|Entry||Database: PDB / ID: 6h60|
|Title||pseudo-atomic structural model of the E3BP component of the human pyruvate dehydrogenase multienzyme complex|
|Components||Pyruvate dehydrogenase protein X component, mitochondrial|
|Keywords||OXIDOREDUCTASE / 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 species||Homo sapiens (human)|
|Method||ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 6 Å|
|Authors||Haselbach, D. / Prajapati, S. / Tittmann, K. / Stark, H.|
|Funding support||Germany , 1件 |
|Citation||Journal: 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.
SummaryFull reportAbout validation report
|Date||Deposition: Jul 25, 2018 / Release: Jun 5, 2019|
|Structure viewer||Molecule: |
Downloads & links
A: Pyruvate dehydrogenase protein X component, mitochondrial
|#1: Protein/peptide|| |
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
|Experiment||Method: ELECTRON MICROSCOPY|
|EM experiment||Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction|
|Component||Name: 1 / Type: COMPLEX / Entity ID: 1 / Source: RECOMBINANT|
|Molecular weight||Experimental value: NO|
|Source (natural)||Organism: Homo sapiens (human)|
|Source (recombinant)||Organism: Escherichia coli (E. coli)|
|Buffer solution||pH: 8|
|Specimen||Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES|
|Vitrification||Cryogen name: ETHANE|
-Electron microscopy imaging
Model: Titan Krios / Image courtesy: FEI Company
|Microscopy||Model: FEI TITAN KRIOS|
|Electron gun||Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: SPOT SCAN|
|Electron lens||Mode: BRIGHT FIELDBright-field microscopy|
|Image recording||Electron dose: 41 e/Å2 / Film or detector model: FEI FALCON II (4k x 4k)|
|CTF correction||Type: PHASE FLIPPING AND AMPLITUDE CORRECTION|
|Symmetry||Point symmetry: I (icosahedral)|
|3D reconstruction||Resolution: 6 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 29788 / Symmetry type: POINT|
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