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- EMDB-0138: core of the human pyruvate dehydrogenase -

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Basic information

Entry
Database: EMDB / ID: EMD-0138
Titlecore of the human pyruvate dehydrogenase
Map data
Sample
  • Complex: single particle cryo EM-derived map of the full-length native human E2-E3BP core of the pyruvate dehydrogenase multienzyme complex
    • Protein or peptide: Dihydrolipoyllysine-residue acetyltransferase component of pyruvate dehydrogenase complex, mitochondrial
KeywordsPyruvate dehydrogenase / human / OXIDOREDUCTASE
Function / homology
Function and homology information


PDH complex synthesizes acetyl-CoA from PYR / dihydrolipoyllysine-residue acetyltransferase / dihydrolipoyllysine-residue acetyltransferase activity / acetyl-CoA biosynthetic process from pyruvate / Regulation of pyruvate dehydrogenase (PDH) complex / Protein lipoylation / pyruvate dehydrogenase complex / Signaling by Retinoic Acid / acyltransferase activity / tricarboxylic acid cycle ...PDH complex synthesizes acetyl-CoA from PYR / dihydrolipoyllysine-residue acetyltransferase / dihydrolipoyllysine-residue acetyltransferase activity / acetyl-CoA biosynthetic process from pyruvate / Regulation of pyruvate dehydrogenase (PDH) complex / Protein lipoylation / pyruvate dehydrogenase complex / Signaling by Retinoic Acid / acyltransferase activity / tricarboxylic acid cycle / glucose metabolic process / mitochondrial matrix / intracellular membrane-bounded organelle / mitochondrion / identical protein binding
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
Pyruvate dehydrogenase protein X component, mitochondrial / Dihydrolipoyllysine-residue acetyltransferase component of pyruvate dehydrogenase complex, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 6.0 Å
AuthorsHaselbach D / Prajapati S
Funding support Germany, 1 items
OrganizationGrant numberCountry
German Research FoundationSFB860 Germany
CitationJournal: Structure / Year: 2019
Title: Structural and Functional Analyses of the Human PDH Complex Suggest a "Division-of-Labor" Mechanism by Local E1 and E3 Clusters.
Authors: Sabin Prajapati / David Haselbach / Sabine Wittig / Mulchand S Patel / Ashwin Chari / Carla Schmidt / Holger Stark / Kai Tittmann /
Abstract: The pseudo-atomic structural model of human pyruvate dehydrogenase complex (PDHc) core composed of full-length E2 and E3BP components, calculated from our cryoelectron microscopy-derived density maps ...The pseudo-atomic structural model of human pyruvate dehydrogenase complex (PDHc) core composed of full-length E2 and E3BP components, calculated from our cryoelectron microscopy-derived density maps at 6-Å resolution, is similar to those of prokaryotic E2 structures. The spatial organization of human PDHc components as evidenced by negative-staining electron microscopy and native mass spectrometry is not homogeneous, and entails the unanticipated formation of local clusters of E1:E2 and E3BP:E3 complexes. Such uneven, clustered organization translates into specific duties for E1-E2 clusters (oxidative decarboxylation and acetyl transfer) and E3BP-E3 clusters (regeneration of reduced lipoamide) corresponding to half-reactions of the PDHc catalytic cycle. The addition of substrate coenzyme A modulates the conformational landscape of PDHc, in particular of the lipoyl domains, extending the postulated multiple random coupling mechanism. The conformational and associated chemical landscapes of PDHc are thus not determined entirely stochastically, but are restrained and channeled through an asymmetric architecture and further modulated by substrate binding.
History
DepositionJul 23, 2018-
Header (metadata) releaseSep 5, 2018-
Map releaseJun 5, 2019-
UpdateMay 15, 2024-
Current statusMay 15, 2024Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.06
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.06
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6h55
  • Surface level: 0.06
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6h60
  • Surface level: 0.06
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-6h55
  • Imaged by Jmol
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-6h60
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_0138.png

Downloads & links

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Map

FileDownload / File: emd_0138.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.27 Å/pix.
x 256 pix.
= 325.12 Å		1.27 Å/pix.
x 256 pix.
= 325.12 Å		1.27 Å/pix.
x 256 pix.
= 325.12 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.27 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.06 / Movie #1: 0.06
Minimum - Maximum-0.11762706 - 0.29477248
Average (Standard dev.)0.003969073 (±0.020067863)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 325.12 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.271.271.27
M x/y/z256256256
origin x/y/z0.0000.0000.000
length x/y/z325.120325.120325.120
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS256256256
D min/max/mean-0.1180.2950.004

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Supplemental data

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Sample components

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Entire : single particle cryo EM-derived map of the full-length native hum...

