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- PDB-8gv3: The cryo-EM structure of GSNOR with NYY001 -

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Basic information

Entry
Database: PDB / ID: 8gv3
TitleThe cryo-EM structure of GSNOR with NYY001
ComponentsAlcohol dehydrogenase class-3
KeywordsOXIDOREDUCTASE / Alcohol dehydrogenase class-3
Function / homology
Function and homology information


formaldehyde dehydrogenase activity / S-(hydroxymethyl)glutathione dehydrogenase / S-(hydroxymethyl)glutathione dehydrogenase (NADP+) activity / S-(hydroxymethyl)glutathione dehydrogenase (NAD+) activity / 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 activity / S-(hydroxymethyl)glutathione dehydrogenase / S-(hydroxymethyl)glutathione dehydrogenase (NADP+) activity / S-(hydroxymethyl)glutathione dehydrogenase (NAD+) activity / fatty acid omega-oxidation / S-(hydroxymethyl)glutathione dehydrogenase (NAD(P)+) activity / formaldehyde catabolic process / response to nitrosative stress / Ethanol oxidation / respiratory system process / alcohol dehydrogenase (NAD+) activity, zinc-dependent / : / 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
Alcohol dehydrogenase class III / Alcohol dehydrogenase, zinc-type, conserved site / Zinc-containing alcohol dehydrogenases signature. / Alcohol dehydrogenase-like, C-terminal / Zinc-binding dehydrogenase / Alcohol dehydrogenase, N-terminal / Alcohol dehydrogenase GroES-like domain / GroES-like superfamily / NAD(P)-binding domain superfamily
Similarity search - Domain/homology
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Chem-WKZ / Alcohol dehydrogenase class-3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.05 Å
AuthorsXia, Y. / Zhang, Q. / Yao, D. / Zhao, S. / Xie, L. / Ji, Y. / Cao, Y.
Funding support China, 2items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, China)2018YFC1004704 China
National Natural Science Foundation of China (NSFC)82072468 China
CitationJournal: To Be Published
Title: The cryo-EM structure of GSNOR with NYY001
Authors: Cao, Y. / Xia, Y.
History
DepositionSep 14, 2022Deposition site: PDBJ / Processing site: RCSB
Revision 1.0Sep 20, 2023Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Alcohol dehydrogenase class-3
B: Alcohol dehydrogenase class-3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,39010
Polymers79,8032
Non-polymers2,5888
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein Alcohol dehydrogenase class-3 / Alcohol dehydrogenase 5 / Alcohol dehydrogenase class chi chain / Alcohol dehydrogenase class-III / ...Alcohol dehydrogenase 5 / Alcohol dehydrogenase class chi chain / Alcohol dehydrogenase class-III / Glutathione-dependent formaldehyde dehydrogenase / FALDH / FDH / GSH-FDH / S-(hydroxymethyl)glutathione dehydrogenase


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 / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Nicotinamide adenine dinucleotide


Mass: 663.425 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#4: Chemical ChemComp-WKZ / (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


Mass: 499.584 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H25N5O3S / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Alcohol dehydrogenase class-3 / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Homo sapiens (human)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: SPOT SCAN
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 26000 nm / Nominal defocus min: 10000 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.19.2_4158: / Classification: refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.05 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 288334 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0075836
ELECTRON MICROSCOPYf_angle_d0.6647918
ELECTRON MICROSCOPYf_dihedral_angle_d8.712810
ELECTRON MICROSCOPYf_chiral_restr0.051908
ELECTRON MICROSCOPYf_plane_restr0.005992

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