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- EMDB-27176: Cryo-electron microscopy structure of human kidney Aldehyde Dehyd... -

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Basic information

Entry
Database: EMDB / ID: EMD-27176
TitleCryo-electron microscopy structure of human kidney Aldehyde Dehydrogenase 1A1
Map data
Sample
  • Complex: Aldehyde dehydrogenase 1A1
    • Protein or peptide: Retinal dehydrogenase 1
Keywordsaldehyde dehydrogenase / ALDH1A1 / HYDROLASE
Function / homology
Function and homology information


fructosamine catabolic process / 3-deoxyglucosone dehydrogenase activity / benzaldehyde dehydrogenase (NAD+) / acetaldehyde dehydrogenase (NAD+) activity / benzaldehyde dehydrogenase (NAD+) activity / aminobutyraldehyde dehydrogenase / retinal dehydrogenase / gamma-aminobutyric acid biosynthetic process / aminobutyraldehyde dehydrogenase (NAD+) activity / maintenance of lens transparency ...fructosamine catabolic process / 3-deoxyglucosone dehydrogenase activity / benzaldehyde dehydrogenase (NAD+) / acetaldehyde dehydrogenase (NAD+) activity / benzaldehyde dehydrogenase (NAD+) activity / aminobutyraldehyde dehydrogenase / retinal dehydrogenase / gamma-aminobutyric acid biosynthetic process / aminobutyraldehyde dehydrogenase (NAD+) activity / maintenance of lens transparency / Fructose catabolism / aldehyde metabolic process / Ethanol oxidation / RA biosynthesis pathway / aldehyde dehydrogenase (NAD+) / androgen binding / cellular detoxification of aldehyde / aldehyde dehydrogenase (NAD+) activity / retinal dehydrogenase (NAD+) activity / retinol metabolic process / negative regulation of cold-induced thermogenesis / retinoid metabolic process / GTPase activator activity / NAD binding / axon / synapse / extracellular exosome / cytoplasm / cytosol
Similarity search - Function
Aldehyde dehydrogenase, glutamic acid active site / Aldehyde dehydrogenases glutamic acid active site. / Aldehyde dehydrogenase, cysteine active site / Aldehyde dehydrogenases cysteine active site. / Aldehyde dehydrogenase domain / Aldehyde dehydrogenase family / Aldehyde dehydrogenase, C-terminal / Aldehyde dehydrogenase, N-terminal / Aldehyde/histidinol dehydrogenase
Similarity search - Domain/homology
Aldehyde dehydrogenase 1A1
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.84 Å
AuthorsLyu M / Yu EW
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01 AI145069 United States
CitationJournal: To Be Published
Title: Cryo-electron microscopy structure of human kidney Aldehyde Dehydrogenase 1A1
Authors: Lyu M / Yu EW
History
DepositionJun 1, 2022-
Header (metadata) releaseNov 16, 2022-
Map releaseNov 16, 2022-
UpdateJun 12, 2024-
Current statusJun 12, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_27176.png

Downloads & links

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Map

FileDownload / File: emd_27176.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.07 Å/pix.
x 300 pix.
= 321. Å		1.07 Å/pix.
x 300 pix.
= 321. Å		1.07 Å/pix.
x 300 pix.
= 321. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.07 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.15
Minimum - Maximum-1.8644 - 2.6129408
Average (Standard dev.)-0.000014375085 (±0.050346844)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 321.00003 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_27176_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_27176_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 : Aldehyde dehydrogenase 1A1

EntireName: Aldehyde dehydrogenase 1A1
Components
  • Complex: Aldehyde dehydrogenase 1A1
    • Protein or peptide: Retinal dehydrogenase 1

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Supramolecule #1: Aldehyde dehydrogenase 1A1

SupramoleculeName: Aldehyde dehydrogenase 1A1 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Retinal dehydrogenase 1

MacromoleculeName: Retinal dehydrogenase 1 / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO
EC number: Oxidoreductases; Acting on the aldehyde or oxo group of donors; With NAD+ or NADP+ as acceptor
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 54.924617 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MSSSGTPDLP VLLTDLKIQY TKIFINNEWH DSVSGKKFPV FNPATEEELC QVEEGDKEDV DKAVKAARQA FQIGSPWRTM DASERGRLL YKLADLIERD RLLLATMESM NGGKLYSNAY LNDLAGCIKT LRYCAGWADK IQGRTIPIDG NFFTYTRHEP I GVCGQIIP ...String:
MSSSGTPDLP VLLTDLKIQY TKIFINNEWH DSVSGKKFPV FNPATEEELC QVEEGDKEDV DKAVKAARQA FQIGSPWRTM DASERGRLL YKLADLIERD RLLLATMESM NGGKLYSNAY LNDLAGCIKT LRYCAGWADK IQGRTIPIDG NFFTYTRHEP I GVCGQIIP WNFPLVMLIW KIGPALSCGN TVVVKPAEQT PLTALHVASL IKEAGFPPGV VNIVPGYGPT AGAAISSHMD ID KVAFTGS TEVGKLIKEA AGKSNLKRVT LELGGKSPCI VLADADLDNA VEFAHHGVFY HQGQCCIAAS RIFVEESIYD EFV RRSVER AKKYILGNPL TPGVTQGPQI DKEQYDKILD LIESGKKEGA KLECGGGPWG NKGYFVQPTV FSNVTDEMRI AKEE IFGPV QQIMKFKSLD DVIKRANNTF YGLSAGVFTK DIDKAITISS ALQAGTVWVN CYGVVSAQCP FGGFKMSGNG RELGE YGFH EYTEVKTVTV KISQKNS

UniProtKB: Aldehyde dehydrogenase 1A1

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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

Concentration.7 mg/mL
BufferpH: 7.5
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Support film - Material: CARBON / Support film - topology: HOLEY
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.5 K / Instrument: FEI VITROBOT MARK I / Details: blot 15 seconds before plunging.

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 39.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.84 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 95743
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: OTHER
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementProtocol: AB INITIO MODEL
Output model

PDB-8d46:
Cryo-electron microscopy structure of human kidney Aldehyde Dehydrogenase 1A1

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