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- EMDB-22805: Symmetry in Yeast Alcohol Dehydrogenase 1 -Closed Form with NADH -
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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-22805 | |||||||||
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Title | Symmetry in Yeast Alcohol Dehydrogenase 1 -Closed Form with NADH | |||||||||
![]() | YADH with NADH and PZO. PZO not found in map | |||||||||
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Function / homology | ![]() alcohol dehydrogenase (NAD+) activity / alcohol dehydrogenase / zinc ion binding / cytoplasm Similarity search - Function | |||||||||
Biological species | ![]() ![]() ![]() ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.67 Å | |||||||||
![]() | 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: Yeast alcohol dehydrogenase structure and catalysis. Authors: Raj SB / Ramaswamy S / Plapp BV #2: ![]() 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) | ![]() ![]() | 14.5 KB 14.5 KB | Display Display | ![]() |
Images | ![]() | 235 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 345.9 KB | Display | ![]() |
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Full document | ![]() | 345.5 KB | Display | |
Data in XML | ![]() | 5.6 KB | Display | |
Data in CIF | ![]() | 6.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7kc2MC ![]() 7kcbC ![]() 7kcqC ![]() 7kjyC 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 with NADH and PZO. PZO not found in map | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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 : Alcohol Dehydrogenase NAD+ Pyrazole complex
Entire | Name: Alcohol Dehydrogenase NAD+ Pyrazole complex |
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Components |
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-Supramolecule #1: Alcohol Dehydrogenase NAD+ Pyrazole complex
Supramolecule | Name: Alcohol Dehydrogenase NAD+ Pyrazole 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: alcohol dehydrogenase |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 36.749824 KDa |
Sequence | String: SIPETQKGVI FYESHGKLEY KDIPVPKPKA NELLINVKYS GVCHTDLHAW HGDWPLPTKL PLVGGHEGAG VVVGMGENVK GWKIGDYAG IKWLNGSCMA CEYCELGNES NCPHADLSGY THDGSFQEYA TADAVQAAHI PQGTDLAEVA PVLCAGITVY K ALKSANLM ...String: SIPETQKGVI FYESHGKLEY KDIPVPKPKA NELLINVKYS GVCHTDLHAW HGDWPLPTKL PLVGGHEGAG VVVGMGENVK GWKIGDYAG IKWLNGSCMA CEYCELGNES NCPHADLSGY THDGSFQEYA TADAVQAAHI PQGTDLAEVA PVLCAGITVY 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 |
-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: |
-Macromolecule #4: water
Macromolecule | Name: water / type: ligand / ID: 4 / Number of copies: 4 / Formula: HOH |
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Molecular weight | Theoretical: 18.015 Da |
Chemical component information | ![]() ChemComp-HOH: |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
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 | Model: Quantifoil / Material: GOLD / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Atmosphere: AIR |
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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Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 54.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: OTHER / Imaging mode: BRIGHT FIELD |
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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Final reconstruction | Applied symmetry - Point group: C1 (asymmetric) / Algorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 2.67 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.0) / Number images used: 923969 |
Initial angle assignment | Type: RANDOM ASSIGNMENT |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |