Da
Chemical component information

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

-
Experimental details

-
Structure determination

Methodcryo EM
Processinghelical reconstruction
Aggregation statefilament

-
Sample preparation

BufferpH: 6.4
VitrificationCryogen name: ETHANE-PROPANE

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.8000000000000003 µm / Nominal defocus min: 1.2 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

-
Image processing

Final reconstructionApplied symmetry - Helical parameters - Δz: 53.61 Å
Applied symmetry - Helical parameters - Δ&Phi: 13.03 °
Applied symmetry - Helical parameters - Axial symmetry: C3 (3 fold cyclic)
Resolution.type: BY AUTHOR / Resolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number images used: 17169
Startup modelType of model: OTHER
Details: the initial model is determined from sub-tomogram averaged volume of spread spheroplast.
Final angle assignmentType: NOT APPLICABLE

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbjlvh1.pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more