+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-27575 | |||||||||
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Title | Human Brain Aldehyde Dehydrogenase 1 family, member A1 | |||||||||
Map data | ||||||||||
Sample |
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Keywords | human brain / ALDH1A1 / Oxidoreductase | |||||||||
Function / homology | Function and homology information benzaldehyde dehydrogenase (NAD+) / benzaldehyde dehydrogenase (NAD+) activity / retinal dehydrogenase / aminobutyraldehyde dehydrogenase / aldehyde dehydrogenase (NAD+) / cytosol Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.4 Å | |||||||||
Authors | Tringides ML | |||||||||
Funding support | United States, 1 items
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Citation | Journal: 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 |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_27575.map.gz | 5 MB | EMDB map data format | |
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Header (meta data) | emd-27575-v30.xml emd-27575.xml | 12.9 KB 12.9 KB | Display Display | EMDB header |
Images | emd_27575.png | 650.9 KB | ||
Filedesc metadata | emd-27575.cif.gz | 5 KB | ||
Others | emd_27575_half_map_1.map.gz emd_27575_half_map_2.map.gz | 59.1 MB 59.1 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-27575 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-27575 | HTTPS FTP |
-Validation report
Summary document | emd_27575_validation.pdf.gz | 889.9 KB | Display | EMDB validaton report |
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Full document | emd_27575_full_validation.pdf.gz | 889.5 KB | Display | |
Data in XML | emd_27575_validation.xml.gz | 12.4 KB | Display | |
Data in CIF | emd_27575_validation.cif.gz | 14.5 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-27575 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-27575 | HTTPS FTP |
-Related structure data
Related structure data | 8dnoMC 8dnmC 8dnpC 8dnsC 8dnuC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_27575.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.07 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: #2
File | emd_27575_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_27575_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Aldehyde Dehydrogenase 1 family member A1
Entire | Name: Aldehyde Dehydrogenase 1 family member A1 |
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Components |
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-Supramolecule #1: Aldehyde Dehydrogenase 1 family member A1
Supramolecule | Name: Aldehyde Dehydrogenase 1 family member A1 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: Homo sapiens (human) |
-Macromolecule #1: Retinal dehydrogenase 1
Macromolecule | Name: Retinal dehydrogenase 1 / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 54.89759 KDa |
Sequence | String: 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: Aldehyde dehydrogenase 1A1 |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | tissue |
-Sample preparation
Buffer | pH: 7.5 |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | TFS KRIOS |
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Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 36.5 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination 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 |
-Image processing
Startup model | Type of model: PDB ENTRY PDB model - PDB ID: |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 6684 |
Initial angle assignment | Type: ANGULAR RECONSTITUTION |
Final angle assignment | Type: ANGULAR RECONSTITUTION |