EntireName: single particle cryo EM-derived map of the full-length native human E2-E3BP core of the pyruvate dehydrogenase multienzyme complex
Components
  • Complex: single particle cryo EM-derived map of the full-length native human E2-E3BP core of the pyruvate dehydrogenase multienzyme complex
    • Protein or peptide: Dihydrolipoyllysine-residue acetyltransferase component of pyruvate dehydrogenase complex, mitochondrial

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Supramolecule #1: single particle cryo EM-derived map of the full-length native hum...

SupramoleculeName: single particle cryo EM-derived map of the full-length native human E2-E3BP core of the pyruvate dehydrogenase multienzyme complex
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Dihydrolipoyllysine-residue acetyltransferase component of pyruva...

MacromoleculeName: Dihydrolipoyllysine-residue acetyltransferase component of pyruvate dehydrogenase complex, mitochondrial
type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO / EC number: dihydrolipoyllysine-residue acetyltransferase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 69.069398 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MWRVCARRAQ NVAPWAGLEA RWTALQEVPG TPRVTSRSGP APARRNSVTT GYGGVRALCG WTPSSGATPR NRLLLQLLGS PGRRYYSLP PHQKVPLPSL SPTMQAGTIA RWEKKEGDKI NEGDLIAEVE TDKATVGFES LEECYMAKIL VAEGTRDVPI G AIICITVG ...String:
MWRVCARRAQ NVAPWAGLEA RWTALQEVPG TPRVTSRSGP APARRNSVTT GYGGVRALCG WTPSSGATPR NRLLLQLLGS PGRRYYSLP PHQKVPLPSL SPTMQAGTIA RWEKKEGDKI NEGDLIAEVE TDKATVGFES LEECYMAKIL VAEGTRDVPI G AIICITVG KPEDIEAFKN YTLDSSAAPT PQAAPAPTPA ATASPPTPSA QAPGSSYPPH MQVLLPALSP TMTMGTVQRW EK KVGEKLS EGDLLAEIET DKATIGFEVQ EEGYLAKILV PEGTRDVPLG TPLCIIVEKE ADISAFADYR PTEVTDLKPQ VPP PTPPPV AAVPPTPQPL APTPSAPCPA TPAGPKGRVF VSPLAKKLAV EKGIDLTQVK GTGPDGRITK KDIDSFVPSK VAPA PAAVV PPTGPGMAPV PTGVFTDIPI SNIRRVIAQR LMQSKQTIPH YYLSIDVNMG EVLLVRKELN KILEGRSKIS VNDFI IKAS ALACLKVPEA NSSWMDTVIR QNHVVDVSVA VSTPAGLITP IVFNAHIKGV ETIANDVVSL ATKAREGKLQ PHEFQG GTF TISNLGMFGI KNFSAIINPP QACILAIGAS EDKLVPADNE KGFDVASMMS VTLSCDHRVV DGAVGAQWLA EFRKYLE KP ITMLL

UniProtKB: Dihydrolipoyllysine-residue acetyltransferase component of pyruvate dehydrogenase complex, mitochondrial

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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: 8
GridModel: Quantifoil R3.5/1 / Support film - #0 - Film type ID: 1 / Support film - #0 - Material: CARBON / Support film - #0 - topology: CONTINUOUS / Support film - #1 - Film type ID: 2 / Support film - #1 - Material: CARBON / Support film - #1 - topology: HOLEY
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Specialist opticsSpherical aberration corrector: Microscope was modified with a Cs corrector with two hexapole elements
Image recordingFilm or detector model: FEI FALCON II (4k x 4k) / Detector mode: INTEGRATING / Number grids imaged: 1 / Number real images: 2250 / Average exposure time: 1.0 sec. / Average electron dose: 41.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Cs: 0.01 mm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: INSILICO MODEL
Final reconstructionApplied symmetry - Point group: I (icosahedral) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 6.0 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 29788
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: PROJECTION MATCHING

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