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Yorodumi- EMDB-34369: Cryo-EM Structure of Membrane-Bound Aldehyde Dehydrogenase from G... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-34369 | |||||||||
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Title | Cryo-EM Structure of Membrane-Bound Aldehyde Dehydrogenase from Gluconobacter oxydans | |||||||||
Map data | ||||||||||
Sample |
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Keywords | Complex / Oxidoreductase / Membrane-bound protein | |||||||||
Function / homology | Function and homology information oxidoreductase activity, acting on CH-OH group of donors / 2 iron, 2 sulfur cluster binding / oxidoreductase activity / electron transfer activity / iron ion binding / heme binding / metal ion binding / plasma membrane Similarity search - Function | |||||||||
Biological species | Gluconobacter oxydans (bacteria) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.7 Å | |||||||||
Authors | Adachi T / Miyata T / Makino F / Tanaka H / Namba K / Sowa K / Kitazumi Y / Shirai O | |||||||||
Funding support | Japan, 2 items
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Citation | Journal: Acs Catalysis / Year: 2023 Title: Experimental and Theoretical Insights into Bienzymatic Cascade for Mediatorless Bioelectrochemical Ethanol Oxidation with Alcohol and Aldehyde Dehydrogenases Authors: Adachi T / Miyata T / Makino F / Tanaka H / Namba K / Kano 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_34369.map.gz | 62.6 MB | EMDB map data format | |
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Header (meta data) | emd-34369-v30.xml emd-34369.xml | 23.9 KB 23.9 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_34369_fsc.xml | 10.5 KB | Display | FSC data file |
Images | emd_34369.png | 87.4 KB | ||
Masks | emd_34369_msk_1.map | 125 MB | Mask map | |
Others | emd_34369_half_map_1.map.gz emd_34369_half_map_2.map.gz | 116.1 MB 116.1 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-34369 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-34369 | HTTPS FTP |
-Validation report
Summary document | emd_34369_validation.pdf.gz | 923 KB | Display | EMDB validaton report |
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Full document | emd_34369_full_validation.pdf.gz | 922.6 KB | Display | |
Data in XML | emd_34369_validation.xml.gz | 18.9 KB | Display | |
Data in CIF | emd_34369_validation.cif.gz | 24.3 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-34369 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-34369 | HTTPS FTP |
-Related structure data
Related structure data | 8gy3MC 8gy2C 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_34369.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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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
File | emd_34369_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_34369_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_34369_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Aldehyde dehydrogenase from Gluconobacter oxydans
Entire | Name: Aldehyde dehydrogenase from Gluconobacter oxydans |
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Components |
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-Supramolecule #1: Aldehyde dehydrogenase from Gluconobacter oxydans
Supramolecule | Name: Aldehyde dehydrogenase from Gluconobacter oxydans / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3 |
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Source (natural) | Organism: Gluconobacter oxydans (bacteria) |
Molecular weight | Theoretical: 150 KDa |
-Macromolecule #1: Cytochrome c subunit of aldehyde dehydrogenase
Macromolecule | Name: Cytochrome c subunit of aldehyde dehydrogenase / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO / EC number: aldehyde dehydrogenase (FAD-independent) |
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Source (natural) | Organism: Gluconobacter oxydans (bacteria) |
Molecular weight | Theoretical: 48.5195 KDa |
Recombinant expression | Organism: Gluconobacter oxydans (bacteria) |
Sequence | String: MLKRIAAAVI GLGAVGGIGF LAYAWYPAIA PIPRPAASSF SADAISRGEI VANGGYCAEC HTRVDGKPGP ELAGDFKMAT PFGDIFSSN ITPDEEWGIG NWSLAAFKRA MNKGIARDGS QLYPAFPFDH FTKVSDQDVS DLYAYLMTRP AVHLKPRDNT V PFPINIRL ...String: MLKRIAAAVI GLGAVGGIGF LAYAWYPAIA PIPRPAASSF SADAISRGEI VANGGYCAEC HTRVDGKPGP ELAGDFKMAT PFGDIFSSN ITPDEEWGIG NWSLAAFKRA MNKGIARDGS QLYPAFPFDH FTKVSDQDVS DLYAYLMTRP AVHLKPRDNT V PFPINIRL IGQGFWKLLF FTPGRYQNDP KHDAQWNRGA YLAEGNEHCG ACHTPRNLLG AEKMSSVYDG AVIDGWIAPP LN DHNPTPV VWTEDELFQY LRFGVAPLHG SAAGPMSPVP HRFLSKIPEE DVHAIAHYYA DVDKAAQRSS GDQAAITRAM QMS GRDLTG PQPLDEDARL YQGACGACHY NSGPNPVLGR PELALNNALW LDEPNNLYQV MLHGITAEEG QDHISMPSFY SGLS DHDMA RIAAYLRRTR TTLPPWTDLE KKAASARATL EAPPVNASH UniProtKB: Aldehyde dehydrogenase |
