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Yorodumi- EMDB-16135: Escherichia coli anaerobic fatty acid beta oxidation trifunctiona... -
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-Basic information
Entry | Database: EMDB / ID: EMD-16135 | ||||||||||||
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Title | Escherichia coli anaerobic fatty acid beta oxidation trifunctional enzyme (anEcTFE) tetrameric complex | ||||||||||||
Map data | anEcTFE A2B2 half map 1 | ||||||||||||
Sample |
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Keywords | complex / heterotetramer / MEMBRANE PROTEIN | ||||||||||||
Function / homology | Function and homology information fatty acid beta-oxidation, unsaturated, even number / fatty acid beta-oxidation multienzyme complex / 3-hydroxybutyryl-CoA epimerase / 3-hydroxybutyryl-CoA epimerase activity / acetyl-CoA C-acyltransferase / acetyl-CoA C-acyltransferase activity / long-chain-3-hydroxyacyl-CoA dehydrogenase activity / 3-hydroxyacyl-CoA dehydrogenase / enoyl-CoA hydratase / 3-hydroxyacyl-CoA dehydrogenase activity ...fatty acid beta-oxidation, unsaturated, even number / fatty acid beta-oxidation multienzyme complex / 3-hydroxybutyryl-CoA epimerase / 3-hydroxybutyryl-CoA epimerase activity / acetyl-CoA C-acyltransferase / acetyl-CoA C-acyltransferase activity / long-chain-3-hydroxyacyl-CoA dehydrogenase activity / 3-hydroxyacyl-CoA dehydrogenase / enoyl-CoA hydratase / 3-hydroxyacyl-CoA dehydrogenase activity / enoyl-CoA hydratase activity / fatty acid beta-oxidation / NAD+ binding / cytosol / cytoplasm Similarity search - Function | ||||||||||||
Biological species | Escherichia coli (E. coli) / Escherichia coli K-12 (bacteria) | ||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.55 Å | ||||||||||||
Authors | Sah-Teli SK / Pinkas M / Novacek J / Venkatesan R | ||||||||||||
Funding support | Czech Republic, Finland, European Union, 3 items
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Citation | Journal: Structure / Year: 2023 Title: Structural basis for different membrane-binding properties of E. coli anaerobic and human mitochondrial β-oxidation trifunctional enzymes. Authors: Shiv K Sah-Teli / Matyas Pinkas / Mikko J Hynönen / Sarah J Butcher / Rik K Wierenga / Jiri Novacek / Rajaram Venkatesan / Abstract: Facultative anaerobic bacteria such as Escherichia coli have two αβ heterotetrameric trifunctional enzymes (TFE), catalyzing the last three steps of the β-oxidation cycle: soluble aerobic TFE ...Facultative anaerobic bacteria such as Escherichia coli have two αβ heterotetrameric trifunctional enzymes (TFE), catalyzing the last three steps of the β-oxidation cycle: soluble aerobic TFE (EcTFE) and membrane-associated anaerobic TFE (anEcTFE), closely related to the human mitochondrial TFE (HsTFE). The cryo-EM structure of anEcTFE and crystal structures of anEcTFE-α show that the overall assembly of anEcTFE and HsTFE is similar. However, their membrane-binding properties differ considerably. The shorter A5-H7 and H8 regions of anEcTFE-α result in weaker α-β as well as α-membrane interactions, respectively. The protruding H-H region of anEcTFE-β is therefore more critical for membrane-association. Mutational studies also show that this region is important for the stability of the anEcTFE-β dimer and anEcTFE heterotetramer. The fatty acyl tail binding tunnel of the anEcTFE-α hydratase domain, as in HsTFE-α, is wider than in EcTFE-α, accommodating longer fatty acyl tails, in good agreement with their respective substrate specificities. | ||||||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_16135.map.gz | 12.1 MB | EMDB map data format | |
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Header (meta data) | emd-16135-v30.xml emd-16135.xml | 19.8 KB 19.8 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_16135_fsc.xml | 12.8 KB | Display | FSC data file |
Images | emd_16135.png | 91.7 KB | ||
Others | emd_16135_half_map_1.map.gz emd_16135_half_map_2.map.gz | 164.9 MB 164.9 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-16135 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-16135 | HTTPS FTP |
-Related structure data
Related structure data | 8bnuMC 8bnrC 8brjC 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_16135.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Annotation | anEcTFE A2B2 half map 1 | ||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.828 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: anEcTFE A2B2 half map 2
File | emd_16135_half_map_1.map | ||||||||||||
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Annotation | anEcTFE A2B2 half map 2 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: anEcTFE A2B2 half map 2
