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Yorodumi- EMDB-26649: Endogenous dihydrolipoamide succinyltransferase (E2) core of 2-ox... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-26649 | ||||||||||||
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Title | Endogenous dihydrolipoamide succinyltransferase (E2) core of 2-oxoglutarate dehydrogenase complex from bovine kidney | ||||||||||||
Map data | |||||||||||||
Sample |
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Keywords | e2 / 2-oxoglutarate / dehydrogenase / complex / TRANSFERASE | ||||||||||||
Function / homology | Function and homology information : / succinyl-CoA metabolic process / L-lysine catabolic process to acetyl-CoA via saccharopine / dihydrolipoyllysine-residue succinyltransferase / dihydrolipoyllysine-residue succinyltransferase activity / oxoglutarate dehydrogenase complex / 2-oxoglutarate metabolic process / acyltransferase activity / tricarboxylic acid cycle / mitochondrial matrix ...: / succinyl-CoA metabolic process / L-lysine catabolic process to acetyl-CoA via saccharopine / dihydrolipoyllysine-residue succinyltransferase / dihydrolipoyllysine-residue succinyltransferase activity / oxoglutarate dehydrogenase complex / 2-oxoglutarate metabolic process / acyltransferase activity / tricarboxylic acid cycle / mitochondrial matrix / mitochondrion / nucleus Similarity search - Function | ||||||||||||
Biological species | Bos taurus (cattle) | ||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.5 Å | ||||||||||||
Authors | Liu S / Xia X / Zhen J / Li ZH / Zhou ZH | ||||||||||||
Funding support | United States, 3 items
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Citation | Journal: Cell Discov / Year: 2022 Title: Structures and comparison of endogenous 2-oxoglutarate and pyruvate dehydrogenase complexes from bovine kidney. Authors: Shiheng Liu / Xian Xia / James Zhen / Zihang Li / Z Hong Zhou / Abstract: The α-keto acid dehydrogenase complex family catalyzes the essential oxidative decarboxylation of α-keto acids to yield acyl-CoA and NADH. Despite performing the same overarching reaction, members ...The α-keto acid dehydrogenase complex family catalyzes the essential oxidative decarboxylation of α-keto acids to yield acyl-CoA and NADH. Despite performing the same overarching reaction, members of the family have different component structures and structural organization between each other and across phylogenetic species. While native structures of α-keto acid dehydrogenase complexes from bacteria and fungi became available recently, the atomic structure and organization of their mammalian counterparts in native states remain unknown. Here, we report the cryo-electron microscopy structures of the endogenous cubic 2-oxoglutarate dehydrogenase complex (OGDC) and icosahedral pyruvate dehydrogenase complex (PDC) cores from bovine kidney determined at resolutions of 3.5 Å and 3.8 Å, respectively. The structures of multiple proteins were reconstructed from a single lysate sample, allowing direct structural comparison without the concerns of differences arising from sample preparation and structure determination. Although native and recombinant E2 core scaffold structures are similar, the native structures are decorated with their peripheral E1 and E3 subunits. Asymmetric sub-particle reconstructions support heterogeneity in the arrangements of these peripheral subunits. In addition, despite sharing a similar monomeric fold, OGDC and PDC E2 cores have distinct interdomain and intertrimer interactions, which suggests a means of modulating self-assembly to mitigate heterologous binding between mismatched E2 species. The lipoyl moiety lies near a mobile gatekeeper within the interdomain active site of OGDC E2 and PDC E2. Analysis of the twofold related intertrimer interface identified secondary structural differences and chemical interactions between icosahedral and cubic geometries of the core. Taken together, our study provides a direct structural comparison of OGDC and PDC from the same source and offers new insights into determinants of interdomain interactions and of architecture diversity among α-keto acid dehydrogenase complexes. | ||||||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_26649.map.gz | 13.2 MB | EMDB map data format | |
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Header (meta data) | emd-26649-v30.xml emd-26649.xml | 17 KB 17 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_26649_fsc.xml | 13.5 KB | Display | FSC data file |
Images | emd_26649.png | 172.5 KB | ||
Masks | emd_26649_msk_1.map | 216 MB | Mask map | |
Filedesc metadata | emd-26649.cif.gz | 5.8 KB | ||
Others | emd_26649_half_map_1.map.gz emd_26649_half_map_2.map.gz | 165.1 MB 164.9 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-26649 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-26649 | HTTPS FTP |
-Related structure data
Related structure data | 7uolMC 7uomC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_26649.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.36 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
File | emd_26649_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_26649_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_26649_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Endogenous dihydrolipoamide succinyltransferase (E2) core of 2-ox...
