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Yorodumi- EMDB-35042: Cryo-EM structure of the the 2-oxoglutarate dehydrogenase (E1) wi... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-35042 | |||||||||
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Title | Cryo-EM structure of the the 2-oxoglutarate dehydrogenase (E1) with TCAIM complex | |||||||||
Map data | ||||||||||
Sample |
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Keywords | TCAIM / Mitochondria / alpha ketoglutarate dehydrogenase / OGDH / proteostasis / DNAJC / single particle cryoEM / PROTEIN BINDING | |||||||||
Function / homology | Function and homology information oxoglutarate dehydrogenase (NAD+) activity / olfactory bulb mitral cell layer development / oxoglutarate dehydrogenase (succinyl-transferring) / : / succinyl-CoA metabolic process / oxoglutarate dehydrogenase (succinyl-transferring) activity / tangential migration from the subventricular zone to the olfactory bulb / oxoglutarate dehydrogenase complex / cerebellar cortex development / Lysine catabolism ...oxoglutarate dehydrogenase (NAD+) activity / olfactory bulb mitral cell layer development / oxoglutarate dehydrogenase (succinyl-transferring) / : / succinyl-CoA metabolic process / oxoglutarate dehydrogenase (succinyl-transferring) activity / tangential migration from the subventricular zone to the olfactory bulb / oxoglutarate dehydrogenase complex / cerebellar cortex development / Lysine catabolism / pyramidal neuron development / Citric acid cycle (TCA cycle) / thalamus development / 2-oxoglutarate metabolic process / striatum development / Glyoxylate metabolism and glycine degradation / thiamine pyrophosphate binding / tricarboxylic acid cycle / generation of precursor metabolites and energy / hippocampus development / mitochondrial membrane / glycolytic process / mitochondrial matrix / mitochondrion / metal ion binding / nucleus Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.86 Å | |||||||||
Authors | Yu X / Yang W | |||||||||
Funding support | China, 1 items
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Citation | Journal: To Be Published Title: Cryo-electron microscopic structure of the 2-oxoglutarate dehydrogenase (E1) with TCAIM complex Authors: Yu X / Yang W / Zhong YH / Ma XM / Gao YZ | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_35042.map.gz | 44.9 MB | EMDB map data format | |
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Header (meta data) | emd-35042-v30.xml emd-35042.xml | 13.3 KB 13.3 KB | Display Display | EMDB header |
Images | emd_35042.png | 50.1 KB | ||
Filedesc metadata | emd-35042.cif.gz | 5.2 KB | ||
Others | emd_35042_half_map_1.map.gz emd_35042_half_map_2.map.gz | 59.3 MB 59.3 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-35042 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-35042 | HTTPS FTP |
-Related structure data
Related structure data | 8i0kMC 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_35042.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Voxel size | X=Y=Z: 0.855 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: #2
File | emd_35042_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_35042_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : 2-oxoglutarate dehydrogenase, OGDH and T cell activation inhibito...
Entire | Name: 2-oxoglutarate dehydrogenase, OGDH and T cell activation inhibitor mitochondrial, TCAIMOxoglutarate dehydrogenase complex |
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Components |
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-Supramolecule #1: 2-oxoglutarate dehydrogenase, OGDH and T cell activation inhibito...
Supramolecule | Name: 2-oxoglutarate dehydrogenase, OGDH and T cell activation inhibitor mitochondrial, TCAIM type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: Homo sapiens (human) |
-Macromolecule #1: 2-oxoglutarate dehydrogenase(E1)
Macromolecule | Name: 2-oxoglutarate dehydrogenase(E1) / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO EC number: oxoglutarate dehydrogenase (succinyl-transferring) |
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Source (natural) | Organism: Homo sapiens (human) |
Sequence | String: HNEMDEPMFT QPLMYKQIRK QKPVLQKYAE LLVSQGVVNQ PEYEEEISKY DKICEEAFAR SKDEKILHIK HWLDSPWPGF FTLDGQPRS MSCPSTGLTE DILTHIGNVA SSVPVENFTI HGGLSRILKT RGEMVKNRTV DWALAEYMAF GSLLKEGIHI R LSGQDVER ...String: HNEMDEPMFT QPLMYKQIRK QKPVLQKYAE LLVSQGVVNQ PEYEEEISKY DKICEEAFAR SKDEKILHIK HWLDSPWPGF FTLDGQPRS MSCPSTGLTE DILTHIGNVA SSVPVENFTI HGGLSRILKT RGEMVKNRTV DWALAEYMAF GSLLKEGIHI R LSGQDVER GTFSHRHHVL HDQNVDKRTC IPMNHLWPNQ APYTVCNSSL SEYGVLGFEL GFAMASPNAL VLWEAQFGDF HN TAQCIID QFICPGQAKW VRQNGIVLLL PHGMEGMGPE HSSARPERFL QMCNDDPDVL PDLKEANFDI NQLYDCNWVV VNC STPGNF FHVLRRQILL PFRKPLIIFT PKSLLRHPEA RSSFDEMLPG THFQRVIPED GPAAQNPENV KRLLFCTGKV YYDL TRERK ARDMVGQVAI TRIEQLSPFP FDLLLKEVQK YPNAELAWCQ EEHKNQGYYD YVKPRLRTTI SRAKPVWYAG RDPAA APAT GNKKTHLTEL QRLLDTAFDL DVFKNFS |
-Macromolecule #2: T-cell activation inhibitor, mitochondrial
Macromolecule | Name: T-cell activation inhibitor, mitochondrial / type: protein_or_peptide / ID: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Sequence | String: TTLTSWLDNN GKSAVKKLKN SLPLRKELDR LKDELSHQLQ LSDIRWQRSW GIAHRCSQLH SLSRLAQQNL ETLKKAKGCT IIFTDRSGM SAVGHVMLGT MDVHHHWTKL FERLPSYFDL QRRLMILEDQ ISYLLGGIQV VYIEELQPVL TLEEYYSLLD V FYNRLLKS ...String: TTLTSWLDNN GKSAVKKLKN SLPLRKELDR LKDELSHQLQ LSDIRWQRSW GIAHRCSQLH SLSRLAQQNL ETLKKAKGCT IIFTDRSGM SAVGHVMLGT MDVHHHWTKL FERLPSYFDL QRRLMILEDQ ISYLLGGIQV VYIEELQPVL TLEEYYSLLD V FYNRLLKS RILFHPRSLR GLQMILNSDR YAPSLHELGH FNIPTLCDPA NLQWFILTKA QQARENMKRK EELKVIENEL IQ ASTKKFS LEKLYKEPSI SSIQMVDCCK RLLEQSLPYL HGMHLCISHF YSVMQDGDLC IPWNW |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.4 |
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Vitrification | Cryogen name: ETHANE-PROPANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm |
Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 60.0 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Startup model | Type of model: NONE |
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Initial angle assignment | Type: ANGULAR RECONSTITUTION |
Final angle assignment | Type: ANGULAR RECONSTITUTION |
Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 2.86 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 1342786 |