+Open data
-Basic information
Entry | Database: PDB / ID: 8gv3 | |||||||||
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Title | The cryo-EM structure of GSNOR with NYY001 | |||||||||
Components | Alcohol dehydrogenase class-3 | |||||||||
Keywords | OXIDOREDUCTASE / Alcohol dehydrogenase class-3 | |||||||||
Function / homology | Function and homology information 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 / : ...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 / extracellular exosome / zinc ion binding / identical protein binding / cytosol Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.05 Å | |||||||||
Authors | Xia, Y. / Zhang, Q. / Yao, D. / Zhao, S. / Xie, L. / Ji, Y. / Cao, Y. | |||||||||
Funding support | China, 2items
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Citation | Journal: To Be Published Title: The cryo-EM structure of GSNOR with NYY001 Authors: Cao, Y. / Xia, Y. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8gv3.cif.gz | 138.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8gv3.ent.gz | 106.3 KB | Display | PDB format |
PDBx/mmJSON format | 8gv3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8gv3_validation.pdf.gz | 1.3 MB | Display | wwPDB validaton report |
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Full document | 8gv3_full_validation.pdf.gz | 1.3 MB | Display | |
Data in XML | 8gv3_validation.xml.gz | 35.3 KB | Display | |
Data in CIF | 8gv3_validation.cif.gz | 50.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gv/8gv3 ftp://data.pdbj.org/pub/pdb/validation_reports/gv/8gv3 | HTTPS FTP |
-Related structure data
Related structure data | 34282MC 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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1 |
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-Components
#1: Protein | Mass: 39901.305 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: ADH5, ADHX, FDH / Production host: Homo sapiens (human) References: UniProt: P11766, alcohol dehydrogenase, Oxidoreductases; Acting on the CH-OH group of donors; With NAD+ or NADP+ as acceptor, S-(hydroxymethyl)glutathione dehydrogenase #2: Chemical | ChemComp-ZN / #3: Chemical | #4: Chemical | 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: Alcohol dehydrogenase class-3 / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT |
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Molecular weight | Experimental value: NO |
Source (natural) | Organism: Homo sapiens (human) |
Source (recombinant) | Organism: Homo sapiens (human) |
Buffer solution | pH: 7.5 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
-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: SPOT SCAN |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 26000 nm / Nominal defocus min: 10000 nm |
Image recording | Electron dose: 50 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) |
-Processing
Software | Name: PHENIX / Version: 1.19.2_4158: / Classification: refinement | ||||||||||||||||||||||||
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
3D reconstruction | Resolution: 3.05 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 288334 / Symmetry type: POINT | ||||||||||||||||||||||||
Refine LS restraints |
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