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- EMDB-16900: Cryo-EM reconstruction of the native 24-mer E2o core of the 2-oxo... -
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Open data
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Basic information
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Title | Cryo-EM reconstruction of the native 24-mer E2o core of the 2-oxoglutarate dehydrogenase complex of C. thermophilum at 3.35 A resolution | |||||||||
![]() | Cryo-EM reconstruction of the native 24-mer E2o core of the 2-oxoglutarate dehydrogenase complex of C. thermophilum. | |||||||||
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![]() | Dihydrolipoyl Succinyltransferase / E2 / Oxoglutarate / a-Ketoglutarate / TRANSFERASE | |||||||||
Function / homology | ![]() L-lysine catabolic process to acetyl-CoA via saccharopine / dihydrolipoyllysine-residue succinyltransferase / dihydrolipoyllysine-residue succinyltransferase activity / oxoglutarate dehydrogenase complex / tricarboxylic acid cycle / mitochondrion / cytosol Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.35 Å | |||||||||
![]() | Skalidis I / Tueting C / Kyrilis FL / Hamdi F / Kastritis PL | |||||||||
Funding support | 1 items
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![]() | ![]() Title: Structural analysis of an endogenous 4-megadalton succinyl-CoA-generating metabolon. Authors: Ioannis Skalidis / Fotis L Kyrilis / Christian Tüting / Farzad Hamdi / Toni K Träger / Jaydeep Belapure / Gerd Hause / Marta Fratini / Francis J O'Reilly / Ingo Heilmann / Juri Rappsilber ...Authors: Ioannis Skalidis / Fotis L Kyrilis / Christian Tüting / Farzad Hamdi / Toni K Träger / Jaydeep Belapure / Gerd Hause / Marta Fratini / Francis J O'Reilly / Ingo Heilmann / Juri Rappsilber / Panagiotis L Kastritis / ![]() ![]() ![]() ![]() Abstract: The oxoglutarate dehydrogenase complex (OGDHc) participates in the tricarboxylic acid cycle and, in a multi-step reaction, decarboxylates α-ketoglutarate, transfers succinyl to CoA, and reduces NAD+. ...The oxoglutarate dehydrogenase complex (OGDHc) participates in the tricarboxylic acid cycle and, in a multi-step reaction, decarboxylates α-ketoglutarate, transfers succinyl to CoA, and reduces NAD+. Due to its pivotal role in metabolism, OGDHc enzymatic components have been studied in isolation; however, their interactions within the endogenous OGDHc remain elusive. Here, we discern the organization of a thermophilic, eukaryotic, native OGDHc in its active state. By combining biochemical, biophysical, and bioinformatic methods, we resolve its composition, 3D architecture, and molecular function at 3.35 Å resolution. We further report the high-resolution cryo-EM structure of the OGDHc core (E2o), which displays various structural adaptations. These include hydrogen bonding patterns confining interactions of OGDHc participating enzymes (E1o-E2o-E3), electrostatic tunneling that drives inter-subunit communication, and the presence of a flexible subunit (E3BPo), connecting E2o and E3. This multi-scale analysis of a succinyl-CoA-producing native cell extract provides a blueprint for structure-function studies of complex mixtures of medical and biotechnological value. | |||||||||
History |
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Structure visualization
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 32.3 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 21.9 KB 21.9 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 7.7 KB | Display | ![]() |
Images | ![]() | 84.2 KB | ||
Masks | ![]() | 34.3 MB | ![]() | |
Others | ![]() ![]() ![]() | 2.5 MB 31.8 MB 31.8 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 823.9 KB | Display | ![]() |
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Full document | ![]() | 823.4 KB | Display | |
Data in XML | ![]() | 14.5 KB | Display | |
Data in CIF | ![]() | 18.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8oiuMC M: atomic model generated by this map C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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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 | Cryo-EM reconstruction of the native 24-mer E2o core of the 2-oxoglutarate dehydrogenase complex of C. thermophilum. | ||||||||||||||||||||
Voxel size | X=Y=Z: 1.5678 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
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Density Histograms |
-Additional map: Cryo-EM reconstruction of the native asymmetric complex of...
