[English] 日本語
Yorodumi
- EMDB-16672: Pyruvate dehydrogenase complex core (E2, dihydrolipoyl transacetylase) -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-16672
TitlePyruvate dehydrogenase complex core (E2, dihydrolipoyl transacetylase)
Map dataPyruvate dehydrogenase complex core
Sample
  • Organelle or cellular component: ruptured mitochondrial membrane samples
    • Protein or peptide: dihydrolipoyl transacetylase
Keywordstransferase / dodecahedron / mitochondrion
Biological speciesRattus norvegicus (Norway rat)
Methodsubtomogram averaging / cryo EM / Resolution: 17.0 Å
AuthorsPlokhikh KS / Chesnokov YM
Funding support1 items
OrganizationGrant numberCountry
Other government
CitationJournal: FEBS J / Year: 2024
Title: Association of 2-oxoacid dehydrogenase complexes with respirasomes in mitochondria.
Authors: Konstantin S Plokhikh / Semen V Nesterov / Yuriy M Chesnokov / Anton G Rogov / Roman A Kamyshinsky / Aleksandr L Vasiliev / Lev S Yaguzhinsky / Raif G Vasilov /
Abstract: In the present study, cryo-electron tomography was used to investigate the localization of 2-oxoacid dehydrogenase complexes (OADCs) in cardiac mitochondria and mitochondrial inner membrane samples. ...In the present study, cryo-electron tomography was used to investigate the localization of 2-oxoacid dehydrogenase complexes (OADCs) in cardiac mitochondria and mitochondrial inner membrane samples. Two classes of ordered OADC inner cores with different symmetries were distinguished and their quaternary structures modeled. One class corresponds to pyruvate dehydrogenase complexes and the other to dehydrogenase complexes of α-ketoglutarate and branched-chain α-ketoacids. OADCs were shown to be localized in close proximity to membrane-embedded respirasomes, as observed both in densely packed lamellar cristae of cardiac mitochondria and in ruptured mitochondrial samples where the dense packing is absent. This suggests the specificity of the OADC-respirasome interaction, which allows localized NADH/NAD exchange between OADCs and complex I of the respiratory chain. The importance of this local coupling is based on OADCs being the link between respiration, glycolysis and amino acid metabolism. The coupling of these basic metabolic processes can vary in different tissues and conditions and may be involved in the development of various pathologies. The present study shows that this important and previously missing parameter of mitochondrial complex coupling can be successfully assessed using cryo-electron tomography.
History
DepositionFeb 9, 2023-
Header (metadata) releaseOct 11, 2023-
Map releaseOct 11, 2023-
UpdateJan 17, 2024-
Current statusJan 17, 2024Processing site: PDBe / Status: Released

-
Structure visualization

Supplemental images

emd_16672.png

Downloads & links

-
Map

FileDownload / File: emd_16672.map.gz / Format: CCP4 / Size: 8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationPyruvate dehydrogenase complex core
Voxel sizeX=Y=Z: 3.7 Å
Density
Contour LevelBy AUTHOR: 12.0
Minimum - Maximum-33.359859999999998 - 54.073512999999998
Average (Standard dev.)0.7587497 (±5.3990088)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions128128128
Spacing128128128
CellA=B=C: 473.6 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Mask #1

Fileemd_16672_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #2

Fileemd_16672_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_16672_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : ruptured mitochondrial membrane samples

EntireName: ruptured mitochondrial membrane samples
Components
  • Organelle or cellular component: ruptured mitochondrial membrane samples
    • Protein or peptide: dihydrolipoyl transacetylase

-
Supramolecule #1: ruptured mitochondrial membrane samples

SupramoleculeName: ruptured mitochondrial membrane samples / type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Rattus norvegicus (Norway rat) / Strain: Wistar rat / Organ: heart / Tissue: cardiac muscle / Organelle: mitochondrion / Location in cell: mitochondrion matrix

-
Macromolecule #1: dihydrolipoyl transacetylase

MacromoleculeName: dihydrolipoyl transacetylase / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO / EC number: dihydrolipoyllysine-residue acetyltransferase
Source (natural)Organism: Rattus norvegicus (Norway rat) / Strain: Wistar rat / Organ: heart / Tissue: cardiac muscle
SequenceString: MWRVCARRVQ SAVPRAGFRA RWATLKGPRT GPAAVRCGSG IPSYGVRSLC GWSYGSATVP RNRILQQLLG SPSRRSYSLP PHQKVPLPSL SPTMQAGTIA RWEKKEGEKI SEGDLIAEVE TDKATVGFES LEECYMAKIL VPEGTRDVPV GSIICITVEK PQDIEAFKNY ...String:
MWRVCARRVQ SAVPRAGFRA RWATLKGPRT GPAAVRCGSG IPSYGVRSLC GWSYGSATVP RNRILQQLLG SPSRRSYSLP PHQKVPLPSL SPTMQAGTIA RWEKKEGEKI SEGDLIAEVE TDKATVGFES LEECYMAKIL VPEGTRDVPV GSIICITVEK PQDIEAFKNY TLDSATAATQ AAPAPAAAPA AAPAAPSASA PGSSYPVHMQ IVLPALSPTM TMGTVQRWEK KVGEKLSEGD LLAEIETDKA TIGFEVQEEG YLAKILVPEG TRDVPLGTPL CIIVEKQEDI AAFADYRPTE VTSLKPQAPP PVPPPVAAVP PIPQPLAPTP SAAPAGPKGR VFVSPLAKKL AAEKGIDLTQ VKGTGPEGRI IKKDIDSFVP TKAAPAAAAA APPGPRVAPT PAGVFIDIPI SNIRRVIAQR LMQSKQTIPH YYLSVDVNMG EVLLVRKELN KMLEGKGKIS VNDFIIKASA LACLKVPEAN SSWMDTVIRQ NHVVDVSVAV STPAGLITPI VFNAHIKGLE TIASDVVSLA SKAREGKLQP HEFQGGTFTI SNLGMFGIKN FSAIINPPQA CILAIGASED KLIPADNEKG FDVASVMSVT LSCDHRVVDG AVGAQWLAEF KKYLEKPVTM LL

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsubtomogram averaging
Aggregation statecell

-
Sample preparation

BufferpH: 7.4 / Component - Concentration: 10.0 mM / Component - Name: Hepes/KOH
GridModel: EMS Lacey Carbon / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: LACEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec. / Pretreatment - Atmosphere: AIR / Pretreatment - Pressure: 0.026000000000000002 kPa
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 100.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 8.0 µm / Nominal defocus min: 6.0 µm / Nominal magnification: 18000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Image recordingFilm or detector model: FEI FALCON II (4k x 4k) / Average electron dose: 1.7 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

-
Image processing

ExtractionNumber tomograms: 3 / Number images used: 73 / Method: manual / Software - Name: IMOD (ver. 4.11.15)
Final 3D classificationSoftware - Name: RELION (ver. 4.0)
Final angle assignmentType: OTHER / Software - Name: IMOD (ver. 4.11.15)
Final reconstructionApplied symmetry - Point group: I (icosahedral) / Resolution.type: BY AUTHOR / Resolution: 17.0 Å / Resolution method: FSC 0.143 CUT-OFF / Number subtomograms used: 73
FSC plot (resolution estimation)

+
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://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