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Yorodumi- EMDB-36921: Cryo-EM Structure of Membrane-bound Fructose Dehydrogenase from G... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-36921 | ||||||||||||
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Title | Cryo-EM Structure of Membrane-bound Fructose Dehydrogenase from Gluconobacter japonicus variant-N1146A | ||||||||||||
Map data | |||||||||||||
Sample |
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Keywords | Complex / OXIDOREDUCTASE Membrane-bound protein / OXIDEREDUCTASE / OXIDOREDUCTASE | ||||||||||||
Function / homology | Function and homology information oxidoreductase activity, acting on CH-OH group of donors / fructose metabolic process / electron transfer activity / iron ion binding / heme binding / plasma membrane Similarity search - Function | ||||||||||||
Biological species | Gluconobacter japonicus (bacteria) | ||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.4 Å | ||||||||||||
Authors | Fukawa E / Miyata T / Makino F / Adachi T / Suzuki Y / Tanaka H / Namba K / Sowa K / Kitazumi Y / Shirai O | ||||||||||||
Funding support | Japan, 3 items
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Citation | Journal: Electrochim Acta / Year: 2024 Title: Structural and electrochemical elucidation of biocatalytic mechanisms in direct electron transfer-type D-fructose dehydrogenase. Authors: Fukawa E / Suzuki Y / Adachi T / Miyata T / Makino F / Tanaka H / Namba K / Sowa K / Kitazumi Y / Shirai O | ||||||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_36921.map.gz | 42.3 MB | EMDB map data format | |
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Header (meta data) | emd-36921-v30.xml emd-36921.xml | 23.7 KB 23.7 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_36921_fsc.xml | 9.2 KB | Display | FSC data file |
Images | emd_36921.png | 104.3 KB | ||
Masks | emd_36921_msk_1.map | 83.7 MB | Mask map | |
Filedesc metadata | emd-36921.cif.gz | 7.4 KB | ||
Others | emd_36921_half_map_1.map.gz emd_36921_half_map_2.map.gz | 77.7 MB 77.7 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-36921 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-36921 | HTTPS FTP |
-Validation report
Summary document | emd_36921_validation.pdf.gz | 881.4 KB | Display | EMDB validaton report |
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Full document | emd_36921_full_validation.pdf.gz | 881 KB | Display | |
Data in XML | emd_36921_validation.xml.gz | 17.5 KB | Display | |
Data in CIF | emd_36921_validation.cif.gz | 22.5 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-36921 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-36921 | HTTPS FTP |
-Related structure data
Related structure data | 8k6kMC 8k6jC 8xcmC 8xcnC 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_36921.map.gz / Format: CCP4 / Size: 83.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.86 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
File | emd_36921_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_36921_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_36921_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : D-fructose dehydrogenase (N1146A) from Gluconobacter japonicus
Entire | Name: D-fructose dehydrogenase (N1146A) from Gluconobacter japonicus |
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Components |
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-Supramolecule #1: D-fructose dehydrogenase (N1146A) from Gluconobacter japonicus
Supramolecule | Name: D-fructose dehydrogenase (N1146A) from Gluconobacter japonicus type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3 |
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Source (natural) | Organism: Gluconobacter japonicus (bacteria) |
Molecular weight | Theoretical: 140 KDa |
-Macromolecule #1: Fructose dehydrogenase (N1146A) large subunit
Macromolecule | Name: Fructose dehydrogenase (N1146A) 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: Gluconobacter japonicus (bacteria) |
Molecular weight | Theoretical: 59.755285 KDa |
Recombinant expression | Organism: Gluconobacter oxydans (bacteria) |
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 NAHIT GGTI MGHDPRDSVV DKWLRTHDHS NLFLATGATM AASGTVNSTL TMAALSLRAA DAILNDLKQG |
-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: Gluconobacter japonicus (bacteria) |
Molecular weight | Theoretical: 20.106732 KDa |
Recombinant expression | Organism: Gluconobacter oxydans (bacteria) |
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 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Gluconobacter japonicus (bacteria) |
Molecular weight | Theoretical: 52.252652 KDa |
Recombinant expression | Organism: Gluconobacter oxydans (bacteria) |
Sequence | String: MRYFRPLSAT AMTTVLLLAG TNVRAQPTEP TPASAHRPSI SRGHYLAIAA DCAACHTNGR DGQFLAGGYA ISSPMGNIYS TNITPSKTH GIGNYTLEQF SKALRHGIRA DGAQLYPAMP YDAYNRLTDE DVKSLYAYIM TEVKPVDAPS PKTQLPFPFS I RASLGIWK ...String: MRYFRPLSAT AMTTVLLLAG TNVRAQPTEP TPASAHRPSI SRGHYLAIAA DCAACHTNGR DGQFLAGGYA ISSPMGNIYS TNITPSKTH GIGNYTLEQF SKALRHGIRA DGAQLYPAMP YDAYNRLTDE DVKSLYAYIM TEVKPVDAPS PKTQLPFPFS I RASLGIWK IAARIEGKPY VFDHTHNDDW NRGRYLVDEL AHCGECHTPR NFLLAPNQSA YLAGADIGSW RAPNITNAPQ SG IGSWSDQ DLFQYLKTGK TAHARAAGPM AEAIEHSLQY LPDADISAIV TYLRSVPAKA ESGQTVANFE HAGRPSSYSV ANA NSRRSN STLTKTTDGA ALYEAVCASC HQSDGKGSKD GYYPSLVGNT TTGQLNPNDL IASILYGVDR TTDNHEILMP AFGP DSLVQ PLTDEQIATI ADYVLSHFGN AQATVSADAV KQVRAGGKQV PLAKLASPGV MLLLGTGGIL GAILVVAGLW WLISR RKKR SA UniProtKB: 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: 3 / Formula: HEC |
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Molecular weight | Theoretical: 618.503 Da |
Chemical component information | ChemComp-HEC: |
-Macromolecule #7: UBIQUINONE-10
Macromolecule | Name: UBIQUINONE-10 / type: ligand / ID: 7 / Number of copies: 1 / Formula: U10 |
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Molecular weight | Theoretical: 863.343 Da |
Chemical component information | ChemComp-U10: |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 3.6 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. / Pretreatment - Atmosphere: AIR | |||||||||||||||
Vitrification | Cryogen name: ETHANE |
-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: 9439 / Average exposure time: 3.0 sec. / Average electron dose: 80.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
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 |