+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-28465 | |||||||||
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Title | Liver carboxylesterase 1Carboxylesterase 1 | |||||||||
Map data | ||||||||||
Sample |
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Keywords | carboxylesterase / human liver / HYDROLASE | |||||||||
Function / homology | Function and homology information cholesterol ester hydrolysis involved in cholesterol transport / methylumbelliferyl-acetate deacetylase / methylumbelliferyl-acetate deacetylase activity / sterol esterase / sterol esterase activity / medium-chain fatty acid metabolic process / regulation of bile acid secretion / positive regulation of cholesterol metabolic process / Physiological factors / carboxylesterase ...cholesterol ester hydrolysis involved in cholesterol transport / methylumbelliferyl-acetate deacetylase / methylumbelliferyl-acetate deacetylase activity / sterol esterase / sterol esterase activity / medium-chain fatty acid metabolic process / regulation of bile acid secretion / positive regulation of cholesterol metabolic process / Physiological factors / carboxylesterase / carboxylesterase activity / reverse cholesterol transport / cellular response to cholesterol / regulation of bile acid biosynthetic process / carboxylic ester hydrolase activity / Phase I - Functionalization of compounds / Aspirin ADME / cholesterol biosynthetic process / negative regulation of cholesterol storage / positive regulation of cholesterol efflux / cellular response to low-density lipoprotein particle stimulus / Metabolism of Angiotensinogen to Angiotensins / lipid catabolic process / cholesterol metabolic process / epithelial cell differentiation / lipid droplet / cholesterol homeostasis / response to toxic substance / endoplasmic reticulum lumen / endoplasmic reticulum / cytosol / cytoplasm Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.67 Å | |||||||||
Authors | Zhang Z / Yu E | |||||||||
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_28465.map.gz | 97.2 MB | EMDB map data format | |
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Header (meta data) | emd-28465-v30.xml emd-28465.xml | 15.7 KB 15.7 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_28465_fsc.xml | 9.8 KB | Display | FSC data file |
Images | emd_28465.png | 170.1 KB | ||
Filedesc metadata | emd-28465.cif.gz | 5.4 KB | ||
Others | emd_28465_additional_1.map.gz emd_28465_half_map_1.map.gz emd_28465_half_map_2.map.gz | 52 MB 95.5 MB 95.5 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-28465 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-28465 | 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 (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_28465.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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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
File | emd_28465_additional_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_28465_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_28465_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Liver carboxylesterase 1
Entire | Name: Liver carboxylesterase 1Carboxylesterase 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: Homo sapiens (human) |
-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: Homo sapiens (human) |
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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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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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 3.291 µm / Nominal defocus min: 0.17 µm / Nominal magnification: 81000 |
Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 41.25 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |