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- EMDB-12181: Cryo-EM map of Icosahedrally averaged native core of Pyruvate Deh... -
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Basic information
Entry | Database: EMDB / ID: EMD-12181 | |||||||||
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Title | Cryo-EM map of Icosahedrally averaged native core of Pyruvate Dehydrogenase Complex from Ch. thermophilum | |||||||||
![]() | Symmetrically averaged (Icosahedral Symmetry) Pyruvate Dehydrogenase Complex core from Ch. thermophilum. | |||||||||
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![]() | Dihydrolipoyl / transacetylase / E2 / Pyruvate / TRANSFERASE | |||||||||
Function / homology | ![]() dihydrolipoyllysine-residue acetyltransferase / dihydrolipoyllysine-residue acetyltransferase activity / acetyl-CoA biosynthetic process from pyruvate / pyruvate dehydrogenase complex / mitochondrion Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 6.9 Å | |||||||||
![]() | Skalidis I / Kyrilis FL / Tueting C / Semchonok DA / Kastritis PL | |||||||||
![]() | ![]() Title: Integrative structure of a 10-megadalton eukaryotic pyruvate dehydrogenase complex from native cell extracts. Authors: Fotis L Kyrilis / Dmitry A Semchonok / Ioannis Skalidis / Christian Tüting / Farzad Hamdi / Francis J O'Reilly / Juri Rappsilber / Panagiotis L Kastritis / ![]() ![]() Abstract: The pyruvate dehydrogenase complex (PDHc) is a giant enzymatic assembly involved in pyruvate oxidation. PDHc components have been characterized in isolation, but the complex's quaternary structure ...The pyruvate dehydrogenase complex (PDHc) is a giant enzymatic assembly involved in pyruvate oxidation. PDHc components have been characterized in isolation, but the complex's quaternary structure has remained elusive due to sheer size, heterogeneity, and plasticity. Here, we identify fully assembled Chaetomium thermophilum α-keto acid dehydrogenase complexes in native cell extracts and characterize their domain arrangements utilizing mass spectrometry, activity assays, crosslinking, electron microscopy (EM), and computational modeling. We report the cryo-EM structure of the PDHc core and observe unique features of the previously unknown native state. The asymmetric reconstruction of the 10-MDa PDHc resolves spatial proximity of its components, agrees with stoichiometric data (60 E2p:12 E3BP:∼20 E1p: ≤ 12 E3), and proposes a minimum reaction path among component enzymes. The PDHc shows the presence of a dynamic pyruvate oxidation compartment, organized by core and peripheral protein species. Our data provide a framework for further understanding PDHc and α-keto acid dehydrogenase complex structure and function. | |||||||||
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 | ![]() | 45.8 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 30.8 KB 30.8 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 11.4 KB | Display | ![]() |
Images | ![]() | 64.6 KB | ||
Filedesc metadata | ![]() | 6.3 KB | ||
Others | ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() | 46.2 MB 46.2 MB 46.2 MB 46.2 MB 46.2 MB 46.1 MB 45.9 MB 45.9 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7bgjMC M: atomic model generated by this map C: citing same article ( |
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Similar structure data | |
EM raw data | ![]() Data size: 5.4 TB Data #1: Unaligned multiframe and summed frame mrc files of the datasets presented in the corresponding Cell Reports manuscript, by Kastritis et al. Please read the README file for more information ...Data #1: Unaligned multiframe and summed frame mrc files of the datasets presented in the corresponding Cell Reports manuscript, by Kastritis et al. Please read the README file for more information [micrographs - multiframe]) |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
File | ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Symmetrically averaged (Icosahedral Symmetry) Pyruvate Dehydrogenase Complex core from Ch. thermophilum. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 3.1765 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Additional map: Asymmetrical Pyruvate Dehydrogenase Complex from Ch. thermophilum.
File | emd_12181_additional_1.map | ||||||||||||
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Annotation | Asymmetrical Pyruvate Dehydrogenase Complex from Ch. thermophilum. | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: Asymmetrical Pyruvate Dehydrogenase Complex from Ch. thermophilum, Half-map...
File | emd_12181_additional_2.map | ||||||||||||
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Annotation | Asymmetrical Pyruvate Dehydrogenase Complex from Ch. thermophilum, Half-map 1. | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: Asymmetrical Pyruvate Dehydrogenase Complex from Ch. thermophilum, Half-map...
File | emd_12181_additional_3.map | ||||||||||||
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Annotation | Asymmetrical Pyruvate Dehydrogenase Complex from Ch. thermophilum, Half-map 2. | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: Asymmetrical Pyruvate Dehydrogenase Complex core from Ch. thermophilum....
File | emd_12181_additional_4.map | ||||||||||||
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Annotation | Asymmetrical Pyruvate Dehydrogenase Complex core from Ch. thermophilum. Half-map 1 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: Asymmetrical Pyruvate Dehydrogenase Complex core from Ch. thermophilum....
