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- EMDB-61725: Cryo-EM Structure of Fructose Dehydrogenase Variant from Gluconob... -
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Open data
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Basic information
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Title | Cryo-EM Structure of Fructose Dehydrogenase Variant from Gluconobacter japonicus Truncating Heme 1c and C-Terminal Hydrophobic Regions | ||||||||||||
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![]() | Complex / OXIDOREDUCTASE Membrane-bound protein / OXIDOREDUCTASE | ||||||||||||
Function / homology | ![]() fructose 5-dehydrogenase / fructose 5-dehydrogenase activity / oxidoreductase activity, acting on CH-OH group of donors / fructose metabolic process / flavin adenine dinucleotide binding / electron transfer activity / iron ion binding / heme binding / plasma membrane Similarity search - Function | ||||||||||||
Biological species | ![]() | ||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.15 Å | ||||||||||||
![]() | Adachi T / Ichikawa K / Miyata T / Makino F / Tanaka H / Namba K / Sowa K / Shirai O | ||||||||||||
Funding support | ![]()
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![]() | ![]() Title: Improved Direct Bioelectrochemical Fructose Oxidation with Surfactant-Free Heterotrimeric Fructose Dehydrogenase Variant Truncating Heme 1c and C-Terminal Hydrophobic Regions Authors: Adachi T / Ichikawa K / Miyata T / Makino F / Tanaka H / Namba K / Sowa K | ||||||||||||
History |
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Structure visualization
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 63.1 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 24.1 KB 24.1 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 10.5 KB | Display | ![]() |
Images | ![]() | 92.8 KB | ||
Masks | ![]() | 125 MB | ![]() | |
Filedesc metadata | ![]() | 7.1 KB | ||
Others | ![]() ![]() | 116.2 MB 116.2 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 713.2 KB | Display | ![]() |
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Full document | ![]() | 712.8 KB | Display | |
Data in XML | ![]() | 18.9 KB | Display | |
Data in CIF | ![]() | 24.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 9jqaMC M: atomic model generated by this map C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
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Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.87 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_61725_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_61725_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
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Sample components
-Entire : D-fructose dehydrogenase Variant from Gluconobacter japonicus Tru...
Entire | Name: D-fructose dehydrogenase Variant from Gluconobacter japonicus Truncating Heme 1c and C-terminal Hydrophobic Regions |
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Components |
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-Supramolecule #1: D-fructose dehydrogenase Variant from Gluconobacter japonicus Tru...
Supramolecule | Name: D-fructose dehydrogenase Variant from Gluconobacter japonicus Truncating Heme 1c and C-terminal Hydrophobic Regions type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3 |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 110 KDa |
-Macromolecule #1: Fructose dehydrogenase large subunit
Macromolecule | Name: Fructose dehydrogenase large subunit / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO / EC number: ec: 1.1.99.11 |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 59.798309 KDa |
Recombinant expression | Organism: ![]() |
Sequence | String: MSNETLSADV VIIGAGICGS LLAHKLVRNG LSVLLLDAGP RRDRSQIVEN WRNMPPDNKS QYDYATPYPS VPWAPHTNYF PDNNYLIVK GPDRTAYKQG IIKGVGGTTW HWAASSWRYL PNDFKLHSTY GVGRDYAMSY DELEPYYYEA ECEMGVMGPN G EEITPSAP ...String: MSNETLSADV VIIGAGICGS LLAHKLVRNG LSVLLLDAGP RRDRSQIVEN WRNMPPDNKS QYDYATPYPS VPWAPHTNYF PDNNYLIVK GPDRTAYKQG IIKGVGGTTW HWAASSWRYL PNDFKLHSTY GVGRDYAMSY DELEPYYYEA ECEMGVMGPN G EEITPSAP RQNPWPMTSM PYGYGDRTFT EIVSKLGFSN TPVPQARNSR PYDGRPQCCG NNNCMPICPI GAMYNGVYAA IK AEKLGAK IIPNAVVYAM ETDAKNRITA ISFYDPDKQS HRVVAKTFVI AANGIETPKL LLLAANDRNP HGIANSSDLV GRN MMDHPG IGMSFQSAEP IWAGGGSVQM SSITNFRDGD FRSEYAATQI GYNNTAQNSR AGMKALSMGL VGKKLDEEIR RRTA HGVDI YANHEVLPDP NNRLVLSKDY KDALGIPHPE VTYDVGEYVR KSAAISRQRL MDIAKAMGGT EIEMTPYFTP NNHIT GGTI MGHDPRDSVV DKWLRTHDHS NLFLATGATM AASGTVNSTL TMAALSLRAA DAILNDLKQG UniProtKB: Fructose dehydrogenase large subunit |
