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

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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

mitochondrial acetyl-CoA biosynthetic process from pyruvate / pyruvate dehydrogenase complex / pyruvate metabolic process / transferase activity, transferring acyl groups / mitochondrial matrix
2-oxoacid dehydrogenase acyltransferase, catalytic domain / Biotin/lipoyl attachment / 2-oxo acid dehydrogenase, lipoyl-binding site / Peripheral subunit-binding domain / Single hybrid motif / Chloramphenicol acetyltransferase-like domain superfamily / E3-binding domain superfamily / 2-oxoacid dehydrogenases acyltransferase (catalytic domain) / Biotin-requiring enzyme / e3 binding domain
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 support Germany, 1items
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.
Validation Report
SummaryFull reportAbout validation report
DepositionJul 25, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 5, 2019Provider: repository / Type: Initial release
Revision 1.1Jul 10, 2019Group: Data collection / Database references / Category: citation / pdbx_database_proc
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Dec 11, 2019Group: Other / Category: atom_sites
Item: _atom_sites.fract_transf_matrix[1][1] / _atom_sites.fract_transf_matrix[2][2] / _atom_sites.fract_transf_matrix[3][3]

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Deposited unit
A: Pyruvate dehydrogenase protein X component, mitochondrial

Theoretical massNumber of molelcules
Total (without water)54,1911

TypeNameSymmetry operationNumber
identity operation1_5551


#1: Protein Pyruvate dehydrogenase protein X component, mitochondrial / / Dihydrolipoamide dehydrogenase-binding protein of pyruvate dehydrogenase complex / E3-binding ...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

Experimental details


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

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

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)


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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