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Yorodumi- PDB-7ntm: Cryo-EM structure of S.cerevisiae native alcohol dehydrogenase 1 ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7ntm | ||||||
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Title | Cryo-EM structure of S.cerevisiae native alcohol dehydrogenase 1 (ADH1) in its tetrameric apo state | ||||||
Components | Alcohol dehydrogenase 1 | ||||||
Keywords | OXIDOREDUCTASE / ADH1 / tetramer / S.cerevisiae | ||||||
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 / alcohol dehydrogenase (NAD+) activity / melatonin binding / 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 / alcohol dehydrogenase (NAD+) activity / melatonin binding / 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) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.86 Å | ||||||
Authors | Nzigou Mandouckou, J.A. / Carroni, M. / Haeggstrom, J.Z. / Thulasingam, M. | ||||||
Funding support | Sweden, 1items
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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, J.A. / Carroni, M. / Haeggstrom, J.Z. / Thulasingam, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7ntm.cif.gz | 255.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7ntm.ent.gz | 207 KB | Display | PDB format |
PDBx/mmJSON format | 7ntm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nt/7ntm ftp://data.pdbj.org/pub/pdb/validation_reports/nt/7ntm | HTTPS FTP |
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-Related structure data
Related structure data | 12591MC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
NCS ensembles :
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-Components
#1: Protein | Mass: 36759.906 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / References: UniProt: P00330, alcohol dehydrogenase #2: Chemical | ChemComp-ZN / Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: Tetrameric structure of native ADH1 from S. cereviciae in its apo state. Type: COMPLEX Details: Stable homotetramer, composed of four monomers labelled as A, B, C and D. Entity ID: #1 / Source: NATURAL |
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Molecular weight | Value: 0.147 MDa / Experimental value: YES |
Source (natural) | Organism: Saccharomyces cerevisiae S288C (yeast) |
Buffer solution | pH: 7.4 |
Specimen | Conc.: 2 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Grid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3 |
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 130000 X / Nominal defocus max: 3000 nm / Nominal defocus min: 1000 nm / Cs: 2.7 mm / Alignment procedure: COMA FREE |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Residual tilt: 130 mradians |
Image recording | Average exposure time: 2.5 sec. / Electron dose: 60 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Num. of grids imaged: 1 / Num. of real images: 14964 |
EM imaging optics | Energyfilter name: GIF Bioquantum / Energyfilter slit width: 10 eV |
-Processing
Software | Name: REFMAC / Version: 5.8.0257 / Classification: refinement | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 639189 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: D2 (2x2 fold dihedral) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 2.86 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 222802 / Symmetry type: POINT | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Atomic model building | B value: 123 / Protocol: BACKBONE TRACE / Space: REAL 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. ...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. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Atomic model building | PDB-ID: 5ENV Pdb chain-ID: A / Pdb chain residue range: 1-347 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | Resolution: 2.86→242.88 Å / Cor.coef. Fo:Fc: 0.997 / SU B: 0.244 / SU ML: 0.005 / ESU R: 0.012 Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
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Solvent computation | Solvent model: PARAMETERS FOR MASK CACLULATION | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 54.33 Å2
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Refinement step | Cycle: 1 / Total: 10336 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
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