-Macromolecule #2: Small subunit of aldehyde dehydrogenase
Macromolecule | Name: Small subunit of aldehyde dehydrogenase / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO / EC number: aldehyde dehydrogenase (FAD-independent) |
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Source (natural) | Organism: Gluconobacter oxydans (bacteria) |
Molecular weight | Theoretical: 16.799998 KDa |
Recombinant expression | Organism: Gluconobacter oxydans (bacteria) |
Sequence | String: MTTKFELNGQ PVTVDAPADT PLLWVIRDDL NLTGTKFGCG IGECGACTVH VGGRATRSCI TPLSAVEGAS ITTIEGLDPA GNHVVQVAW RDQQVPQCGY CQSGQIMQAA SLLKDYPNPT DDQIDGVMGG SLCRCMTYIR IRKAIKEAAS RQQEGANNG UniProtKB: Isoquinoline 1-oxidoreductase alpha subunit |
-Macromolecule #3: Large subunit of aldehyde dehydrogenase
Macromolecule | Name: Large subunit of aldehyde dehydrogenase / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO / EC number: aldehyde dehydrogenase (FAD-independent) |
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Source (natural) | Organism: Gluconobacter oxydans (bacteria) |
Molecular weight | Theoretical: 83.302164 KDa |
Recombinant expression | Organism: Gluconobacter oxydans (bacteria) |
Sequence | String: MAKIEQIAKK SDATRLSRRN FLMTAAGAGL MFGFARKAGA ATTLPSAMPP EAAFEPNIWC AIAPDGSINV NIVRAEMGQH VGTALARII ADEMDADWDK IKITQVDTAP KWAGKYVTGG SWSVWDTWDT FRQAGAAARS VMIEEGAKLL GTTPDRCTAH E SVVSAGSK ...String: MAKIEQIAKK SDATRLSRRN FLMTAAGAGL MFGFARKAGA ATTLPSAMPP EAAFEPNIWC AIAPDGSINV NIVRAEMGQH VGTALARII ADEMDADWDK IKITQVDTAP KWAGKYVTGG SWSVWDTWDT FRQAGAAARS VMIEEGAKLL GTTPDRCTAH E SVVSAGSK SISFGDIVAR AKPTRTFTPE EMAKLPLKPT GNRRLISKQV PALDIPDKTT GKAIYGIDVK LDGMVYGRPK MP PTRYAAK VISVDDSAAK KIPGYLRYVV LDDPSGIVPG WVVALAKTYP AAIRAADALK VQWNPGPTIN VSEADIIEHG RKL AADPKN GTRVFNDKGV DEALTIHPGQ VFERSYTCAS VAHYQLEPVN AVARHIDGMW EIHTGNQWQS LILPQLAKSL QVPE EQVVM RTYMLGGGFG RRLNGDYCIP AALASKAIGG APVKLILTRS DDMELDSIRS PSIQTIKVAL DNDRKKIVGM DYVAV AGWP TQVMAPAFLA TGEDGKKYDP FAIAGADHWY ETGPTRVRAI SNDLANATFR PGWLRSVSAG WTPWALECFL DELAHS TKQ DPLAFRLSMF TAQGRNAGQA PNSVGGAKRQ AAVLQRLADK IGYANKQLPA DTGIGIATSF GQERGMPTWT AAAAQIH VD RKTGVVTCQK LWLVLDAGTI VDPGGALAQT EGAALWGFSM ALFEGTEIVN GTIKDRNLNT YTPLRIPDVP DIDIEFIQ N TEKPTGLGEP GVTVVAPAIG NAIFNAVGIR LRHMPMRPAD VRRELQQHTS UniProtKB: CO/xanthine dehydrogenase Mo-binding subunit |
-Macromolecule #4: HEME C
Macromolecule | Name: HEME C / type: ligand / ID: 4 / Number of copies: 3 / Formula: HEC |
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Molecular weight | Theoretical: 618.503 Da |
Chemical component information | ChemComp-HEC: |
-Macromolecule #5: UBIQUINONE-10
Macromolecule | Name: UBIQUINONE-10 / type: ligand / ID: 5 / Number of copies: 1 / Formula: U10 |
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Molecular weight | Theoretical: 863.343 Da |
Chemical component information | ChemComp-U10: |
-Macromolecule #6: FE2/S2 (INORGANIC) CLUSTER
Macromolecule | Name: FE2/S2 (INORGANIC) CLUSTER / type: ligand / ID: 6 / Number of copies: 2 / Formula: FES |
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Molecular weight | Theoretical: 175.82 Da |
Chemical component information | ChemComp-FES: |
-Macromolecule #7: (MOLYBDOPTERIN-CYTOSINE DINUCLEOTIDE-S,S)-DIOXO-AQUA-MOLYBDENUM(V)
Macromolecule | Name: (MOLYBDOPTERIN-CYTOSINE DINUCLEOTIDE-S,S)-DIOXO-AQUA-MOLYBDENUM(V) type: ligand / ID: 7 / Number of copies: 1 / Formula: PCD |
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Molecular weight | Theoretical: 844.471 Da |
Chemical component information | ChemComp-PCD: |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 10 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 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec. | |||||||||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV |
-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: 12747 / Average exposure time: 3.0 sec. / Average electron dose: 2.0 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 |
+Image processing
-Atomic model buiding 1
Refinement | Space: REAL / Protocol: FLEXIBLE FIT |
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Output model | PDB-8gy3: |