[English] 日本語
![](img/lk-miru.gif)
- EMDB-27176: Cryo-electron microscopy structure of human kidney Aldehyde Dehyd... -
+
Open data
-
Basic information
Entry | ![]() | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Cryo-electron microscopy structure of human kidney Aldehyde Dehydrogenase 1A1 | |||||||||
![]() | ||||||||||
![]() |
| |||||||||
![]() | aldehyde dehydrogenase / ALDH1A1 / HYDROLASE | |||||||||
Function / homology | ![]() 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 / cellular 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 / cytoplasm / cytosol Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.84 Å | |||||||||
![]() | Lyu M / Yu EW | |||||||||
Funding support | ![]()
| |||||||||
![]() | ![]() Title: Cryo-electron microscopy structure of human kidney Aldehyde Dehydrogenase 1A1 Authors: Lyu M / Yu EW | |||||||||
History |
|
-
Structure visualization
Supplemental images |
---|
-
Downloads & links
-EMDB archive
Map data | ![]() | 97.3 MB | ![]() | |
---|---|---|---|---|
Header (meta data) | ![]() ![]() | 13.5 KB 13.5 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 13.6 KB | Display | ![]() |
Images | ![]() | 230.8 KB | ||
Filedesc metadata | ![]() | 5.4 KB | ||
Others | ![]() ![]() | 95.5 MB 95.5 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 861.4 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 860.9 KB | Display | |
Data in XML | ![]() | 18.4 KB | Display | |
Data in CIF | ![]() | 23.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8d46MC M: atomic model generated by this map C: citing same article ( |
---|---|
Similar structure data | Similarity search - Function & homology ![]() |
-
Links
EMDB pages | ![]() ![]() |
---|---|
Related items in Molecule of the Month |
-
Map
File | ![]() | ||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Voxel size | X=Y=Z: 1.07 Å | ||||||||||||||||||||
Density |
| ||||||||||||||||||||
Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
|
-Supplemental data
-Half map: #2
File | emd_27176_half_map_1.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Projections & Slices |
| ||||||||||||
Density Histograms |
-Half map: #1
File | emd_27176_half_map_2.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Projections & Slices |
| ||||||||||||
Density Histograms |
-
Sample components
-Entire : Aldehyde dehydrogenase 1A1
Entire | Name: Aldehyde dehydrogenase 1A1 |
---|---|
Components |
|
-Supramolecule #1: Aldehyde dehydrogenase 1A1
Supramolecule | Name: Aldehyde dehydrogenase 1A1 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
---|---|
Source (natural) | Organism: ![]() |
-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 |
---|---|
Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 54.924617 KDa |
Recombinant expression | Organism: ![]() |
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 |
-Experimental details
-Structure determination
Method | cryo EM |
---|---|
![]() | single particle reconstruction |
Aggregation state | particle |
-
Sample preparation
Concentration | .7 mg/mL |
---|---|
Buffer | pH: 7.5 |
Grid | Model: Quantifoil R1.2/1.3 / Material: COPPER / Support film - Material: CARBON / Support film - topology: HOLEY |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.5 K / Instrument: FEI VITROBOT MARK I / Details: blot 15 seconds before plunging. |
-
Electron microscopy
Microscope | FEI TITAN KRIOS |
---|---|
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 39.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination 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 |
+
Image processing
-Atomic model buiding 1
Refinement | Protocol: AB INITIO MODEL |
---|---|
Output model | ![]() PDB-8d46: |