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- EMDB-1448: Structures of the human pyruvate dehydrogenase complex cores: a h... -
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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-1448 | |||||||||
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Title | Structures of the human pyruvate dehydrogenase complex cores: a highly conserved catalytic center with flexible N-terminal domains. | |||||||||
![]() | This is the half density map for the truncated human dihydrolipoyl acetyltransferase(E2)dodecahedron | |||||||||
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Function / homology | ![]() dihydrolipoyllysine-residue acetyltransferase / dihydrolipoyllysine-residue acetyltransferase activity / acetyl-CoA biosynthetic process from pyruvate / : / pyruvate dehydrogenase complex / Pyruvate metabolism / Glyoxylate metabolism and glycine degradation / Regulation of pyruvate dehydrogenase (PDH) complex / Signaling by Retinoic Acid / tricarboxylic acid cycle ...dihydrolipoyllysine-residue acetyltransferase / dihydrolipoyllysine-residue acetyltransferase activity / acetyl-CoA biosynthetic process from pyruvate / : / pyruvate dehydrogenase complex / Pyruvate metabolism / Glyoxylate metabolism and glycine degradation / Regulation of pyruvate dehydrogenase (PDH) complex / Signaling by Retinoic Acid / tricarboxylic acid cycle / glucose metabolic process / mitochondrial matrix / intracellular membrane-bounded organelle / mitochondrion / identical protein binding Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 8.8 Å | |||||||||
![]() | Yu X / Hiromasa Y / Tsen H / Stoops JK / Roche TE / Zhou ZH | |||||||||
![]() | ![]() Title: Structures of the human pyruvate dehydrogenase complex cores: a highly conserved catalytic center with flexible N-terminal domains. Authors: Xuekui Yu / Yasuaki Hiromasa / Hua Tsen / James K Stoops / Thomas E Roche / Z Hong Zhou / ![]() Abstract: Dihydrolipoyl acetyltransferase (E2) is the central component of pyruvate dehydrogenase complex (PDC), which converts pyruvate to acetyl-CoA. Structural comparison by cryo-electron microscopy (cryo- ...Dihydrolipoyl acetyltransferase (E2) is the central component of pyruvate dehydrogenase complex (PDC), which converts pyruvate to acetyl-CoA. Structural comparison by cryo-electron microscopy (cryo-EM) of the human full-length and truncated E2 (tE2) cores revealed flexible linkers emanating from the edges of trimers of the internal catalytic domains. Using the secondary structure constraints revealed in our 8 A cryo-EM reconstruction and the prokaryotic tE2 atomic structure as a template, we derived a pseudo atomic model of human tE2. The active sites are conserved between prokaryotic tE2 and human tE2. However, marked structural differences are apparent in the hairpin domain and in the N-terminal helix connected to the flexible linker. These permutations away from the catalytic center likely impart structures needed to integrate a second component into the inner core and provide a sturdy base for the linker that holds the pyruvate dehydrogenase for access by the E2-bound regulatory kinase/phosphatase components in humans. | |||||||||
History |
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Structure visualization
Movie |
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 29.5 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 9.9 KB 9.9 KB | Display Display | ![]() |
Images | ![]() | 16.1 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 377.5 KB | Display | ![]() |
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Full document | ![]() | 377.1 KB | Display | |
Data in XML | ![]() | 6.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3b8kMC M: atomic model generated by this map C: citing same article ( |
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Similar structure data |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
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Annotation | This is the half density map for the truncated human dihydrolipoyl acetyltransferase(E2)dodecahedron | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.09 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
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Sample components
-Entire : the truncated human dihydrolipoyl acetyltransferase
Entire | Name: the truncated human dihydrolipoyl acetyltransferase |
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Components |
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-Supramolecule #1000: the truncated human dihydrolipoyl acetyltransferase
Supramolecule | Name: the truncated human dihydrolipoyl acetyltransferase / type: sample / ID: 1000 / Oligomeric state: dodecahedrial assembly of tE2 / Number unique components: 1 |
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Molecular weight | Theoretical: 1.6 MDa |
-Macromolecule #1: truncated human dihydrolipoyl acetyltransferase
Macromolecule | Name: truncated human dihydrolipoyl acetyltransferase / type: protein_or_peptide / ID: 1 / Name.synonym: tE2 Details: Human tE2 was prepared from scE2, which contains a PreScission site in the third linker region. Treatment of scE2 with the PreScission protease (Amersham Biosciences) removed the N-terminal 319 amino acids. Number of copies: 60 / Oligomeric state: Dodecahedron / Recombinant expression: Yes |
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Source (natural) | Organism: ![]() |
Molecular weight | Experimental: 1.6 MDa / Theoretical: 1.6 MDa |
Recombinant expression | Organism: ![]() ![]() |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Concentration | 0.2 mg/mL |
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Buffer | pH: 7.2 / Details: PBS |
Grid | Details: 200 mesh holey carbon grid |
Vitrification | Cryogen name: ETHANE / Instrument: HOMEMADE PLUNGER / Details: Vitrification instrument: lab-made plunger / Method: Blot for 1 second before plunging |
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Electron microscopy
Microscope | JEOL 2010F |
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Temperature | Min: 100 K / Max: 100 K / Average: 100 K |
Date | Oct 10, 2003 |
Image recording | Category: CCD / Film or detector model: GENERIC GATAN / Average electron dose: 12 e/Å2 |
Electron beam | Acceleration voltage: 200 kV / Electron source: ![]() |
Electron optics | Calibrated magnification: 69250 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 1.0 mm / Nominal defocus max: 2.1 µm / Nominal defocus min: 0.6 µm / Nominal magnification: 69250 |
Sample stage | Specimen holder: Eucentric / Specimen holder model: GATAN LIQUID NITROGEN |
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Image processing
CTF correction | Details: each image |
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Final reconstruction | Applied symmetry - Point group: I (icosahedral) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 8.8 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: IMIRS / Number images used: 2432 |