+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-28271 | |||||||||
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Title | Aldehyde dehydrogenase 1 family member A1 from human liver | |||||||||
Map data | ||||||||||
Sample |
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Keywords | aldehyde dehydrogenase / human liver / OXIDOREDUCTASE | |||||||||
Function / homology | Function and homology information fructosamine catabolic process / 3-deoxyglucosone dehydrogenase activity / benzaldehyde dehydrogenase (NAD+) / benzaldehyde dehydrogenase (NAD+) activity / maintenance of lens transparency / gamma-aminobutyric acid biosynthetic process / retinal dehydrogenase / aminobutyraldehyde dehydrogenase / aminobutyraldehyde dehydrogenase (NAD+) activity / Fructose catabolism ...fructosamine catabolic process / 3-deoxyglucosone dehydrogenase activity / benzaldehyde dehydrogenase (NAD+) / benzaldehyde dehydrogenase (NAD+) activity / maintenance of lens transparency / gamma-aminobutyric acid biosynthetic process / retinal dehydrogenase / aminobutyraldehyde dehydrogenase / aminobutyraldehyde dehydrogenase (NAD+) activity / Fructose catabolism / Ethanol oxidation / aldehyde metabolic process / RA biosynthesis pathway / glyceraldehyde-3-phosphate dehydrogenase (NAD+) (non-phosphorylating) activity / aldehyde dehydrogenase (NAD+) / cellular detoxification of aldehyde / androgen binding / aldehyde dehydrogenase (NAD+) activity / retinal dehydrogenase activity / negative regulation of cold-induced thermogenesis / retinol metabolic process / retinoid metabolic process / GTPase activator activity / NAD binding / axon / synapse / extracellular exosome / cytosol / cytoplasm Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.64 Å | |||||||||
Authors | Zhang Z | |||||||||
Funding support | United States, 1 items
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Citation | Journal: Cell Rep / Year: 2023 Title: High-resolution structural-omics of human liver enzymes. Authors: Chih-Chia Su / Meinan Lyu / Zhemin Zhang / Masaru Miyagi / Wei Huang / Derek J Taylor / Edward W Yu / Abstract: We applied raw human liver microsome lysate to a holey carbon grid and used cryo-electron microscopy (cryo-EM) to define its composition. From this sample we identified and simultaneously determined ...We applied raw human liver microsome lysate to a holey carbon grid and used cryo-electron microscopy (cryo-EM) to define its composition. From this sample we identified and simultaneously determined high-resolution structural information for ten unique human liver enzymes involved in diverse cellular processes. Notably, we determined the structure of the endoplasmic bifunctional protein H6PD, where the N- and C-terminal domains independently possess glucose-6-phosphate dehydrogenase and 6-phosphogluconolactonase enzymatic activity, respectively. We also obtained the structure of heterodimeric human GANAB, an ER glycoprotein quality-control machinery that contains a catalytic α subunit and a noncatalytic β subunit. In addition, we observed a decameric peroxidase, PRDX4, which directly contacts a disulfide isomerase-related protein, ERp46. Structural data suggest that several glycosylations, bound endogenous compounds, and ions associate with these human liver enzymes. These results highlight the importance of cryo-EM in facilitating the elucidation of human 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_28271.map.gz | 97.3 MB | EMDB map data format | |
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Header (meta data) | emd-28271-v30.xml emd-28271.xml | 15.9 KB 15.9 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_28271_fsc.xml | 11.3 KB | Display | FSC data file |
Images | emd_28271.png | 224.6 KB | ||
Filedesc metadata | emd-28271.cif.gz | 5.3 KB | ||
Others | emd_28271_additional_1.map.gz emd_28271_half_map_1.map.gz emd_28271_half_map_2.map.gz | 52 MB 95.3 MB 95.3 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-28271 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-28271 | HTTPS FTP |
-Validation report
Summary document | emd_28271_validation.pdf.gz | 1006.4 KB | Display | EMDB validaton report |
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Full document | emd_28271_full_validation.pdf.gz | 1006 KB | Display | |
Data in XML | emd_28271_validation.xml.gz | 18.2 KB | Display | |
Data in CIF | emd_28271_validation.cif.gz | 23.4 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-28271 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-28271 | HTTPS FTP |
-Related structure data
Related structure data | 8eneMC 7uzmC 8ekwC 8ekyC 8em2C 8emrC 8emsC 8emtC 8eojC 8eorC 23428 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_28271.map.gz / Format: CCP4 / Size: 103 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: 1.08 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Additional map: #1
File | emd_28271_additional_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_28271_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_28271_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: #1 |
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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 EC number: Oxidoreductases; Acting on the aldehyde or oxo group of donors; With NAD+ or NADP+ as acceptor |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 54.924617 KDa |
Sequence | String: 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 |
-Macromolecule #2: NICOTINAMIDE-ADENINE-DINUCLEOTIDE
Macromolecule | Name: NICOTINAMIDE-ADENINE-DINUCLEOTIDE / type: ligand / ID: 2 / Number of copies: 4 / Formula: NAD |
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Molecular weight | Theoretical: 663.425 Da |
Chemical component information | ChemComp-NAD: |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.5 |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 41.25 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: 3.291 µm / Nominal defocus min: 0.17 µm / Nominal magnification: 81000 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |