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- EMDB-22902: Symmetry in Yeast Alcohol Dehydrogenase 1 - Open Form with NADH -
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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-22902 | |||||||||
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Title | Symmetry in Yeast Alcohol Dehydrogenase 1 - Open Form with NADH![]() | |||||||||
![]() | YADH - NADH | |||||||||
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Function / homology | ![]() alcohol dehydrogenase (NAD+) activity / ![]() ![]() Similarity search - Function | |||||||||
Biological species | ![]() ![]() ![]() ![]() ![]() ![]() | |||||||||
Method | ![]() ![]() | |||||||||
![]() | Subramanian R / Chang L / Li Z / Plapp BV | |||||||||
![]() | ![]() Title: Cryo-Electron Microscopy Structures of Yeast Alcohol Dehydrogenase. Authors: Sai Rohit Guntupalli / Zhuang Li / Leifu Chang / Bryce V Plapp / Ramaswamy Subramanian / ![]() ![]() Abstract: Structures of yeast alcohol dehydrogenase determined by X-ray crystallography show that the subunits have two different conformational states in each of the two dimers that form the tetramer. ...Structures of yeast alcohol dehydrogenase determined by X-ray crystallography show that the subunits have two different conformational states in each of the two dimers that form the tetramer. Apoenzyme and holoenzyme complexes relevant to the catalytic mechanism were described, but the asymmetry led to questions about the cooperativity of the subunits in catalysis. This study used cryo-electron microscopy (cryo-EM) to provide structures for the apoenzyme, two different binary complexes with NADH, and a ternary complex with NAD and 2,2,2-trifluoroethanol. All four subunits in each of these complexes are identical, as the tetramers have 2 symmetry, suggesting that there is no preexisting asymmetry and that the subunits can be independently active. The apoenzyme and one enzyme-NADH complex have "open" conformations and the inverted coordination of the catalytic zinc with Cys-43, His-66, Glu-67, and Cys-153, whereas another enzyme-NADH complex and the ternary complex have closed conformations with the classical coordination of the zinc with Cys-43, His-66, Cys-153, and a water or the oxygen of trifluoroethanol. The conformational change involves interactions of Arg-340 with the pyrophosphate group of the coenzyme and Glu-67. The cryo-EM and X-ray crystallography studies provide structures relevant for the catalytic mechanism. #1: ![]() Title: Mechanistic implications from structures of yeast alcohol dehydrogenase complexed with coenzyme and an alcohol. Authors: Plapp BV / Charlier HA / Ramaswamy S | |||||||||
History |
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Structure visualization
Movie |
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 2.4 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 13.4 KB 13.4 KB | Display Display | ![]() |
Images | ![]() | 235 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7kjyMC ![]() 7kc2C ![]() 7kcbC ![]() 7kcqC M: atomic model generated by this map C: citing same article ( |
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Similar structure data |
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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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Annotation | YADH - NADH | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.05 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
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Sample components
-Entire : Sc Alcohol Dehydrogenase NADH Complex
Entire | Name: Sc Alcohol Dehydrogenase NADH Complex |
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Components |
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-Supramolecule #1: Sc Alcohol Dehydrogenase NADH Complex
Supramolecule | Name: Sc Alcohol Dehydrogenase NADH Complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1 |
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Source (natural) | Organism: ![]() ![]() ![]() |
Molecular weight | Theoretical: 370 KDa |
-Macromolecule #1: Alcohol dehydrogenase
Macromolecule | Name: Alcohol dehydrogenase / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO / EC number: ![]() |
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Source (natural) | Organism: ![]() ![]() ![]() |
Molecular weight | Theoretical: 36.881016 KDa |
Sequence | String: MSIPETQKGV IFYESHGKLE YKDIPVPKPK ANELLINVKY SGVCHTDLHA WHGDWPLPTK LPLVGGHEGA GVVVGMGENV KGWKIGDYA GIKWLNGSCM ACEYCELGNE SNCPHADLSG YTHDGSFQEY ATADAVQAAH IPQGTDLAEV APVLCAGITV Y KALKSANL ...String: MSIPETQKGV IFYESHGKLE YKDIPVPKPK ANELLINVKY SGVCHTDLHA WHGDWPLPTK LPLVGGHEGA GVVVGMGENV KGWKIGDYA GIKWLNGSCM ACEYCELGNE SNCPHADLSG YTHDGSFQEY ATADAVQAAH IPQGTDLAEV APVLCAGITV Y KALKSANL MAGHWVAISG AAGGLGSLAV QYAKAMGYRV LGIDGGEGKE ELFRSIGGEV FIDFTKEKDI VGAVLKATDG GA HGVINVS VSEAAIEAST RYVRANGTTV LVGMPAGAKC CSDVFNQVVK SISIVGSYVG NRADTREALD FFARGLVKSP IKV VGLSTL PEIYEKMEKG QIVGRYVVDT SK |
-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 |
-Macromolecule #3: NICOTINAMIDE-ADENINE-DINUCLEOTIDE
Macromolecule | Name: NICOTINAMIDE-ADENINE-DINUCLEOTIDE / type: ligand / ID: 3 / Number of copies: 4 / Formula: NAD |
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Molecular weight | Theoretical: 663.425 Da |
Chemical component information | ![]() ChemComp-NAD: |
-Experimental details
-Structure determination
Method | ![]() |
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Aggregation state | particle |
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Sample preparation
Concentration | 5 mg/mL |
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Buffer | pH: 8.2 / Component - Concentration: 50.0 mM / Component - Formula: C4H11NO3 / Component - Name: Tris![]() Details: Tris HCl buffer 5mM with 200mM KCl adjusted to pH 8.2. |
Grid | Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Atmosphere: AIR / Details: unspecified |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 298 K / Instrument: FEI VITROBOT MARK II |
Details | Purified by Size Exclusion chromatography |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | C2 aperture diameter: 100.0 µm / Illumination mode: OTHER / Imaging mode: BRIGHT FIELD![]() |
Sample stage | Cooling holder cryogen: NITROGEN |
Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 54.0 e/Å2 |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Image processing
CTF correction | Software - Name: Gctf (ver. 1.06) |
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Initial angle assignment | Type: RANDOM ASSIGNMENT |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |
Final reconstruction | Applied symmetry - Point group: D2 (2x2 fold dihedral![]() |