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Open data
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Basic information
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Title | The cryo-EM structure of GSNOR with NYY001 | |||||||||
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![]() | Alcohol dehydrogenase class-3 / OXIDOREDUCTASE | |||||||||
Function / homology | ![]() formaldehyde dehydrogenase (NAD+) activity / S-(hydroxymethyl)glutathione dehydrogenase (NADP+) activity / S-(hydroxymethyl)glutathione dehydrogenase (NAD+) activity / S-(hydroxymethyl)glutathione dehydrogenase / fatty acid omega-oxidation / S-(hydroxymethyl)glutathione dehydrogenase [NAD(P)+] activity / formaldehyde catabolic process / response to nitrosative stress / Ethanol oxidation / respiratory system process ...formaldehyde dehydrogenase (NAD+) activity / S-(hydroxymethyl)glutathione dehydrogenase (NADP+) activity / S-(hydroxymethyl)glutathione dehydrogenase (NAD+) activity / S-(hydroxymethyl)glutathione dehydrogenase / fatty acid omega-oxidation / S-(hydroxymethyl)glutathione dehydrogenase [NAD(P)+] activity / formaldehyde catabolic process / response to nitrosative stress / Ethanol oxidation / respiratory system process / : / positive regulation of blood pressure / alcohol dehydrogenase / Oxidoreductases; Acting on the CH-OH group of donors; With NAD+ or NADP+ as acceptor / response to redox state / retinoid metabolic process / fatty acid binding / response to lipopolysaccharide / electron transfer activity / mitochondrion / zinc ion binding / extracellular exosome / identical protein binding / cytosol Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.05 Å | |||||||||
![]() | Xia Y / Zhang Q / Yao D / Zhao S / Xie L / Ji Y / Cao Y | |||||||||
Funding support | ![]()
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![]() | ![]() Title: The cryo-EM structure of GSNOR with NYY001 Authors: Cao Y / Xia Y | |||||||||
History |
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Structure visualization
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 20.9 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 13.9 KB 13.9 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 5.9 KB | Display | ![]() |
Images | ![]() | 108.7 KB | ||
Others | ![]() ![]() | 20.6 MB 20.6 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8gv3MC M: atomic model generated by this map C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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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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Voxel size | X=Y=Z: 1.1 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: #2
File | emd_34282_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_34282_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
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Sample components
-Entire : Alcohol dehydrogenase class-3
Entire | Name: Alcohol dehydrogenase class-3 |
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Components |
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-Supramolecule #1: Alcohol dehydrogenase class-3
Supramolecule | Name: Alcohol dehydrogenase class-3 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1 |
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Source (natural) | Organism: ![]() |
-Macromolecule #1: Alcohol dehydrogenase class-3
Macromolecule | Name: Alcohol dehydrogenase class-3 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO / EC number: alcohol dehydrogenase |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 39.901305 KDa |
Recombinant expression | Organism: ![]() |
Sequence | String: MANEVIKCKA AVAWEAGKPL SIEEIEVAPP KAHEVRIKII ATAVCHTDAY TLSGADPEGC FPVILGHEGA GIVESVGEGV TKLKAGDTV IPLYIPQCGE CKFCLNPKTN LCQKIRVTQG KGLMPDGTSR FTCKGKTILH YMGTSTFSEY TVVADISVAK I DPLAPLDK ...String: MANEVIKCKA AVAWEAGKPL SIEEIEVAPP KAHEVRIKII ATAVCHTDAY TLSGADPEGC FPVILGHEGA GIVESVGEGV TKLKAGDTV IPLYIPQCGE CKFCLNPKTN LCQKIRVTQG KGLMPDGTSR FTCKGKTILH YMGTSTFSEY TVVADISVAK I DPLAPLDK VCLLGCGIST GYGAAVNTAK LEPGSVCAVF GLGGVGLAVI MGCKVAGASR IIGVDINKDK FARAKEFGAT EC INPQDFS KPIQEVLIEM TDGGVDYSFE CIGNVKVMRA ALEACHKGWG VSVVVGVAAS GEEIATRPFQ LVTGRTWKGT AFG GWKSVE SVPKLVSEYM SKKIKVDEFV THNLSFDEIN KAFELMHSGK SIRTVVKIE UniProtKB: Alcohol dehydrogenase class-3 |
-Macromolecule #2: ZINC ION
Macromolecule | Name: ZINC ION / type: ligand / ID: 2 / Number of copies: 4 / 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: 2 / Formula: NAD |
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Molecular weight | Theoretical: 663.425 Da |
Chemical component information | ![]() ChemComp-NAD: |
-Macromolecule #4: (4P)-4-{2-[4-(1H-imidazol-1-yl)phenyl]-5-[3-oxo-3-(2-oxo-1,3-thia...
Macromolecule | Name: (4P)-4-{2-[4-(1H-imidazol-1-yl)phenyl]-5-[3-oxo-3-(2-oxo-1,3-thiazolidin-3-yl)propyl]-1H-pyrrol-1-yl}-3-methylbenzamide type: ligand / ID: 4 / Number of copies: 2 / Formula: WKZ |
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Molecular weight | Theoretical: 499.584 Da |
Chemical component information | ![]() ChemComp-WKZ: |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Buffer | pH: 7.5 |
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Vitrification | Cryogen name: ETHANE |
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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: 50.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Nominal defocus max: 26.0 µm / Nominal defocus min: 10.0 µm |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |