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- EMDB-37969: Structure of mitochondrial soluble protein -

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Basic information

Entry
Database: EMDB / ID: EMD-37969
TitleStructure of mitochondrial soluble protein
Map data
Sample
  • Complex: Structure of mitochondrial soluble protein
    • Protein or peptide: Acetyltransferase component of pyruvate dehydrogenase complex
KeywordsStructure of mitochondrial enzyme complex / TRANSFERASE
Function / homology
Function and homology information


dihydrolipoyllysine-residue acetyltransferase / dihydrolipoyllysine-residue acetyltransferase activity / pyruvate decarboxylation to acetyl-CoA / pyruvate dehydrogenase complex / glucose metabolic process / mitochondrial matrix
Similarity search - Function
Dihydrolipoyllysine-residue acetyltransferase component of pyruvate dehydrogenase complex / Dihydrolipoamide acetyltransferase/Pyruvate dehydrogenase protein X component / Peripheral subunit-binding domain / e3 binding domain / Peripheral subunit-binding (PSBD) domain profile. / E3-binding domain superfamily / 2-oxo acid dehydrogenase, lipoyl-binding site / 2-oxo acid dehydrogenases acyltransferase component lipoyl binding site. / 2-oxoacid dehydrogenase acyltransferase, catalytic domain / 2-oxoacid dehydrogenases acyltransferase (catalytic domain) ...Dihydrolipoyllysine-residue acetyltransferase component of pyruvate dehydrogenase complex / Dihydrolipoamide acetyltransferase/Pyruvate dehydrogenase protein X component / Peripheral subunit-binding domain / e3 binding domain / Peripheral subunit-binding (PSBD) domain profile. / E3-binding domain superfamily / 2-oxo acid dehydrogenase, lipoyl-binding site / 2-oxo acid dehydrogenases acyltransferase component lipoyl binding site. / 2-oxoacid dehydrogenase acyltransferase, catalytic domain / 2-oxoacid dehydrogenases acyltransferase (catalytic domain) / Biotin-requiring enzyme / Biotinyl/lipoyl domain profile. / Biotin/lipoyl attachment / Single hybrid motif / Chloramphenicol acetyltransferase-like domain superfamily
Similarity search - Domain/homology
Acetyltransferase component of pyruvate dehydrogenase complex
Similarity search - Component
Biological speciesSus scrofa (pig)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.66 Å
AuthorsZhang SS / Chen MF
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)21532004, 31570733 China
CitationJournal: Protein Cell / Year: 2025
Title: Molecular architecture of mammalian pyruvate dehydrogenase complex.
Authors: Maofei Chen / Yutong Song / Sensen Zhang / Yitang Zhang / Xudong Chen / Minghui Zhang / Meng Han / Xin Gao / Sai Li / Maojun Yang /
History
DepositionNov 3, 2023-
Header (metadata) releaseNov 6, 2024-
Map releaseNov 6, 2024-
UpdateJan 15, 2025-
Current statusJan 15, 2025Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_37969.png

Downloads & links

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Map

FileDownload / File: emd_37969.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.1 Å/pix.
x 360 pix.
= 395.1 Å		1.1 Å/pix.
x 360 pix.
= 395.1 Å		1.1 Å/pix.
x 360 pix.
= 395.1 Å

Surface

Projections

Slices (1/3)

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.0975 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.019
Minimum - Maximum-0.06881734 - 0.12851226
Average (Standard dev.)0.00061518885 (±0.005583935)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 395.09998 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_37969_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_37969_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Structure of mitochondrial soluble protein

EntireName: Structure of mitochondrial soluble protein
Components
  • Complex: Structure of mitochondrial soluble protein
    • Protein or peptide: Acetyltransferase component of pyruvate dehydrogenase complex

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Supramolecule #1: Structure of mitochondrial soluble protein

SupramoleculeName: Structure of mitochondrial soluble protein / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Sus scrofa (pig)

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Macromolecule #1: Acetyltransferase component of pyruvate dehydrogenase complex

MacromoleculeName: Acetyltransferase component of pyruvate dehydrogenase complex
type: protein_or_peptide / ID: 1 / Number of copies: 60 / Enantiomer: LEVO
Source (natural)Organism: Sus scrofa (pig)
Molecular weightTheoretical: 69.262477 KDa
SequenceString: MWRVCARRAQ NAAPRAGFGA RWTALREEPG APCAAPRAGS VPARCSSTTR GYGRSRALCG WSASSWATPQ NRILLQLWGS PNRRWYSLP PHQKVPLPSL SPTMQAGTIA RWEKKEGDKI NEGELIAEVE TDKATVGFES LEECYMAKIL VAEGTRDVPV G AIICITVE ...String:
MWRVCARRAQ NAAPRAGFGA RWTALREEPG APCAAPRAGS VPARCSSTTR GYGRSRALCG WSASSWATPQ NRILLQLWGS PNRRWYSLP PHQKVPLPSL SPTMQAGTIA RWEKKEGDKI NEGELIAEVE TDKATVGFES LEECYMAKIL VAEGTRDVPV G AIICITVE KPEDIEAFKN YTLDSSAAPA PQAAPAPTPA AAAPAPTPSA QAPGSSYPTH MQVVLPALSP TMTMGTVQRW EK KVGEKLS EGDLLAEIET DKATIGFEVQ EEGYLAKILI PEGTRDVPLG TPLCIIVEKE ADIPAFADYR PTEVTDLKPP APP PTPSPV TPVPPAPQPV APTPAATRPA TPAGPKGRLF VSPLAKKLAS EKGIDLTQIK GTGPDGRIIK KDIDSFVPTK AAPT PAAAV PPPSPGVAPV PTGVFTDIPI SNIRRVIAQR LMQSKQTIPH YYLSVDVNMG EVLLVRKELN KMLEGRSKIS VNDFI IKAS ALACLKVPEA NSSWLDTVIR QNHVVDISVA VSTPAGLITP IVFNAHIKGL ETIANDVVSL ATKAREGKLQ PHEFQG GTF TISNLGMFGI KNFSAIINPP QACILAVGAS EDRLFPADNE KGFDVASMMS VTLSCDHRVV DGAVGAQWLA EFRKYLE KP ITMLL

UniProtKB: Acetyltransferase component of pyruvate dehydrogenase complex

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.5 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.66 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 35220
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION

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