[English] 日本語
Yorodumi
- EMDB-19549: cryoEM structure of the central Ald4 filament determined by FilamentID -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-19549
TitlecryoEM structure of the central Ald4 filament determined by FilamentID
Map data
Sample
  • Complex: Ald4 polymers from the spread mitochondria of meiotic yeast cells
    • Protein or peptide: Potassium-activated aldehyde dehydrogenase, mitochondrial
  • Ligand: NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
Keywordsmetabolic enzyme / filament / cryoEM / CYTOSOLIC PROTEIN
Function / homology
Function and homology information


Metabolism of serotonin / Smooth Muscle Contraction / Fructose catabolism / Ethanol oxidation / RA biosynthesis pathway / aldehyde dehydrogenase (NADP+) / acetate biosynthetic process / ethanol metabolic process / aldehyde dehydrogenase [NAD(P)+] activity / NADPH regeneration ...Metabolism of serotonin / Smooth Muscle Contraction / Fructose catabolism / Ethanol oxidation / RA biosynthesis pathway / aldehyde dehydrogenase (NADP+) / acetate biosynthetic process / ethanol metabolic process / aldehyde dehydrogenase [NAD(P)+] activity / NADPH regeneration / Oxidoreductases; Acting on the aldehyde or oxo group of donors; With NAD+ or NADP+ as acceptor / Mitochondrial protein degradation / aldehyde dehydrogenase (NAD+) activity / pyruvate metabolic process / mitochondrial nucleoid / mitochondrion
Similarity search - Function
Aldehyde dehydrogenase, glutamic acid active site / Aldehyde dehydrogenases glutamic acid active site. / Aldehyde dehydrogenase, cysteine active site / Aldehyde dehydrogenases cysteine active site. / Aldehyde dehydrogenase domain / Aldehyde dehydrogenase family / Aldehyde dehydrogenase, N-terminal / Aldehyde dehydrogenase, C-terminal / Aldehyde/histidinol dehydrogenase
Similarity search - Domain/homology
Potassium-activated aldehyde dehydrogenase, mitochondrial
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast) / Saccharomyces cerevisiae SK1 (yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.8 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_19549.png

Downloads & links

-
Map

FileDownload / File: emd_19549.map.gz / Format: CCP4 / Size: 30.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1.1 Å
Density
Contour LevelBy AUTHOR: 0.025
Minimum - Maximum-0.07571765 - 0.13205372
Average (Standard dev.)0.00033282005 (±0.0045615667)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions200200200
Spacing200200200
CellA=B=C: 220.0 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Mask #1

Fileemd_19549_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Additional map: cryoEM map that is further processed by DeepEMhancer.

Fileemd_19549_additional_1.map
AnnotationcryoEM map that is further processed by DeepEMhancer.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #2

Fileemd_19549_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_19549_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Ald4 polymers from the spread mitochondria of meiotic yeast cells

EntireName: Ald4 polymers from the spread mitochondria of meiotic yeast cells
Components
  • Complex: Ald4 polymers from the spread mitochondria of meiotic yeast cells
    • Protein or peptide: Potassium-activated aldehyde dehydrogenase, mitochondrial
  • Ligand: NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE

-
Supramolecule #1: Ald4 polymers from the spread mitochondria of meiotic yeast cells

SupramoleculeName: Ald4 polymers from the spread mitochondria of meiotic yeast cells
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast) / Strain: SK1

-
Macromolecule #1: Potassium-activated aldehyde dehydrogenase, mitochondrial

MacromoleculeName: Potassium-activated aldehyde dehydrogenase, mitochondrial
type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO
EC number: Oxidoreductases; Acting on the aldehyde or oxo group of donors; With NAD+ or NADP+ as acceptor
Source (natural)Organism: Saccharomyces cerevisiae SK1 (yeast)
Molecular weightTheoretical: 56.787391 KDa
SequenceString: MFSRSTLCLK TSASSIGRLQ LRYFSHLPMT VPIKLPNGLE YEQPTGLFIN NKFVPSKQNK TFEVINPSTE EEICHIYEGR EDDVEEAVQ AADRAFSNGS WNGIDPIDRG KALYRLAELI EQDKDVIASI ETLDNGKAIS SSRGDVDLVI NYLKSSAGFA D KIDGRMID ...String:
MFSRSTLCLK TSASSIGRLQ LRYFSHLPMT VPIKLPNGLE YEQPTGLFIN NKFVPSKQNK TFEVINPSTE EEICHIYEGR EDDVEEAVQ AADRAFSNGS WNGIDPIDRG KALYRLAELI EQDKDVIASI ETLDNGKAIS SSRGDVDLVI NYLKSSAGFA D KIDGRMID TGRTHFSYTK RQPLGVCGQI IPWNFPLLMW AWKIAPALVT GNTVVLKTAE STPLSALYVS KYIPQAGIPP GV INIVSGF GKIVGEAITN HPKIKKVAFT GSTATGRHIY QSAAAGLKKV TLELGGKSPN IVFADAELKK AVQNIILGIY YNS GEVCCA GSRVYVEESI YDKFIEEFKA ASESIKVGDP FDESTFQGAQ TSQMQLNKIL KYVDIGKNEG ATLITGGERL GSKG YFIKP TVFGDVKEDM RIVKEEIFGP VVTVTKFKSA DEVINMANDS EYGLAAGIHT SNINTALKVA DRVNAGTVWI NTYND FHHA VPFGGFNASG LGREMSVDAL QNYLQVKAVR AKLDE

UniProtKB: Potassium-activated aldehyde dehydrogenase, mitochondrial

-
Macromolecule #2: NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE

MacromoleculeName: NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / type: ligand / ID: 2 / Number of copies: 4 / Formula: NAP
Molecular weightTheoretical: 743.405 Da
Chemical component information

ChemComp-NAP:
NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation statehelical array

-
Sample preparation

BufferpH: 7.2
VitrificationCryogen name: ETHANE-PROPANE

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k 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

Startup modelType of model: OTHER
Details: the initial model is determined by sub-tomogram averaging of the same filament in the purified mitochondria.
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number images used: 29307
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION

+
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