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- EMDB-16672: Pyruvate dehydrogenase complex core (E2, dihydrolipoyl transacetylase) -

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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

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Structure visualization

Supplemental images

emd_16672.png

Downloads & links

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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
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
3.7 Å/pix.
x 128 pix.
= 473.6 Å		3.7 Å/pix.
x 128 pix.
= 473.6 Å		3.7 Å/pix.
x 128 pix.
= 473.6 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 3.7 Å
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Histogram

Histogram (log scale)
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 °

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Supplemental data

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Mask #1

Fileemd_16672_msk_1.map
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Half map: #2

Fileemd_16672_half_map_1.map
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Half map: #1

Fileemd_16672_half_map_2.map
Projections & Slices
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Sample components

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Entire : ruptured mitochondrial membrane samples

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

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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

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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

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Experimental details

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Structure determination

Methodcryo EM
Processingsubtomogram averaging
Aggregation statecell

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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

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: FEI FALCON II (4k x 4k) / Average electron dose: 1.7 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 100.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / 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
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

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
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)
FSC plot (resolution estimation)

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