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Open data
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Basic information
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Title | Liver carboxylesterase 1 | |||||||||
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![]() | carboxylesterase / human liver / HYDROLASE | |||||||||
Function / homology | ![]() cholesterol ester hydrolysis involved in cholesterol transport / methylumbelliferyl-acetate deacetylase / methylumbelliferyl-acetate deacetylase activity / sterol esterase / sterol ester esterase activity / medium-chain fatty acid metabolic process / regulation of bile acid secretion / carboxylesterase / Physiological factors / carboxylesterase activity ...cholesterol ester hydrolysis involved in cholesterol transport / methylumbelliferyl-acetate deacetylase / methylumbelliferyl-acetate deacetylase activity / sterol esterase / sterol ester esterase activity / medium-chain fatty acid metabolic process / regulation of bile acid secretion / carboxylesterase / Physiological factors / carboxylesterase activity / cellular response to cholesterol / regulation of bile acid biosynthetic process / positive regulation of cholesterol metabolic process / reverse cholesterol transport / carboxylic ester hydrolase activity / Phase I - Functionalization of compounds / Aspirin ADME / negative regulation of cholesterol storage / cholesterol biosynthetic process / cellular response to low-density lipoprotein particle stimulus / positive regulation of cholesterol efflux / Metabolism of Angiotensinogen to Angiotensins / lipid catabolic process / epithelial cell differentiation / cholesterol metabolic process / lipid droplet / cholesterol homeostasis / response to toxic substance / endoplasmic reticulum lumen / endoplasmic reticulum / cytoplasm / cytosol Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.67 Å | |||||||||
![]() | Zhang Z / Yu E | |||||||||
Funding support | ![]()
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![]() | ![]() 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 | ![]() | 97.2 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 15.7 KB 15.7 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 9.8 KB | Display | ![]() |
Images | ![]() | 170.1 KB | ||
Filedesc metadata | ![]() | 5.4 KB | ||
Others | ![]() ![]() ![]() | 52 MB 95.5 MB 95.5 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 836.6 KB | Display | ![]() |
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Full document | ![]() | 836.2 KB | Display | |
Data in XML | ![]() | 18.3 KB | Display | |
Data in CIF | ![]() | 23.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8eorMC ![]() 7uzmC ![]() 8ekwC ![]() 8ekyC ![]() 8em2C ![]() 8emrC ![]() 8emsC ![]() 8emtC ![]() 8eneC ![]() 8eojC ![]() 23427 M: atomic model generated by this map C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
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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
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-Half map: #2
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Density Histograms |
-Half map: #1
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Sample components
-Entire : Liver carboxylesterase 1
Entire | Name: Liver carboxylesterase 1 |
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Components |
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-Supramolecule #1: Liver carboxylesterase 1
Supramolecule | Name: Liver carboxylesterase 1 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1 |
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Source (natural) | Organism: ![]() |
-Macromolecule #1: Liver carboxylesterase 1
Macromolecule | Name: Liver carboxylesterase 1 / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO / EC number: carboxylesterase |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 62.587773 KDa |
Sequence | String: MWLRAFILAT LSASAAWGHP SSPPVVDTVH GKVLGKFVSL EGFAQPVAIF LGIPFAKPPL GPLRFTPPQP AEPWSFVKNA TSYPPMCTQ DPKAGQLLSE LFTNRKENIP LKLSEDCLYL NIYTPADLTK KNRLPVMVWI HGGGLMVGAA STYDGLALAA H ENVVVVTI ...String: MWLRAFILAT LSASAAWGHP SSPPVVDTVH GKVLGKFVSL EGFAQPVAIF LGIPFAKPPL GPLRFTPPQP AEPWSFVKNA TSYPPMCTQ DPKAGQLLSE LFTNRKENIP LKLSEDCLYL NIYTPADLTK KNRLPVMVWI HGGGLMVGAA STYDGLALAA H ENVVVVTI QYRLGIWGFF STGDEHSRGN WGHLDQVAAL RWVQDNIASF GGNPGSVTIF GESAGGESVS VLVLSPLAKN LF HRAISES GVALTSVLVK KGDVKPLAEQ IAITAGCKTT TSAVMVHCLR QKTEEELLET TLKMKFLSLD LQGDPRESQP LLG TVIDGM LLLKTPEELQ AERNFHTVPY MVGINKQEFG WLIPMQLMSY PLSEGQLDQK TAMSLLWKSY PLVCIAKELI PEAT EKYLG GTDDTVKKKD LFLDLIADVM FGVPSVIVAR NHRDAGAPTY MYEFQYRPSF SSDMKPKTVI GDHGDELFSV FGAPF LKEG ASEEEIRLSK MVMKFWANFA RNGNPNGEGL PHWPEYNQKE GYLQIGANTQ AAQKLKDKEV AFWTNLFAKK AVEKPP QTE HIEL UniProtKB: Liver carboxylesterase 1 |
-Macromolecule #3: ETHYL ACETATE
Macromolecule | Name: ETHYL ACETATE / type: ligand / ID: 3 / Number of copies: 3 / Formula: EEE |
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Molecular weight | Theoretical: 88.105 Da |
Chemical component information | ![]() ChemComp-EEE: |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Buffer | pH: 7.5 |
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Vitrification | Cryogen name: ETHANE |
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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: ![]() |
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 |