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Yorodumi- EMDB-21156: Cryo-EM Structure of Escherichia coli 2-oxoglutarate dehydrogenas... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-21156 | |||||||||
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Title | Cryo-EM Structure of Escherichia coli 2-oxoglutarate dehydrogenase E1 component sucA | |||||||||
Map data | Escherichia coli 2-oxoglutarate dehydrogenase E1 component sucA | |||||||||
Sample |
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Keywords | TCA cycle / 2-oxoglutarate dehydrogenase complex (OGDH) / E1 component / sucA / AMP / Oxaloacetate (OAA) / Dimer / OXIDOREDUCTASE | |||||||||
Function / homology | Function and homology information oxoglutarate dehydrogenase (succinyl-transferring) / oxoglutarate dehydrogenase (succinyl-transferring) activity / oxoglutarate dehydrogenase complex / thiamine pyrophosphate binding / tricarboxylic acid cycle / nucleotide binding / magnesium ion binding / identical protein binding / cytoplasm / cytosol Similarity search - Function | |||||||||
Biological species | Escherichia coli K-12 (bacteria) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.08 Å | |||||||||
Authors | Gao H | |||||||||
Citation | Journal: To Be Published Title: Cryo-EM Structure of Escherichia coli 2-oxoglutarate dehydrogenase E1 component sucA Authors: Gao H | |||||||||
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_21156.map.gz | 28.5 MB | EMDB map data format | |
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Header (meta data) | emd-21156-v30.xml emd-21156.xml | 11.6 KB 11.6 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_21156_fsc.xml | 9.3 KB | Display | FSC data file |
Images | emd_21156.png | 158.5 KB | ||
Filedesc metadata | emd-21156.cif.gz | 5.5 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-21156 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-21156 | HTTPS FTP |
-Validation report
Summary document | emd_21156_validation.pdf.gz | 587.1 KB | Display | EMDB validaton report |
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Full document | emd_21156_full_validation.pdf.gz | 586.6 KB | Display | |
Data in XML | emd_21156_validation.xml.gz | 9.6 KB | Display | |
Data in CIF | emd_21156_validation.cif.gz | 12.3 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-21156 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-21156 | HTTPS FTP |
-Related structure data
Related structure data | 6vefMC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_21156.map.gz / Format: CCP4 / Size: 30.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Escherichia coli 2-oxoglutarate dehydrogenase E1 component sucA | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.877 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 : Escherichia coli 2-oxoglutarate dehydrogenase E1 component sucA
Entire | Name: Escherichia coli 2-oxoglutarate dehydrogenase E1 component sucA |
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Components |
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-Supramolecule #1: Escherichia coli 2-oxoglutarate dehydrogenase E1 component sucA
Supramolecule | Name: Escherichia coli 2-oxoglutarate dehydrogenase E1 component sucA type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1 |
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Source (natural) | Organism: Escherichia coli K-12 (bacteria) |
-Macromolecule #1: 2-oxoglutarate dehydrogenase E1 component
Macromolecule | Name: 2-oxoglutarate dehydrogenase E1 component / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO EC number: oxoglutarate dehydrogenase (succinyl-transferring) |
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Source (natural) | Organism: Escherichia coli K-12 (bacteria) / Strain: K12 |
Molecular weight | Theoretical: 94.942508 KDa |
Sequence | String: DTNVKQVKVL QLINAYRFRG HQHANLDPLG LYQQDKVADL DPSFHDLTEA DFQETFNVGS FASGKETMKL GELLEALKQT YCGPIGAEY MHITSTEEKR WIQQRIESGR ATFNSEEKKR FLSELTAAEG LERYLGAKFP GAKRFSLEGD ALIPMLKEMI R HAGNSGTR ...String: DTNVKQVKVL QLINAYRFRG HQHANLDPLG LYQQDKVADL DPSFHDLTEA DFQETFNVGS FASGKETMKL GELLEALKQT YCGPIGAEY MHITSTEEKR WIQQRIESGR ATFNSEEKKR FLSELTAAEG LERYLGAKFP GAKRFSLEGD ALIPMLKEMI R HAGNSGTR EVVLGMAHRG RLNVLVNVLG KKPQDLFDEF AGKHKEHLGT GDVKYHMGFS SDFQTDGGLV HLALAFNPSH LE IVSPVVI GSVRARLDRL DEPSSNKVLP ITIHGDAAVT GQGVVQETLN MSKARGYEVG GTVRIVINNQ VGFTTSNPLD ARS TPYMTD IGKMVQAPIF HVNADDPEAV AFVTRLALDF RNTFKRDVFI DLVCYRRHGH NEADEPSATQ KIKKHPTPRK IYAD KLEQE KVATLEDATE MVNLYRDALD AGDCVVAEWR PMNMHSFTWS PYLNHEWDEE YPNKVEMKRL QELAKRISTV PEAVE MQSR VAKIYGDRQA MAAGEKLFDW GGAENLAYAT LVDEGIPVRL SGEDSGRGTF FHRHAVIHNQ SNGSTYTPLQ HIHNGQ GAF RVWDSVLSEE AVLAFEYGYA TAEPRTLTIW EAQFGDFANG AQVVIDQFIS SGEQKWGRMC GLVMLLPHGY EGQGPEH SS ARLERYLQLC AEQNMQVCVP STPAQVYHML RRQALRGMRR PLVVMSPKSL LRHPLAVSSL EELANGTFLP AIGEIDEL D PKGVKRVVMC SGKVYYDLLE QRRKNNQHDV AIVRIEQLYP FPHKAMQEVL QQFAHVKDFV WCQEEPLNQG AWYCSQHHF REVIPFGASL RYAGRPASAS PAVGHMSVHQ KQQQDLVNDA LNVE UniProtKB: Oxoglutarate dehydrogenase (succinyl-transferring) |
-Macromolecule #2: ADENOSINE MONOPHOSPHATE
Macromolecule | Name: ADENOSINE MONOPHOSPHATE / type: ligand / ID: 2 / Number of copies: 2 / Formula: AMP |
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Molecular weight | Theoretical: 347.221 Da |
Chemical component information | ChemComp-AMP: |
-Macromolecule #3: OXALOACETATE ION
Macromolecule | Name: OXALOACETATE ION / type: ligand / ID: 3 / Number of copies: 2 / Formula: OAA |
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Molecular weight | Theoretical: 131.064 Da |
Chemical component information | ChemComp-OAA: |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.5 |
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Grid | Model: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 80 sec. |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | FEI TECNAI ARCTICA |
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Image recording | Film or detector model: GATAN K3 (6k x 4k) / Number grids imaged: 1 / Number real images: 800 / Average exposure time: 2.0 sec. / Average electron dose: 80.0 e/Å2 |
Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm |
Experimental equipment | Model: Talos Arctica / Image courtesy: FEI Company |