-Macromolecule #2: Fructose dehydrogenase small subunit
Macromolecule | Name: Fructose dehydrogenase small subunit / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 20.106732 KDa |
Recombinant expression | Organism: ![]() |
Sequence | String: MEKIADSGPV QIFLSRRKLL AFSGASLTVA AIGAPSKGST QDVVASNRDS ISDFMQLSAF ATGHKNLDLN IGSALLLAFE AQKHDFSTQ IKALREHITK NNYQDVEALD AAMKDDPLHP TLIQIIRAWY SGVIEDETNA KVYAFEKALM YQPSRDVVVI P TYAHNGPN YWVSEPASVD VMPAF UniProtKB: Fructose dehydrogenase small subunit |
-Macromolecule #3: Fructose dehydrogenase cytochrome subunit
Macromolecule | Name: Fructose dehydrogenase cytochrome subunit / type: protein_or_peptide / ID: 3 / Details: deltaP27-I169 deltaG454-W476 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 34.431387 KDa |
Recombinant expression | Organism: ![]() |
Sequence | String: MRYFRPLSAT AMTTVLLLAG TNVRAQAARI EGKPYVFDHT HNDDWNRGRY LVDELAHCGE CHTPRNFLLA PNQSAYLAGA DIGSWRAPN ITNAPQSGIG SWSDQDLFQY LKTGKTAHAR AAGPMAEAIE HSLQYLPDAD ISAIVTYLRS VPAKAESGQT V ANFEHAGR ...String: MRYFRPLSAT AMTTVLLLAG TNVRAQAARI EGKPYVFDHT HNDDWNRGRY LVDELAHCGE CHTPRNFLLA PNQSAYLAGA DIGSWRAPN ITNAPQSGIG SWSDQDLFQY LKTGKTAHAR AAGPMAEAIE HSLQYLPDAD ISAIVTYLRS VPAKAESGQT V ANFEHAGR PSSYSVANAN SRRSNSTLTK TTDGAALYEA VCASCHQSDG KGSKDGYYPS LVGNTTTGQL NPNDLIASIL YG VDRTTDN HEILMPAFGP DSLVQPLTDE QIATIADYVL SHFGNAQATV SADAVKQVRA GGKQVPLAKL ASPLISRRKK RSA UniProtKB: Fructose dehydrogenase cytochrome subunit, Fructose dehydrogenase cytochrome subunit |
-Macromolecule #4: FLAVIN-ADENINE DINUCLEOTIDE
Macromolecule | Name: FLAVIN-ADENINE DINUCLEOTIDE / type: ligand / ID: 4 / Number of copies: 1 / Formula: FAD |
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Molecular weight | Theoretical: 785.55 Da |
Chemical component information | ![]() ChemComp-FAD: |
-Macromolecule #5: FE3-S4 CLUSTER
Macromolecule | Name: FE3-S4 CLUSTER / type: ligand / ID: 5 / Number of copies: 1 / Formula: F3S |
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Molecular weight | Theoretical: 295.795 Da |
Chemical component information | ![]() ChemComp-F3S: |
-Macromolecule #6: HEME C
Macromolecule | Name: HEME C / type: ligand / ID: 6 / Number of copies: 2 / Formula: HEC |
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Molecular weight | Theoretical: 618.503 Da |
Chemical component information | ![]() ChemComp-HEC: |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Concentration | 5 mg/mL | ||||||||||||
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Buffer | pH: 6 Component:
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Grid | Model: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 200 / Support film - Material: CARBON / Support film - topology: HOLEY / Support film - Film thickness: 500 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 20 sec. | ||||||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV |
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Electron microscopy
Microscope | JEOL CRYO ARM 300 |
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Temperature | Min: 80.0 K / Max: 80.0 K |
Alignment procedure | Coma free - Residual tilt: 0.01 mrad |
Specialist optics | Energy filter - Name: In-column Omega Filter / Energy filter - Slit width: 20 eV |
Image recording | Film or detector model: GATAN K3 (6k x 4k) / Number grids imaged: 1 / Number real images: 20066 / Average exposure time: 3.0 sec. / Average electron dose: 80.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | C2 aperture diameter: 50.0 µm / Calibrated defocus max: 2.5 µm / Calibrated defocus min: 0.5 µm / Calibrated magnification: 56754 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.5 µm / Nominal magnification: 60000 |
Sample stage | Specimen holder model: JEOL CRYOSPECPORTER / Cooling holder cryogen: NITROGEN |
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Image processing
-Atomic model buiding 1
Refinement | Space: REAL / Protocol: FLEXIBLE FIT |
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Output model | ![]() PDB-9jqa: |