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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
Samplesingle particle cryo EM-derived map of the full-length native human E2-E3BP core of the pyruvate dehydrogenase multienzyme complex
  • Dihydrolipoyllysine-residue acetyltransferase component of pyruvate dehydrogenase complex, mitochondrialDihydrolipoyl transacetylase
Function / homology
Function and homology information


Regulation of pyruvate dehydrogenase (PDH) complex / Glyoxylate metabolism and glycine degradation / Signaling by Retinoic Acid / Pyruvate metabolism / mitochondrial acetyl-CoA biosynthetic process from pyruvate / acetyl-CoA biosynthetic process from pyruvate / mitochondrial pyruvate dehydrogenase complex / ec:2.3.1.12: / dihydrolipoyllysine-residue acetyltransferase activity / pyruvate dehydrogenase complex ...Regulation of pyruvate dehydrogenase (PDH) complex / Glyoxylate metabolism and glycine degradation / Signaling by Retinoic Acid / Pyruvate metabolism / mitochondrial acetyl-CoA biosynthetic process from pyruvate / acetyl-CoA biosynthetic process from pyruvate / mitochondrial pyruvate dehydrogenase complex / ec:2.3.1.12: / dihydrolipoyllysine-residue acetyltransferase activity / pyruvate dehydrogenase complex / sleep / pyruvate metabolic process / transferase activity, transferring acyl groups / tricarboxylic acid cycle / glucose metabolic process / mitochondrial matrix / mitochondrion / identical protein binding
Peripheral subunit-binding domain / e3 binding domain / Single hybrid motif / Dihydrolipoyllysine-residue acetyltransferase component of pyruvate dehydrogenase complex / 2-oxoacid dehydrogenases acyltransferase (catalytic domain) / 2-oxo acid dehydrogenase, lipoyl-binding site / 2-oxoacid dehydrogenase acyltransferase, catalytic domain / Biotin/lipoyl attachment / Biotin-requiring enzyme / 2-oxo acid dehydrogenases acyltransferase component lipoyl binding site. ...Peripheral subunit-binding domain / e3 binding domain / Single hybrid motif / Dihydrolipoyllysine-residue acetyltransferase component of pyruvate dehydrogenase complex / 2-oxoacid dehydrogenases acyltransferase (catalytic domain) / 2-oxo acid dehydrogenase, lipoyl-binding site / 2-oxoacid dehydrogenase acyltransferase, catalytic domain / Biotin/lipoyl attachment / Biotin-requiring enzyme / 2-oxo acid dehydrogenases acyltransferase component lipoyl binding site. / E3-binding domain superfamily / Biotinyl/lipoyl domain profile. / Peripheral subunit-binding (PSBD) domain profile. / Chloramphenicol acetyltransferase-like domain superfamily
Pyruvate dehydrogenase protein X component, mitochondrial / Dihydrolipoyllysine-residue acetyltransferase component of pyruvate dehydrogenase complex, mitochondrial
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 6 Å
AuthorsHaselbach D / Prajapati S / Tittmann K / Stark H
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.
Validation ReportPDB-ID: 6h55

SummaryFull report
PDB-ID: 6h60

SummaryFull report
About validation report
DateDeposition: Jul 23, 2018 / Header (metadata) release: Sep 5, 2018 / Map release: Jun 5, 2019 / Update: Jun 12, 2019

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Structure visualization

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

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
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
Number of components: 2

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Component #1: protein, single particle cryo EM-derived map of the full-length n...

ProteinName: single particle cryo EM-derived map of the full-length native human E2-E3BP core of the pyruvate dehydrogenase multienzyme complex
Recombinant expression: No
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Escherichia coli (E. coli)

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Component #2: protein, Dihydrolipoyllysine-residue acetyltransferase component ...

ProteinName: Dihydrolipoyllysine-residue acetyltransferase component of pyruvate dehydrogenase complex, mitochondrialDihydrolipoyl transacetylase
Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 69.069398 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Escherichia coli (E. coli)

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Experimental details

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Sample preparation

SpecimenSpecimen state: Particle / Method: cryo EM
Sample solutionpH: 8
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
ImagingMicroscope: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 41 e/Å2 / Illumination mode: SPOT SCAN
LensCs: 0.01 mm / Imaging mode: BRIGHT FIELD
Specimen HolderModel: OTHER
CameraDetector: FEI FALCON II (4k x 4k)

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Image acquisition

Image acquisitionNumber of digital images: 2250

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Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: I (icosahedral) / Number of projections: 29788
3D reconstructionAlgorithm: FOURIER SPACE / Resolution: 6 Å / Resolution method: FSC 0.143 CUT-OFF

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Atomic model buiding

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