File | emd_12181_additional_5.map | ||||||||||||
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Annotation | Asymmetrical Pyruvate Dehydrogenase Complex core from Ch. thermophilum. Half-map 2 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: Asymmetrical Pyruvate Dehydrogenase Complex core from Ch. thermophilum....
File | emd_12181_additional_6.map | ||||||||||||
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Annotation | Asymmetrical Pyruvate Dehydrogenase Complex core from Ch. thermophilum. | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Symmetrically averaged (Icosahedral Symmetry) Pyruvate Dehydrogenase Complex core...
File | emd_12181_half_map_1.map | ||||||||||||
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Annotation | Symmetrically averaged (Icosahedral Symmetry) Pyruvate Dehydrogenase Complex core from Ch. thermophilum, Half-map 1. | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Symmetrically averaged (Icosahedral Symmetry) Pyruvate Dehydrogenase Complex core...
File | emd_12181_half_map_2.map | ||||||||||||
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Annotation | Symmetrically averaged (Icosahedral Symmetry) Pyruvate Dehydrogenase Complex core from Ch. thermophilum, Half-map 2. | ||||||||||||
Projections & Slices |
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Density Histograms |
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Sample components
-Entire : Native 60-mer core of Pyruvate Dehydrogenase Complex
Entire | Name: Native 60-mer core of Pyruvate Dehydrogenase Complex |
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Components |
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-Supramolecule #1: Native 60-mer core of Pyruvate Dehydrogenase Complex
Supramolecule | Name: Native 60-mer core of Pyruvate Dehydrogenase Complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 3 MDa |
-Macromolecule #1: Acetyltransferase component of pyruvate dehydrogenase complex
Macromolecule | Name: Acetyltransferase component of pyruvate dehydrogenase complex type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO / EC number: dihydrolipoyllysine-residue acetyltransferase |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 48.777488 KDa |
Sequence | String: MLAQVLRRQA LQHVRLARAA APSLTRWYAS YPPHTIVKMP ALSPTMTSGN IGAWQKKPGD AITPGEVLVE IETDKAQMDF EFQEEGVLA KILKETGEKD VAVGSPIAVL VEEGTDINAF QNFTLEDAGG DAAAPAAPAK EELAKAETAP TPASTSAPEP E ETTSTGKL ...String: MLAQVLRRQA LQHVRLARAA APSLTRWYAS YPPHTIVKMP ALSPTMTSGN IGAWQKKPGD AITPGEVLVE IETDKAQMDF EFQEEGVLA KILKETGEKD VAVGSPIAVL VEEGTDINAF QNFTLEDAGG DAAAPAAPAK EELAKAETAP TPASTSAPEP E ETTSTGKL EPALDREPNV SFAAKKLAHE LDVPLKALKG TGPGGKITEE DVKKAASAPA AAAAAPGAAY QDIPISNMRK TI ATRLKES VSENPHFFVT SELSVSKLLK LRQALNSSAE GRYKLSVNDF LIKAIAVACK RVPAVNSSWR DGVIRQFDTV DVS VAVATP TGLITPIVKG VEAKGLETIS ATVKELAKKA RDGKLKPEDY QGGTISISNM GMNPAVERFT AIINPPQAAI LAVG TTKKV AVPVENEDGT TGVEWDDQIV VTASFDHKVV DGAVGAEWMR ELKKVVENPL ELLL UniProtKB: Dihydrolipoyllysine-residue acetyltransferase component of pyruvate dehydrogenase complex, mitochondrial |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Concentration | 0.3 mg/mL |
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Buffer | pH: 7.4 / Component - Concentration: 200.0 mM / Component - Formula: NH4CH2COOH / Component - Name: Ammonium acetate |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV Details: For plunging, blot force 2 and blotting time of 6 sec were applied.. |
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Electron microscopy
Microscope | TFS GLACIOS |
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Temperature | Min: 77.15 K / Max: 103.15 K |
Alignment procedure | Coma free - Residual tilt: 14.7 mrad |
Image recording | Film or detector model: FEI FALCON III (4k x 4k) / Detector mode: INTEGRATING / Number real images: 2593 / Average electron dose: 30.0 e/Å2 |
Electron beam | Acceleration voltage: 200 kV / Electron source: ![]() |
Electron optics | C2 aperture diameter: 100.0 µm / Calibrated magnification: 44067 / Illumination mode: OTHER / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 45000 |
Sample stage | Specimen holder model: OTHER / Cooling holder cryogen: NITROGEN |
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Image processing
-Atomic model buiding 1
Initial model | PDB ID: Chain - Chain ID: A / Chain - Residue range: 444-647 / Chain - Source name: PDB / Chain - Initial model type: experimental model |
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Details | The initial model was used to generate our model using MODELLER. This inital model was fitted into the density using ChimeraX and refined in real space using PHENIX. |
Refinement | Space: REAL / Protocol: FLEXIBLE FIT / Overall B value: 103.25 |
Output model | ![]() PDB-7bgj: |