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Yorodumi- EMDB-10556: Cryo-EM map of human dihydrolipoamide succinyltransferase catalyt... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-10556 | |||||||||
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Title | Cryo-EM map of human dihydrolipoamide succinyltransferase catalytic domain (DLST) | |||||||||
Map data | Human dihydrolipoamide succinyltransferase (E2) component of the 2-oxoglutarate dehydrogenase complex | |||||||||
Sample |
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Biological species | Homo sapiens (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 5.0 Å | |||||||||
Authors | Bailey HJ / Bezerra GA / Foster W / Diaz Saez L / Yue WW | |||||||||
Citation | Journal: To Be Published Title: Cryo-EM map of human dihydrolipoamide succinyltransferase (DLST) Authors: Bailey HJ / Bezerra GA / Foster W / Diaz Saez L / Yue WW | |||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_10556.map.gz | 16.6 MB | EMDB map data format | |
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Header (meta data) | emd-10556-v30.xml emd-10556.xml | 11.2 KB 11.2 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_10556_fsc.xml | 12.3 KB | Display | FSC data file |
Images | emd_10556.png | 136.3 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-10556 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-10556 | HTTPS FTP |
-Validation report
Summary document | emd_10556_validation.pdf.gz | 262 KB | Display | EMDB validaton report |
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Full document | emd_10556_full_validation.pdf.gz | 261.2 KB | Display | |
Data in XML | emd_10556_validation.xml.gz | 12.6 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-10556 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-10556 | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_10556.map.gz / Format: CCP4 / Size: 155.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Human dihydrolipoamide succinyltransferase (E2) component of the 2-oxoglutarate dehydrogenase complex | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.96 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
-Entire : human dihydrolipoamide succinyltransferase (DLST)
Entire | Name: human dihydrolipoamide succinyltransferase (DLST) |
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Components |
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-Supramolecule #1: human dihydrolipoamide succinyltransferase (DLST)
Supramolecule | Name: human dihydrolipoamide succinyltransferase (DLST) / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: Homo sapiens (human) |
Recombinant expression | Organism: Spodoptera frugiperda (fall armyworm) |
Molecular weight | Theoretical: 1.059 MDa |
-Macromolecule #1: human dihydrolipoamide succinyltransferase (DLST)
Macromolecule | Name: human dihydrolipoamide succinyltransferase (DLST) / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Recombinant expression | Organism: Spodoptera frugiperda (fall armyworm) |
Sequence | String: MGHHHHHHSS GVDLGTENLY FQSMDDLVTV KTPAFAESVT EGDVRWEKAV GDTVAEDEVV CEIETDKTSV QVPSPANGVI EALLVPDGGK VEGGTPLFTL RKTGAAPAKA KPAEAPAAAA PKAEPTAAAV PPPAAPIPTQ MPPVPSPSQP PSGKPVSAVK PTVAPPLAEP ...String: MGHHHHHHSS GVDLGTENLY FQSMDDLVTV KTPAFAESVT EGDVRWEKAV GDTVAEDEVV CEIETDKTSV QVPSPANGVI EALLVPDGGK VEGGTPLFTL RKTGAAPAKA KPAEAPAAAA PKAEPTAAAV PPPAAPIPTQ MPPVPSPSQP PSGKPVSAVK PTVAPPLAEP GAGKGLRSEH REKMNRMRQR IAQRLKEAQN TCAMLTTFNE IDMSNIQEMR ARHKEAFLKK HNLKLGFMSA FVKASAFALQ EQPVVNAVID DTTKEVVYRD YIDISVAVAT PRGLVVPVIR NVEAMNFADI ERTITELGEK ARKNELAIED MDGGTFTISN GGVFGSLFGT PIINPPQSAI LGMHGIFDRP VAIGGKVEVR PMMYVALTYD HRLIDGREAV TFLRKIKAAV EDPRVLLLDL |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.2 mg/mL | ||||||||
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Buffer | pH: 7.5 Component:
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Grid | Model: Quantifoil R2/1 / Material: GOLD / Pretreatment - Type: GLOW DISCHARGE | ||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K |
-Electron microscopy
Microscope | TFS GLACIOS |
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Image recording | Film or detector model: FEI FALCON III (4k x 4k) / Detector mode: OTHER / Number grids imaged: 1 / Number real images: 619 / Average exposure time: 1.0 sec. / Average electron dose: 32.52 e/Å2 |
Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: OTHER / Imaging mode: OTHER / Nominal magnification: 150000 |