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- EMDB-7610: Atomic Structure of the E2 Inner Core of Human Pyruvate Dehydroge... -

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Basic information

Entry
Database: EMDB / ID: EMD-7610
TitleAtomic Structure of the E2 Inner Core of Human Pyruvate Dehydrogenase Complex
Map data
SampleE2 Inner Core of Human Pyruvate Dehydrogenase 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 / acetyl-CoA biosynthetic process from pyruvate / mitochondrial pyruvate dehydrogenase complex / dihydrolipoyllysine-residue acetyltransferase / dihydrolipoyllysine-residue acetyltransferase activity / pyruvate dehydrogenase complex / sleep ...Regulation of pyruvate dehydrogenase (PDH) complex / Glyoxylate metabolism and glycine degradation / Signaling by Retinoic Acid / Pyruvate metabolism / acetyl-CoA biosynthetic process from pyruvate / mitochondrial pyruvate dehydrogenase complex / dihydrolipoyllysine-residue acetyltransferase / dihydrolipoyllysine-residue acetyltransferase activity / pyruvate dehydrogenase complex / sleep / pyruvate metabolic process / tricarboxylic acid cycle / glucose metabolic process / mitochondrial matrix / mitochondrion / identical protein binding
Peripheral subunit-binding domain / e3 binding domain / Chloramphenicol acetyltransferase-like domain superfamily / Single hybrid motif / Dihydrolipoyllysine-residue acetyltransferase component of pyruvate dehydrogenase complex / Biotin-requiring enzyme / 2-oxo acid dehydrogenase, lipoyl-binding site / 2-oxoacid dehydrogenase acyltransferase, catalytic domain / Biotin/lipoyl attachment / 2-oxo acid dehydrogenases acyltransferase component lipoyl binding site. ...Peripheral subunit-binding domain / e3 binding domain / Chloramphenicol acetyltransferase-like domain superfamily / Single hybrid motif / Dihydrolipoyllysine-residue acetyltransferase component of pyruvate dehydrogenase complex / Biotin-requiring enzyme / 2-oxo acid dehydrogenase, lipoyl-binding site / 2-oxoacid dehydrogenase acyltransferase, catalytic domain / Biotin/lipoyl attachment / 2-oxo acid dehydrogenases acyltransferase component lipoyl binding site. / 2-oxoacid dehydrogenases acyltransferase (catalytic domain) / Biotinyl/lipoyl domain profile. / Peripheral subunit-binding (PSBD) domain profile. / E3-binding domain superfamily
Dihydrolipoyllysine-residue acetyltransferase component of pyruvate dehydrogenase complex, mitochondrial
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.1 Å
AuthorsJiang J / Baiesc FL / Hiromasa Y / Yu X / Hui WH / Dai X / Roche TE / Zhou ZH
CitationJournal: Biochemistry / Year: 2018
Title: Atomic Structure of the E2 Inner Core of Human Pyruvate Dehydrogenase Complex.
Authors: Jiansen Jiang / Flavius L Baiesc / Yasuaki Hiromasa / Xuekui Yu / Wong Hoi Hui / Xinghong Dai / Thomas E Roche / Z Hong Zhou /
Abstract: Pyruvate dehydrogenase complex (PDC) is a large multienzyme complex that catalyzes the irreversible conversion of pyruvate to acetyl-coenzyme A with reduction of NAD. Distinctive from PDCs in lower ...Pyruvate dehydrogenase complex (PDC) is a large multienzyme complex that catalyzes the irreversible conversion of pyruvate to acetyl-coenzyme A with reduction of NAD. Distinctive from PDCs in lower forms of life, in mammalian PDC, dihydrolipoyl acetyltransferase (E2; E2p in PDC) and dihydrolipoamide dehydrogenase binding protein (E3BP) combine to form a complex that plays a central role in the organization, regulation, and integration of catalytic reactions of PDC. However, the atomic structure and organization of the mammalian E2p/E3BP heterocomplex are unknown. Here, we report the structure of the recombinant dodecahedral core formed by the C-terminal inner-core/catalytic (IC) domain of human E2p determined at 3.1 Å resolution by cryo electron microscopy (cryoEM). The structure of the N-terminal fragment and four other surface areas of the human E2p IC domain exhibit significant differences from those of the other E2 crystal structures, which may have implications for the integration of E3BP in mammals. This structure also allowed us to obtain a homology model for the highly homologous IC domain of E3BP. Analysis of the interactions of human E2p or E3BP with their adjacent IC domains in the dodecahedron provides new insights into the organization of the E2p/E3BP heterocomplex and suggests a potential contribution by E3BP to catalysis in mammalian PDC.
Validation ReportPDB-ID: 6ct0

SummaryFull reportAbout validation report
History
DepositionMar 21, 2018-
Header (metadata) releaseApr 18, 2018-
Map releaseApr 18, 2018-
UpdateMay 9, 2018-
Current statusMay 9, 2018Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 2.5
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 2.5
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: : PDB-6ct0
  • Surface level: 2.5
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic models: PDB-6ct0
  • 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_7610.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.)
1.02 Å/pix.
x 256 pix.
= 261.12 Å
1.02 Å/pix.
x 256 pix.
= 261.12 Å
1.02 Å/pix.
x 256 pix.
= 261.12 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.02 Å
Density
Contour LevelBy AUTHOR: 2.5 / Movie #1: 2.5
Minimum - Maximum-6.468645 - 12.254806
Average (Standard dev.)-0.000000001520753 (±1.)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-128-128-128
Dimensions256256256
Spacing256256256
CellA=B=C: 261.12 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.021.021.02
M x/y/z256256256
origin x/y/z0.0000.0000.000
length x/y/z261.120261.120261.120
α/β/γ90.00090.00090.000
start NX/NY/NZ-128-128-128
NX/NY/NZ256256256
MAP C/R/S123
start NC/NR/NS-128-128-128
NC/NR/NS256256256
D min/max/mean-6.46912.255-0.000

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Supplemental data

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Sample components

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Entire E2 Inner Core of Human Pyruvate Dehydrogenase Complex

EntireName: E2 Inner Core of Human Pyruvate Dehydrogenase Complex / Number of components: 2

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Component #1: protein, E2 Inner Core of Human Pyruvate Dehydrogenase Complex

ProteinName: E2 Inner Core of Human Pyruvate Dehydrogenase 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: 7.2
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: 38 e/Å2 / Illumination mode: FLOOD BEAM
LensImaging mode: BRIGHT FIELD
Specimen HolderModel: OTHER
CameraDetector: GATAN K2 SUMMIT (4k x 4k)

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Image processing

ProcessingMethod: single particle reconstruction / Number of projections: 49374
3D reconstructionSoftware: RELION / Resolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF

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Atomic model buiding

Output model

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