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- PDB-6h60: pseudo-atomic structural model of the E3BP component of the human... -

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Entry
Database: PDB / ID: 6h60
Titlepseudo-atomic structural model of the E3BP component of the human pyruvate dehydrogenase multienzyme complex
ComponentsPyruvate dehydrogenase protein X component, mitochondrial
KeywordsOXIDOREDUCTASE / Pyruvate dehydrogenase / human
Function / homology
Function and homology information


Glyoxylate metabolism and glycine degradation / Regulation of pyruvate dehydrogenase (PDH) complex / Pyruvate metabolism / Signaling by Retinoic Acid / mitochondrial acetyl-CoA biosynthetic process from pyruvate / pyruvate dehydrogenase complex / pyruvate metabolic process / transferase activity, transferring acyl groups / mitochondrial matrix
E3-binding domain superfamily / 2-oxoacid dehydrogenases acyltransferase (catalytic domain) / Peripheral subunit-binding (PSBD) domain profile. / Biotinyl/lipoyl domain profile. / 2-oxo acid dehydrogenases acyltransferase component lipoyl binding site. / e3 binding domain / Biotin-requiring enzyme / Chloramphenicol acetyltransferase-like domain superfamily / Single hybrid motif / Peripheral subunit-binding domain ...E3-binding domain superfamily / 2-oxoacid dehydrogenases acyltransferase (catalytic domain) / Peripheral subunit-binding (PSBD) domain profile. / Biotinyl/lipoyl domain profile. / 2-oxo acid dehydrogenases acyltransferase component lipoyl binding site. / e3 binding domain / Biotin-requiring enzyme / Chloramphenicol acetyltransferase-like domain superfamily / Single hybrid motif / Peripheral subunit-binding domain / 2-oxo acid dehydrogenase, lipoyl-binding site / 2-oxoacid dehydrogenase acyltransferase, catalytic domain / Biotin/lipoyl attachment
Pyruvate dehydrogenase protein X component, 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 25, 2018 / Release: Jun 5, 2019
RevisionDateData content typeProviderType
1.0Jun 5, 2019Structure modelrepositoryInitial release

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Assembly

Deposited unit
A: Pyruvate dehydrogenase protein X component, mitochondrial


Theoretical massNumber of molelcules
Total (without water)54,1911
Polymers54,1911
Non-polymers00
Water0
1


TypeNameSymmetry operationNumber
identity operation1_5551
MethodPISA

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Components

#1: Protein/peptide Pyruvate dehydrogenase protein X component, mitochondrial / / Dihydrolipoamide dehydrogenase-binding protein of pyruvate dehydrogenase complex / E3-binding protein / E3BP / Lipoyl-containing pyruvate dehydrogenase complex component X / proX


Mass: 54191.145 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PDHX, PDX1 / Production host: Escherichia coli (E. coli) / References: UniProt: O00330

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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: 1 / Type: COMPLEX / Entity ID: 1 / Source: RECOMBINANT
Molecular weightExperimental value: NO
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
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
Image recordingElectron dose: 41 e/Å2 / Film or detector model: FEI FALCON II (4k x 4k)

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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 / Symmetry type: POINT

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