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Yorodumi- EMDB-12591: Cryo-EM structure of S.cerevisiae native alcohol dehydrogenase 1 ... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-12591 | |||||||||
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Title | Cryo-EM structure of S.cerevisiae native alcohol dehydrogenase 1 (ADH1) in its tetrameric apo state | |||||||||
Map data | Local sharpen cryo-EM map of apo ADH1 | |||||||||
Sample |
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Function / homology | Function and homology information methylglyoxal reductase (NADH) / amino acid catabolic process to alcohol via Ehrlich pathway / octanol dehydrogenase (NAD+) activity / methylglyoxal reductase (NADH) activity / glycolytic fermentation to ethanol / butanol dehydrogenase (NAD+) activity / NADH oxidation / melatonin binding / alcohol dehydrogenase (NAD+) activity / alcohol dehydrogenase ...methylglyoxal reductase (NADH) / amino acid catabolic process to alcohol via Ehrlich pathway / octanol dehydrogenase (NAD+) activity / methylglyoxal reductase (NADH) activity / glycolytic fermentation to ethanol / butanol dehydrogenase (NAD+) activity / NADH oxidation / melatonin binding / alcohol dehydrogenase (NAD+) activity / alcohol dehydrogenase / allyl-alcohol dehydrogenase / allyl-alcohol dehydrogenase activity / zinc ion binding / identical protein binding / plasma membrane / cytoplasm Similarity search - Function | |||||||||
Biological species | Saccharomyces cerevisiae S288C (yeast) / Baker's yeast (brewer's yeast) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.86 Å | |||||||||
Authors | Nzigou Mandouckou JA / Carroni M / Haeggstrom JZ / Thulasingam M | |||||||||
Funding support | Sweden, 1 items
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Citation | Journal: To Be Published Title: Cryo-EM structure of S.cerevisiae native alcohol dehydrogenase 1 (ADH1) in its tetrameric apo state Authors: Nzigou Mandouckou JA / Carroni M / Haeggstrom JZ / Thulasingam M | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_12591.map.gz | 214.3 MB | EMDB map data format | |
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Header (meta data) | emd-12591-v30.xml emd-12591.xml | 20.5 KB 20.5 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_12591_fsc.xml | 14 KB | Display | FSC data file |
Images | emd_12591.png | 78 KB | ||
Masks | emd_12591_msk_1.map | 244.1 MB | Mask map | |
Others | emd_12591_additional_1.map.gz emd_12591_half_map_1.map.gz emd_12591_half_map_2.map.gz | 121.2 MB 226.2 MB 226.2 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-12591 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-12591 | HTTPS FTP |
-Validation report
Summary document | emd_12591_validation.pdf.gz | 929 KB | Display | EMDB validaton report |
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Full document | emd_12591_full_validation.pdf.gz | 928.6 KB | Display | |
Data in XML | emd_12591_validation.xml.gz | 22 KB | Display | |
Data in CIF | emd_12591_validation.cif.gz | 28.3 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-12591 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-12591 | HTTPS FTP |
-Related structure data
Related structure data | 7ntmMC 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_12591.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Annotation | Local sharpen cryo-EM map of apo ADH1 | ||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.6072 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
File | emd_12591_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Additional map: Unfiltered cryo-EM map of apo ADH1
File | emd_12591_additional_1.map | ||||||||||||
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Annotation | Unfiltered cryo-EM map of apo ADH1 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Half map A of cryo-EM map of apo ADH1
File | emd_12591_half_map_1.map | ||||||||||||
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Annotation | Half map A of cryo-EM map of apo ADH1 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Half map B of cryo-EM map of apo ADH1
File | emd_12591_half_map_2.map | ||||||||||||
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Annotation | Half map B of cryo-EM map of apo ADH1 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Tetrameric structure of native ADH1 from S. cereviciae in its apo...
Entire | Name: Tetrameric structure of native ADH1 from S. cereviciae in its apo state. |
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Components |
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-Supramolecule #1: Tetrameric structure of native ADH1 from S. cereviciae in its apo...
Supramolecule | Name: Tetrameric structure of native ADH1 from S. cereviciae in its apo state. type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1 Details: Stable homotetramer, composed of four monomers labelled as A, B, C and D. |
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Source (natural) | Organism: Saccharomyces cerevisiae S288C (yeast) |
Molecular weight | Experimental: 147 KDa |
-Macromolecule #1: Alcohol dehydrogenase 1
Macromolecule | Name: Alcohol dehydrogenase 1 / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO / EC number: alcohol dehydrogenase |
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Source (natural) | Organism: Baker's yeast (brewer's yeast) |
Molecular weight | Theoretical: 36.759906 KDa |
Sequence | String: SIPETQKGVI FYESHGKLEY KDIPVPKPKA NELLINVKYS GVCHTDLHAW HGDWPLPVKL PLVGGHEGAG VVVGMGENVK GWKIGDYAG IKWLNGSCMA CEYCELGNES NCPHADLSGY THDGSFQQYA TADAVQAAHI PQGTDLAQVA PILCAGITVY K ALKSANLM ...String: SIPETQKGVI FYESHGKLEY KDIPVPKPKA NELLINVKYS GVCHTDLHAW HGDWPLPVKL PLVGGHEGAG VVVGMGENVK GWKIGDYAG IKWLNGSCMA CEYCELGNES NCPHADLSGY THDGSFQQYA TADAVQAAHI PQGTDLAQVA PILCAGITVY K ALKSANLM AGHWVAISGA AGGLGSLAVQ YAKAMGYRVL GIDGGEGKEE LFRSIGGEVF IDFTKEKDIV GAVLKATDGG AH GVINVSV SEAAIEASTR YVRANGTTVL VGMPAGAKCC SDVFNQVVKS ISIVGSYVGN RADTREALDF FARGLVKSPI KVV GLSTLP EIYEKMEKGQ IVGRYVVDTS K |
-Macromolecule #2: ZINC ION
Macromolecule | Name: ZINC ION / type: ligand / ID: 2 / Number of copies: 8 / Formula: ZN |
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Molecular weight | Theoretical: 65.409 Da |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 2 mg/mL |
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Buffer | pH: 7.4 |
Grid | Model: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Support film - Material: GOLD / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Atmosphere: AIR |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Alignment procedure | Coma free - Residual tilt: 130.0 mrad |
Specialist optics | Energy filter - Name: GIF Bioquantum / Energy filter - Slit width: 10 eV |
Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Number grids imaged: 1 / Number real images: 14964 / Average exposure time: 2.5 sec. / Average electron dose: 60.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 130000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
+Image processing
-Atomic model buiding 1
Initial model | PDB ID: Chain - Chain ID: A / Chain - Residue range: 1-347 |
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Details | Model building and refinement were done using using CCP-EM software suite (Burnley et al, 2017). The X-ray structure of yeast ADH1 (PDB: 5ENV) was used as a starting model for model building. This model was docked into our Cryo-EM map using MolRep (Brown et al, 2014). The resulting starting model was manually adjusted in Coot (Emsley et al, 2010). REFMAC 5 (Brown et al, 2014) used for structure model refinement. |
Refinement | Space: REAL / Protocol: BACKBONE TRACE / Overall B value: 123 |
Output model | PDB-7ntm: |