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- EMDB-34282: The cryo-EM structure of GSNOR with NYY001 -

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Open data


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Basic information

Entry
Database: EMDB / ID: EMD-34282
TitleThe cryo-EM structure of GSNOR with NYY001
Map data
Sample
  • Complex: Alcohol dehydrogenase class-3
    • Protein or peptide: Alcohol dehydrogenase class-3
  • Ligand: ZINC ION
  • Ligand: NICOTINAMIDE-ADENINE-DINUCLEOTIDE
  • Ligand: (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
KeywordsAlcohol dehydrogenase class-3 / OXIDOREDUCTASE
Function / homology
Function and homology information


formaldehyde dehydrogenase (NAD+) activity / S-nitrosoglutathione reductase (NADH) 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 / response to nitrosative stress / formaldehyde catabolic process / Ethanol oxidation ...formaldehyde dehydrogenase (NAD+) activity / S-nitrosoglutathione reductase (NADH) 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 / response to nitrosative stress / formaldehyde catabolic process / Ethanol oxidation / alcohol dehydrogenase (NAD+) activity / alcohol dehydrogenase / positive regulation of blood pressure / respiratory system process / 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
Alcohol dehydrogenase class-3
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle 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, 2 items
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, 2022-
Header (metadata) releaseSep 20, 2023-
Map releaseSep 20, 2023-
UpdateJun 4, 2025-
Current statusJun 4, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_34282.png

Downloads & links

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Map

FileDownload / File: emd_34282.map.gz / Format: CCP4 / Size: 22.2 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.1 Å/pix.
x 180 pix.
= 198. Å		1.1 Å/pix.
x 180 pix.
= 198. Å		1.1 Å/pix.
x 180 pix.
= 198. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.1 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.7
Minimum - Maximum-5.132504 - 8.057048999999999
Average (Standard dev.)-0.0021636556 (±0.2376401)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions180180180
Spacing180180180
CellA=B=C: 198.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_34282_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_34282_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Alcohol dehydrogenase class-3

EntireName: Alcohol dehydrogenase class-3
Components
  • Complex: Alcohol dehydrogenase class-3
    • Protein or peptide: Alcohol dehydrogenase class-3
  • Ligand: ZINC ION
  • Ligand: NICOTINAMIDE-ADENINE-DINUCLEOTIDE
  • Ligand: (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

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Supramolecule #1: Alcohol dehydrogenase class-3

SupramoleculeName: Alcohol dehydrogenase class-3 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Alcohol dehydrogenase class-3

MacromoleculeName: Alcohol dehydrogenase class-3 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO / EC number: alcohol dehydrogenase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 39.901305 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: 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

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Macromolecule #2: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 2 / Number of copies: 4 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

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Macromolecule #3: NICOTINAMIDE-ADENINE-DINUCLEOTIDE

MacromoleculeName: NICOTINAMIDE-ADENINE-DINUCLEOTIDE / type: ligand / ID: 3 / Number of copies: 2 / Formula: NAD
Molecular weightTheoretical: 663.425 Da
Chemical component information

ChemComp-NAD:
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / NAD*YM

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Macromolecule #4: (4P)-4-{2-[4-(1H-imidazol-1-yl)phenyl]-5-[3-oxo-3-(2-oxo-1,3-thia...

MacromoleculeName: (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
Molecular weightTheoretical: 499.584 Da
Chemical component information

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

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination 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

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.05 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 288334
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: ANGULAR RECONSTITUTION
FSC plot (resolution estimation)

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