File | emd_16135_half_map_2.map | ||||||||||||
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Annotation | anEcTFE A2B2 half map 2 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : anEcTFE tetrameric
Entire | Name: anEcTFE tetrameric |
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Components |
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-Supramolecule #1: anEcTFE tetrameric
Supramolecule | Name: anEcTFE tetrameric / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all / Details: heterotetrameric complex |
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Source (natural) | Organism: Escherichia coli (E. coli) |
-Macromolecule #1: 3-ketoacyl-CoA thiolase FadI
Macromolecule | Name: 3-ketoacyl-CoA thiolase FadI / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO / EC number: acetyl-CoA C-acyltransferase |
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Source (natural) | Organism: Escherichia coli K-12 (bacteria) |
Molecular weight | Theoretical: 46.583379 KDa |
Recombinant expression | Organism: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) |
Sequence | String: MGQVLPLVTR QGDRIAIVSG LRTPFARQAT AFHGIPAVDL GKMVVGELLA RSEIPAEVIE QLVFGQVVQM PEAPNIAREI VLGTGMNVH TDAYSVSRAC ATSFQAVANV AESLMAGTIR AGIAGGADSS SVLPIGVSKK LARVLVDVNK ARTMSQRLKL F SRLRLRDL ...String: MGQVLPLVTR QGDRIAIVSG LRTPFARQAT AFHGIPAVDL GKMVVGELLA RSEIPAEVIE QLVFGQVVQM PEAPNIAREI VLGTGMNVH TDAYSVSRAC ATSFQAVANV AESLMAGTIR AGIAGGADSS SVLPIGVSKK LARVLVDVNK ARTMSQRLKL F SRLRLRDL MPVPPAVAEY STGLRMGDTA EQMAKTYGIT REQQDALAHR SHQRAAQAWS DGKLKEEVMT AFIPPYKQPL VE DNNIRGN SSLADYAKLR PAFDRKHGTV TAANSTPLTD GAAAVILMTE SRAKELGLVP LGYLRSYAFT AIDVWQDMLL GPA WSTPLA LERAGLTMSD LTLIDMHEAF AAQTLANIQL LGSERFAREA LGRAHATGEV DDSKFNVLGG SIAYGHPFAA TGAR MITQT LHELRRRGGG FGLVTACAAG GLGAAMVLEA E UniProtKB: 3-ketoacyl-CoA thiolase FadI |
-Macromolecule #2: Fatty acid oxidation complex subunit alpha
Macromolecule | Name: Fatty acid oxidation complex subunit alpha / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO / EC number: enoyl-CoA hydratase |
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Source (natural) | Organism: Escherichia coli K-12 (bacteria) |
Molecular weight | Theoretical: 76.711656 KDa |
Recombinant expression | Organism: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) |
Sequence | String: MEMTSAFTLN VRLDNIAVIT IDVPGEKMNT LKAEFASQVR AIIKQLRENK ELRGVVFVSA KPDNFIAGAD INMIGNCKTA QEAEALARQ GQQLMAEIHA LPIQVIAAIH GACLGGGLEL ALACHGRVCT DDPKTVLGLP EVQLGLLPGS GGTQRLPRLI G VSTALEMI ...String: MEMTSAFTLN VRLDNIAVIT IDVPGEKMNT LKAEFASQVR AIIKQLRENK ELRGVVFVSA KPDNFIAGAD INMIGNCKTA QEAEALARQ GQQLMAEIHA LPIQVIAAIH GACLGGGLEL ALACHGRVCT DDPKTVLGLP EVQLGLLPGS GGTQRLPRLI G VSTALEMI LTGKQLRAKQ ALKLGLVDDV VPHSILLEAA VELAKKERPS SRPLPVRERI LAGPLGRALL FKMVGKKTEH KT QGNYPAT ERILEVVETG LAQGTSSGYD AEARAFGELA MTPQSQALRS IFFASTDVKK DPGSDAPPAP LNSVGILGGG LMG GGIAYV TACKAGIPVR IKDINPQGIN HALKYSWDQL EGKVRRRHLK ASERDKQLAL ISGTTDYRGF AHRDLIIEAV FENL ELKQQ MVAEVEQNCA AHTIFASNTS SLPIGDIAAH ATRPEQVIGL HFFSPVEKMP LVEIIPHAGT SAQTIATTVK LAKKQ GKTP IVVRDKAGFY VNRILAPYIN EAIRMLTQGE RVEHIDAALV KFGFPVGPIQ LLDEVGIDTG TKIIPVLEAA YGERFS APA NVVSSILNDD RKGRKNGRGF YLYGQKGRKS KKQVDPAIYP LIGTQGQGRI SAPQVAERCV MLMLNEAVRC VDEQVIR SV RDGDIGAVFG IGFPPFLGGP FRYIDSLGAG EVVAIMQRLA TQYGSRFTPC ERLVEMGARG ESFWKTTA UniProtKB: Fatty acid oxidation complex subunit alpha |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.1 mg/mL |
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Buffer | pH: 8 Details: 50 mM Tris, 500 mM NaCl, 5% glycerol, 2.5 mM DTT, 0.0033% amphipol A8-35, pH 8 |
Grid | Model: C-flat-1.2/1.3 / Material: COPPER / Mesh: 300 / Support film - #0 - Film type ID: 1 / Support film - #0 - Material: GRAPHENE / Support film - #0 - topology: CONTINUOUS / Support film - #1 - Film type ID: 2 / Support film - #1 - Material: CARBON / Support film - #1 - topology: HOLEY / Pretreatment - Type: PLASMA CLEANING / Pretreatment - Time: 40 sec. / Pretreatment - Atmosphere: OTHER |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 30.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.2 µm |
Specialist optics | Energy filter - Name: GIF Bioquantum / Energy filter - Slit width: 10 eV |
Image recording | Film or detector model: GATAN K2 QUANTUM (4k x 4k) / Detector mode: COUNTING / Digitization - Dimensions - Width: 3838 pixel / Digitization - Dimensions - Height: 3710 pixel / Number grids imaged: 3 / Number real images: 18669 / Average exposure time: 5.0 sec. / Average electron dose: 48.0 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
-Atomic model buiding 1
Refinement | Space: REAL / Target criteria: cross-correlation coefficient |
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Output model | PDB-8bnu: |