Entire | Name: Endogenous dihydrolipoamide succinyltransferase (E2) core of 2-oxoglutarate dehydrogenase complex from bovine kidney |
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Components |
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-Supramolecule #1: Endogenous dihydrolipoamide succinyltransferase (E2) core of 2-ox...
Supramolecule | Name: Endogenous dihydrolipoamide succinyltransferase (E2) core of 2-oxoglutarate dehydrogenase complex from bovine kidney type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: Bos taurus (cattle) / Organ: kidney / Tissue: kidney / Organelle: mitochondria / Location in cell: mitochondrial matrix |
Molecular weight | Theoretical: 49 KDa |
-Macromolecule #1: Dihydrolipoyllysine-residue succinyltransferase component of 2-ox...
Macromolecule | Name: Dihydrolipoyllysine-residue succinyltransferase component of 2-oxoglutarate dehydrogenase complex, mitochondrial type: protein_or_peptide / ID: 1 / Number of copies: 24 / Enantiomer: LEVO / EC number: dihydrolipoyllysine-residue succinyltransferase |
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Source (natural) | Organism: Bos taurus (cattle) / Organ: kidney / Tissue: kidney |
Molecular weight | Theoretical: 49.034414 KDa |
Sequence | String: MLSRSRCASR AFSRSLSAFQ KGNCPLVRRS LPGISLCQGP GYPDSRKTVI NSSNIFSVRF FRTTAVCKDD VITVKTPAFA ESVTEGDVR WEKAVGDTVA EDEVVCEIET DKTSVQVPSP ANGVIEALLV PDGGKVEGGT PLFTLRKTGA APAKAKPAAA P AAAAPKAE ...String: MLSRSRCASR AFSRSLSAFQ KGNCPLVRRS LPGISLCQGP GYPDSRKTVI NSSNIFSVRF FRTTAVCKDD VITVKTPAFA ESVTEGDVR WEKAVGDTVA EDEVVCEIET DKTSVQVPSP ANGVIEALLV PDGGKVEGGT PLFTLRKTGA APAKAKPAAA P AAAAPKAE PTVSAVPPPP AAPIPTQMPP VPSPSQPLTS KPVSAVKPTA APPRAEAGAG VGLRSEHREK MNRMRQRIAQ RL KEAQNTC AMLTTFNEID MSNIQEMRAR HKDAFLKKHN LKLGFMSAFV KASAFALQEQ PVVNAVIDDA TKEVVYRDYI DIS VAVATP RGLVVPVIRN VETMNYADIE RTISELGEKA RKNELAIEDM DGGTFTISNG GVFGSLFGTP IINPPQSAIL GMHA IVDRP VVIGGKVEVR PMMYVALTYD HRLIDGREAV TFLRKIKAAV EDPRVLLLDL UniProtKB: Dihydrolipoyllysine-residue succinyltransferase component of 2-oxoglutarate dehydrogenase complex, mitochondrial |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7 |
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Grid | Model: PELCO Ultrathin Carbon with Lacey Carbon / Material: COPPER / Support film - Material: CARBON / Support film - topology: LACEY / Pretreatment - Type: GLOW DISCHARGE |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 281 K / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Average exposure time: 8.0 sec. / Average electron dose: 45.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.6 µm / Nominal defocus min: 1.8 µm / Nominal magnification: 105000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
+Image processing
-Atomic model buiding 1
Initial model | PDB ID: Chain - Source name: PDB / Chain - Initial model type: experimental model |
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Software | Name: UCSF ChimeraX |
Refinement | Space: REAL / Protocol: BACKBONE TRACE |
Output model | PDB-7uol: |