File | emd_16900_additional_1.map | ||||||||||||
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Annotation | Cryo-EM reconstruction of the native asymmetric complex of the 2-oxoglutarate dehydrogenase complex of C. thermophilum. | ||||||||||||
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Density Histograms |
-Half map: Cryo-EM reconstruction of the native 24-mer E2o core...
File | emd_16900_half_map_1.map | ||||||||||||
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Annotation | Cryo-EM reconstruction of the native 24-mer E2o core of the 2-oxoglutarate dehydrogenase complex of C. thermophilum, Half-Map A. | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Cryo-EM reconstruction of the native 24-mer E2o core...
File | emd_16900_half_map_2.map | ||||||||||||
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Annotation | Cryo-EM reconstruction of the native 24-mer E2o core of the 2-oxoglutarate dehydrogenase complex of C. thermophilum, Half-Map B. | ||||||||||||
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Density Histograms |
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Sample components
-Entire : Native 24-mer core of Oxoglutarate Dehydrogenase Complex
Entire | Name: Native 24-mer core of Oxoglutarate Dehydrogenase Complex |
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Components |
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-Supramolecule #1: Native 24-mer core of Oxoglutarate Dehydrogenase Complex
Supramolecule | Name: Native 24-mer core of Oxoglutarate 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: Dihydrolipoyllysine-residue succinyltransferase
Macromolecule | Name: Dihydrolipoyllysine-residue succinyltransferase / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO / EC number: dihydrolipoyllysine-residue succinyltransferase |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 45.987004 KDa |
Sequence | String: MLYRGLRMAA RAAPKFAVLN THAALRQLPL QFQHVRTYAD KIIKVPQMAE SITEGTLKQW NKAVGDYVEA DEEIATIETD KIDVAVNAP EAGVIKEFFV NEEDTVLVGQ DLVRLEVGGE KPAEAAKEQP KAAAPEPKVE EKKVPEAPAP EPSKTAAPAP A PPKQEAPA ...String: MLYRGLRMAA RAAPKFAVLN THAALRQLPL QFQHVRTYAD KIIKVPQMAE SITEGTLKQW NKAVGDYVEA DEEIATIETD KIDVAVNAP EAGVIKEFFV NEEDTVLVGQ DLVRLEVGGE KPAEAAKEQP KAAAPEPKVE EKKVPEAPAP EPSKTAAPAP A PPKQEAPA SPKPASKPAE TPAVTLGNRE ERRVKMNRMR LRIAERLKQS QNTAASLTTF NEVDMSALIE FRNKYKDEVL KK TGVKLGF MSAFSRAVVL AIRDLPVVNA SIEGPNGGDT IVYRDYVDIS VAVATEKGLV TPVVRNAETM DLITIEKTIA ELG KKARDG KLTIEDMAGG TFTISNGGVF GSLMGTPIIN LPQSAVLGLH AIKERPVAVN GKVEIRPMMY LALTYDHRLL DGRE AVQFL VKVKEYIEDP RKMLL |
-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 |
Grid | Model: Quantifoil R2/1 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 25 sec. |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV Details: For plunging, blot force 0 and blotting time of 4 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 |
Image recording | Film or detector model: FEI FALCON III (4k x 4k) / Detector mode: INTEGRATING / Number real images: 21381 / Average electron dose: 30.0 e/Å2 |
Electron beam | Acceleration voltage: 200 kV / Electron source: ![]() |
Electron optics | C2 aperture diameter: 100.0 µm / 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: 92000 |
Sample stage | Specimen holder model: OTHER / Cooling holder cryogen: NITROGEN |
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Image processing
-Atomic model buiding 1
Initial model | Chain - Source name: PDB / Chain - Initial model type: experimental model |
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Details | Initial fitting was performed in ChimeraX v1.2, then real-space refined in PHENIX v1.19 |
Refinement | Space: REAL / Protocol: FLEXIBLE FIT |
Output model | ![]() PDB-8oiu: |