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- EMDB-27575: Human Brain Aldehyde Dehydrogenase 1 family, member A1 -

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Basic information

Entry
Database: EMDB / ID: EMD-27575
TitleHuman Brain Aldehyde Dehydrogenase 1 family, member A1
Map data
Sample
  • Complex: Aldehyde Dehydrogenase 1 family member A1
    • Protein or peptide: Retinal dehydrogenase 1
Keywordshuman brain / ALDH1A1 / Oxidoreductase
Function / homology
Function and homology information


oxidoreductase activity, acting on the aldehyde or oxo group of donors, NAD or NADP as acceptor / 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
Epididymis luminal protein 12
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.4 Å
AuthorsTringides ML
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) United States
CitationJournal: Life Sci Alliance / Year: 2023
Title: A cryo-electron microscopic approach to elucidate protein structures from human brain microsomes.
Authors: Marios L Tringides / Zhemin Zhang / Christopher E Morgan / Chih-Chia Su / Edward W Yu /
Abstract: We recently developed a "Build and Retrieve" cryo-electron microscopy (cryo-EM) methodology, which is capable of simultaneously producing near-atomic resolution cryo-EM maps for several individual ...We recently developed a "Build and Retrieve" cryo-electron microscopy (cryo-EM) methodology, which is capable of simultaneously producing near-atomic resolution cryo-EM maps for several individual proteins from a heterogeneous, multiprotein sample. Here we report the use of "Build and Retrieve" to define the composition of a raw human brain microsomal lysate. From this sample, we simultaneously identify and solve cryo-EM structures of five different brain enzymes whose functions affect neurotransmitter recycling, iron metabolism, glycolysis, axonal development, energy homeostasis, and retinoic acid biosynthesis. Interestingly, malfunction of these important proteins has been directly linked to several neurodegenerative disorders, such as Alzheimer's, Huntington's, and Parkinson's diseases. Our work underscores the importance of cryo-EM in facilitating tissue and organ proteomics at the atomic level.
History
DepositionJul 11, 2022-
Header (metadata) releaseNov 16, 2022-
Map releaseNov 16, 2022-
UpdateMay 21, 2025-
Current statusMay 21, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_27575.png

Downloads & links

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Map

FileDownload / File: emd_27575.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
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Others
AxesX (Sec.)Y (Row.)Z (Col.)
1.07 Å/pix.
x 256 pix.
= 273.92 Å		1.07 Å/pix.
x 256 pix.
= 273.92 Å		1.07 Å/pix.
x 256 pix.
= 273.92 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: 0.2
Minimum - Maximum-2.0615182 - 2.8102372
Average (Standard dev.)0.000012704487 (±0.06237589)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderZYX
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 273.92 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_27575_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_27575_half_map_2.map
Projections & Slices
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Histogram

Histogram (log scale)

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Sample components

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Entire : Aldehyde Dehydrogenase 1 family member A1

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

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Supramolecule #1: Aldehyde Dehydrogenase 1 family member A1

SupramoleculeName: Aldehyde Dehydrogenase 1 family member A1 / 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
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 54.89759 KDa
SequenceString: MSSSGTPDLP VLLTDLKIQY TKIFINNEWH DSVSGKKFPV FNPATEEELC QVEEGDKEDV DKAVKAARQA FQIGSPWRTM DASERGRLL YKLADLIERD RLLLATMESM NGGKLYSNAY LSDLAGCIKT LRYCAGWADK IQGRTIPIDG NFFTYTRHEP I GVCGQIIP ...String:
MSSSGTPDLP VLLTDLKIQY TKIFINNEWH DSVSGKKFPV FNPATEEELC QVEEGDKEDV DKAVKAARQA FQIGSPWRTM DASERGRLL YKLADLIERD RLLLATMESM NGGKLYSNAY LSDLAGCIKT 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: Epididymis luminal protein 12

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation statetissue

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Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 36.5 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.706 µm / Nominal defocus min: 1.212 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: PDB ENTRY
PDB model - PDB ID:

4wj9

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 6684
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION

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