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- EMDB-1448: Structures of the human pyruvate dehydrogenase complex cores: a h... -

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Basic information

Entry
Database: EMDB / ID: EMD-1448
TitleStructures of the human pyruvate dehydrogenase complex cores: a highly conserved catalytic center with flexible N-terminal domains.
Map dataThis is the half density map for the truncated human dihydrolipoyl acetyltransferase(E2)dodecahedron
Sample
  • Sample: the truncated human dihydrolipoyl acetyltransferase
  • Protein or peptide: truncated human dihydrolipoyl acetyltransferase
Function / homology
Function and homology information


PDH complex synthesizes acetyl-CoA from PYR / dihydrolipoyllysine-residue acetyltransferase / dihydrolipoyllysine-residue acetyltransferase activity / acetyl-CoA biosynthetic process from pyruvate / Regulation of pyruvate dehydrogenase (PDH) complex / Protein lipoylation / pyruvate dehydrogenase complex / Signaling by Retinoic Acid / tricarboxylic acid cycle / glucose metabolic process ...PDH complex synthesizes acetyl-CoA from PYR / dihydrolipoyllysine-residue acetyltransferase / dihydrolipoyllysine-residue acetyltransferase activity / acetyl-CoA biosynthetic process from pyruvate / Regulation of pyruvate dehydrogenase (PDH) complex / Protein lipoylation / pyruvate dehydrogenase complex / Signaling by Retinoic Acid / tricarboxylic acid cycle / glucose metabolic process / mitochondrial matrix / intracellular membrane-bounded organelle / mitochondrion / identical protein binding
Similarity search - Function
Dihydrolipoyllysine-residue acetyltransferase component of pyruvate dehydrogenase complex / Dihydrolipoamide acetyltransferase/Pyruvate dehydrogenase protein X component / Peripheral subunit-binding domain / e3 binding domain / Peripheral subunit-binding (PSBD) domain profile. / E3-binding domain superfamily / 2-oxo acid dehydrogenase, lipoyl-binding site / 2-oxo acid dehydrogenases acyltransferase component lipoyl binding site. / 2-oxoacid dehydrogenase acyltransferase, catalytic domain / 2-oxoacid dehydrogenases acyltransferase (catalytic domain) ...Dihydrolipoyllysine-residue acetyltransferase component of pyruvate dehydrogenase complex / Dihydrolipoamide acetyltransferase/Pyruvate dehydrogenase protein X component / Peripheral subunit-binding domain / e3 binding domain / Peripheral subunit-binding (PSBD) domain profile. / E3-binding domain superfamily / 2-oxo acid dehydrogenase, lipoyl-binding site / 2-oxo acid dehydrogenases acyltransferase component lipoyl binding site. / 2-oxoacid dehydrogenase acyltransferase, catalytic domain / 2-oxoacid dehydrogenases acyltransferase (catalytic domain) / Biotin-requiring enzyme / Biotinyl/lipoyl domain profile. / Biotin/lipoyl attachment / Single hybrid motif / Chloramphenicol acetyltransferase-like domain superfamily
Similarity search - Domain/homology
Dihydrolipoyllysine-residue acetyltransferase component of pyruvate dehydrogenase complex, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 8.8 Å
AuthorsYu X / Hiromasa Y / Tsen H / Stoops JK / Roche TE / Zhou ZH
CitationJournal: Structure / Year: 2008
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
DepositionNov 1, 2007-
Header (metadata) releaseNov 1, 2007-
Map releaseJan 18, 2008-
UpdateMay 26, 2011-
Current statusMay 26, 2011Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 13
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 13
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

1448.gif

Downloads & links

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Map

FileDownload / File: emd_1448.map.gz / Format: CCP4 / Size: 55.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationThis is the half density map for the truncated human dihydrolipoyl acetyltransferase(E2)dodecahedron
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.09 Å/pix.
x 246 pix.
= 268.14 Å		1.09 Å/pix.
x 246 pix.
= 268.14 Å		1.09 Å/pix.
x 246 pix.
= 268.14 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.09 Å
Density

Histogram

Histogram (log scale)
Contour Level1: 10.699999999999999 / Movie #1: 13
Minimum - Maximum-20.146899999999999 - 31.895600000000002
Average (Standard dev.)0.307676 (±4.82993)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-123-123-123
Dimensions246246246
Spacing246246246
CellA=B=C: 268.14 Å
α=β=γ: 90 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.091.091.09
M x/y/z246246246
origin x/y/z0.0000.0000.000
length x/y/z268.140268.140268.140
α/β/γ90.00090.00090.000
start NX/NY/NZ-60-60-59
NX/NY/NZ120120120
MAP C/R/S123
start NC/NR/NS-123-123-123
NC/NR/NS246246246
D min/max/mean-20.14731.8960.308

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Supplemental data

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Sample components

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Entire : the truncated human dihydrolipoyl acetyltransferase

EntireName: the truncated human dihydrolipoyl acetyltransferase
Components
  • Sample: the truncated human dihydrolipoyl acetyltransferase
  • Protein or peptide: truncated human dihydrolipoyl acetyltransferase

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Supramolecule #1000: the truncated human dihydrolipoyl acetyltransferase

SupramoleculeName: the truncated human dihydrolipoyl acetyltransferase / type: sample / ID: 1000 / Oligomeric state: dodecahedrial assembly of tE2 / Number unique components: 1
Molecular weightTheoretical: 1.6 MDa

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Macromolecule #1: truncated human dihydrolipoyl acetyltransferase

MacromoleculeName: 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
Source (natural)Organism: Homo sapiens (human) / synonym: Human
Molecular weightExperimental: 1.6 MDa / Theoretical: 1.6 MDa
Recombinant expressionOrganism: Escherichia coli (E. coli)

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration0.2 mg/mL
BufferpH: 7.2 / Details: PBS
GridDetails: 200 mesh holey carbon grid
VitrificationCryogen name: ETHANE / Instrument: HOMEMADE PLUNGER / Details: Vitrification instrument: lab-made plunger / Method: Blot for 1 second before plunging

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Electron microscopy

MicroscopeJEOL 2010F
TemperatureMin: 100 K / Max: 100 K / Average: 100 K
DateOct 10, 2003
Image recordingCategory: CCD / Film or detector model: GENERIC GATAN / Average electron dose: 12 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated 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 stageSpecimen holder: Eucentric / Specimen holder model: GATAN LIQUID NITROGEN

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Image processing

CTF correctionDetails: each image
Final reconstructionApplied 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

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Atomic model buiding 1

Initial modelPDB ID:

1eaa


Chain - Chain ID: A
SoftwareName: CHIMERA
DetailsPDBEntryID_givenInChain. Protocol: Rigid Body
RefinementSpace: REAL / Protocol: RIGID BODY FIT / Overall B value: 30
Output model

PDB-3b8k:
Structure of the Truncated Human Dihydrolipoyl Acetyltransferase (E2)

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