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- PDB-6h55: core of the human pyruvate dehydrogenase (E2) -

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Entry
Database: PDB / ID: 6h55
Titlecore of the human pyruvate dehydrogenase (E2)
ComponentsDihydrolipoyllysine-residue acetyltransferase component of pyruvate dehydrogenase complex, mitochondrialDihydrolipoyl transacetylase
KeywordsOXIDOREDUCTASE / Pyruvate dehydrogenase / human
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 / ec:2.3.1.12: / 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 / ec:2.3.1.12: / 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)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 6 Å
AuthorsHaselbach, D. / Prajapati, S. / Tittmann, K. / Stark, H.
Funding supportGermany , 1件
OrganizationGrant numberCountry
German Research FoundationSFB860Germany
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 Report
SummaryFull reportAbout validation report
DateDeposition: Jul 23, 2018 / Release: Jun 5, 2019
RevisionDateData content typeGroupCategoryItemProviderType
1.0Jun 5, 2019Structure modelrepositoryInitial release
1.1Jun 12, 2019Structure modelData collectionem_admin / pdbx_database_proc_em_admin.last_update

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Assembly

Deposited unit
A: Dihydrolipoyllysine-residue acetyltransferase component of pyruvate dehydrogenase complex, mitochondrial


Theoretical massNumber of molelcules
Total (without water)69,0691
Polymers69,0691
Non-polymers00
Water0
1
A: Dihydrolipoyllysine-residue acetyltransferase component of pyruvate dehydrogenase complex, mitochondrial
x 60


Theoretical massNumber of molelcules
Total (without water)4,144,16460
Polymers4,144,16460
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation59
MethodUCSF CHIMERA

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Components

#1: Protein/peptide Dihydrolipoyllysine-residue acetyltransferase component of pyruvate dehydrogenase complex, mitochondrial / Dihydrolipoyl transacetylase / 70 kDa mitochondrial autoantigen of primary biliary cirrhosis / PBC / Dihydrolipoamide acetyltransferase component of pyruvate dehydrogenase complex / M2 antigen complex 70 kDa subunit / Pyruvate dehydrogenase complex component E2 / PDCE2


Mass: 69069.398 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DLAT, DLTA / Production host: Escherichia coli (E. coli) / References: UniProt: P10515, EC: 2.3.1.12

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: single particle cryo EM-derived map of the full-length native human E2-E3BP core of the pyruvate dehydrogenase multienzyme complex
Type: COMPLEX / Entity ID: 1 / Source: RECOMBINANT
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid type: Quantifoil R3.5/1
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: SPOT SCAN
Electron lensMode: BRIGHT FIELDBright-field microscopy / Cs: 0.01 mm
Image recordingAverage exposure time: 1 sec. / Electron dose: 41 e/Å2 / Detector mode: INTEGRATING / Film or detector model: FEI FALCON II (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 2250
EM imaging opticsSpherical aberration corrector: Microscope was modified with a Cs corrector with two hexapole elements
Image scansMovie frames/image: 1

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: I (icosahedral)
3D reconstructionResolution: 6 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 29788 / Algorithm: FOURIER SPACE / Symmetry type: POINT

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