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- PDB-8eor: Liver carboxylesterase 1 -

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Basic information

Entry
Database: PDB / ID: 8eor
TitleLiver carboxylesterase 1
ComponentsLiver carboxylesterase 1
KeywordsHYDROLASE / carboxylesterase / human liver
Function / homology
Function and homology information


cholesterol ester hydrolysis involved in cholesterol transport / methylumbelliferyl-acetate deacetylase / methylumbelliferyl-acetate deacetylase activity / regulation of bile acid secretion / sterol esterase / sterol ester esterase activity / medium-chain fatty acid metabolic process / carboxylesterase / Physiological factors / carboxylesterase activity ...cholesterol ester hydrolysis involved in cholesterol transport / methylumbelliferyl-acetate deacetylase / methylumbelliferyl-acetate deacetylase activity / regulation of bile acid secretion / sterol esterase / sterol ester esterase activity / medium-chain fatty acid metabolic process / carboxylesterase / Physiological factors / carboxylesterase activity / regulation of bile acid biosynthetic process / cellular response to cholesterol / positive regulation of cholesterol metabolic process / reverse cholesterol transport / Phase I - Functionalization of compounds / carboxylic ester hydrolase activity / cholesterol biosynthetic process / Aspirin ADME / negative regulation of cholesterol storage / cellular response to low-density lipoprotein particle stimulus / positive regulation of cholesterol efflux / Metabolism of Angiotensinogen to Angiotensins / cholesterol metabolic process / lipid catabolic process / lipid droplet / epithelial cell differentiation / cholesterol homeostasis / response to toxic substance / endoplasmic reticulum lumen / endoplasmic reticulum / cytoplasm / cytosol
Similarity search - Function
: / Carboxylesterase type B, active site / Carboxylesterases type-B serine active site. / Carboxylesterase type B, conserved site / Carboxylesterases type-B signature 2. / Carboxylesterase, type B / Carboxylesterase family / Alpha/Beta hydrolase fold
Similarity search - Domain/homology
ETHYL ACETATE / Liver carboxylesterase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.67 Å
AuthorsZhang, Z. / Yu, E.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) United States
CitationJournal: 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
DepositionOct 4, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 3, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2023Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 13, 2024Group: Data collection / Structure summary
Category: em_admin / pdbx_entry_details / pdbx_modification_feature
Item: _em_admin.last_update / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Liver carboxylesterase 1
B: Liver carboxylesterase 1
C: Liver carboxylesterase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)189,7879
Polymers187,7633
Non-polymers2,0246
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy
TypeNameSymmetry operationNumber
identity operation1_5551
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1chain "A"
d_2ens_1chain "B"
d_3ens_1chain "C"

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDLabel asym-IDLabel seq-ID
d_11ens_1SERLYSA1 - 532
d_12ens_1NAGNAGB
d_13ens_1NAGNAGC
d_21ens_1SERLYSD1 - 532
d_22ens_1NAGNAGE
d_23ens_1NAGNAGF
d_31ens_1SERLYSG1 - 532
d_32ens_1NAGNAGH
d_33ens_1NAGNAGI

NCS oper:
IDCodeMatrixVector
1given(-0.499924457863, 0.866068295046, 0.00111568234462), (-0.86606897496, -0.499924405841, -0.000345044633023), (0.000258924616202, -0.00113875411569, 0.999999318098)35.4066758646, 163.055295199, 0.0432143667743
2given(-0.500663677489, -0.865641229168, 0.00106976978549), (0.865640963724, -0.500664567389, -0.00084432475262), (0.00126647814354, 0.000503313812436, 0.999999071354)158.962453731, 50.8874986764, -0.105582109572

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Components

#1: Protein Liver carboxylesterase 1 / Acyl-coenzyme A:cholesterol acyltransferase / ACAT / Brain carboxylesterase hBr1 / Carboxylesterase ...Acyl-coenzyme A:cholesterol acyltransferase / ACAT / Brain carboxylesterase hBr1 / Carboxylesterase 1 / CE-1 / hCE-1 / Cholesteryl ester hydrolase / CEH / Cocaine carboxylesterase / Egasyn / HMSE / Methylumbelliferyl-acetate deacetylase 1 / Monocyte/macrophage serine esterase / Retinyl ester hydrolase / REH / Serine esterase 1 / Triacylglycerol hydrolase / TGH


Mass: 62587.773 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human)
References: UniProt: P23141, carboxylesterase, sterol esterase, methylumbelliferyl-acetate deacetylase
#2: Polysaccharide beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 586.542 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}LINUCSPDB-CARE
#3: Chemical ChemComp-EEE / ETHYL ACETATE


Mass: 88.105 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H8O2
Has ligand of interestN
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Liver carboxylesterase 1 / Type: COMPLEX / Entity ID: #1 / Source: NATURAL
Source (natural)Organism: Homo sapiens (human)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 81000 X / Nominal defocus max: 3291 nm / Nominal defocus min: 170 nm
Image recordingElectron dose: 41.25 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.20.1_4487: / Classification: refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.67 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 210633 / Symmetry type: POINT
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 59.34 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00312837
ELECTRON MICROSCOPYf_angle_d0.5317433
ELECTRON MICROSCOPYf_dihedral_angle_d11.1434734
ELECTRON MICROSCOPYf_chiral_restr0.081957
ELECTRON MICROSCOPYf_plane_restr0.0042229
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2AELECTRON MICROSCOPYNCS constraints0.610612544694
ens_1d_3AELECTRON MICROSCOPYNCS constraints0.607880458237

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