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- PDB-6v7n: Crystal Structure of a human Lysosome Resident Glycoprotein, Lyso... -

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Basic information

Entry
Database: PDB / ID: 6v7n
TitleCrystal Structure of a human Lysosome Resident Glycoprotein, Lysosomal Acid Lipase, and its Implications in Cholesteryl Ester Storage Disease (CESD)
ComponentsLysosomal acid lipase/cholesteryl ester hydrolase
KeywordsHYDROLASE / Lysosomal acid lipase / Cholesteryl Ester Storage Disease
Function / homology
Function and homology information


cytokine production / sterol esterase / sterol ester esterase activity / low-density lipoprotein particle clearance / lipase activity / tissue remodeling / sterol metabolic process / LDL clearance / lipid catabolic process / homeostasis of number of cells within a tissue ...cytokine production / sterol esterase / sterol ester esterase activity / low-density lipoprotein particle clearance / lipase activity / tissue remodeling / sterol metabolic process / LDL clearance / lipid catabolic process / homeostasis of number of cells within a tissue / lysosomal lumen / lung development / cell morphogenesis / fibrillar center / cell population proliferation / lysosome / inflammatory response / intracellular membrane-bounded organelle
Similarity search - Function
Lipase, eukaryotic / Lipases, serine active site. / alpha/beta hydrolase fold / Alpha/beta hydrolase fold-1 / Alpha/Beta hydrolase fold, catalytic domain / Alpha/Beta hydrolase fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Lysosomal acid lipase/cholesteryl ester hydrolase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.62 Å
AuthorsHan, S.
CitationJournal: J.Lipid Res. / Year: 2020
Title: Crystal structure of human lysosomal acid lipase and its implications in cholesteryl ester storage disease.
Authors: Rajamohan, F. / Reyes, A.R. / Tu, M. / Nedoma, N.L. / Hoth, L.R. / Schwaid, A.G. / Kurumbail, R.G. / Ward, J. / Han, S.
History
DepositionDec 9, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 17, 2020Provider: repository / Type: Initial release
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.id / _atom_site_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_asym_id / _chem_comp.name / _pdbx_entity_nonpoly.entity_id / _pdbx_entity_nonpoly.name / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Aug 12, 2020Group: Database references / Structure summary / Category: chem_comp / citation
Item: _chem_comp.pdbx_synonyms / _citation.journal_volume ..._chem_comp.pdbx_synonyms / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 2.2Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Lysosomal acid lipase/cholesteryl ester hydrolase
B: Lysosomal acid lipase/cholesteryl ester hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,24010
Polymers87,4392
Non-polymers1,8018
Water2,792155
1
A: Lysosomal acid lipase/cholesteryl ester hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,4614
Polymers43,7201
Non-polymers7423
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Lysosomal acid lipase/cholesteryl ester hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,7786
Polymers43,7201
Non-polymers1,0595
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)97.145, 165.486, 60.360
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Lysosomal acid lipase/cholesteryl ester hydrolase / LAL / Cholesteryl esterase / Lipase A / Sterol esterase


Mass: 43719.535 Da / Num. of mol.: 2 / Mutation: N51Q, N80Q, N300Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: LIPA / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P38571, sterol esterase
#2: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#3: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 155 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.77 Å3/Da / Density % sol: 55.67 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / Details: 1.8 M Ammonium sulfate, 0.1 M CH3COONa, pH 5.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: DECTRIS EIGER2 X 500K / Detector: PIXEL / Date: Dec 10, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.62→97.1 Å / Num. obs: 30000 / % possible obs: 100 % / Redundancy: 6.4 % / CC1/2: 0.996 / Rmerge(I) obs: 0.135 / Net I/σ(I): 13.4
Reflection shellResolution: 2.622→2.63 Å / Rmerge(I) obs: 1.361 / Num. unique obs: 1991 / CC1/2: 0.797

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Processing

Software
NameVersionClassification
BUSTER2.11.7refinement
PDB_EXTRACT3.25data extraction
HKL-3000data reduction
SCALAdata scaling
BUSTERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1HLG

1hlg


Resolution: 2.62→83.78 Å / Cor.coef. Fo:Fc: 0.929 / Cor.coef. Fo:Fc free: 0.901 / SU R Cruickshank DPI: 0.541 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.567 / SU Rfree Blow DPI: 0.263 / SU Rfree Cruickshank DPI: 0.265
RfactorNum. reflection% reflectionSelection details
Rfree0.222 1518 5.07 %RANDOM
Rwork0.185 ---
obs0.187 29950 99.8 %-
Displacement parametersBiso max: 156.49 Å2 / Biso mean: 58.59 Å2 / Biso min: 21.93 Å2
Baniso -1Baniso -2Baniso -3
1--14.5927 Å20 Å20 Å2
2--9.6612 Å20 Å2
3---4.9315 Å2
Refine analyzeLuzzati coordinate error obs: 0.32 Å
Refinement stepCycle: final / Resolution: 2.62→83.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5973 0 113 155 6241
Biso mean--90.45 52.85 -
Num. residues----739
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d2096SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes1048HARMONIC5
X-RAY DIFFRACTIONt_it6276HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion802SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact7012SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d6276HARMONIC20.009
X-RAY DIFFRACTIONt_angle_deg8551HARMONIC21.1
X-RAY DIFFRACTIONt_omega_torsion3.12
X-RAY DIFFRACTIONt_other_torsion22.48
LS refinement shellResolution: 2.62→2.71 Å / Rfactor Rfree error: 0 / Total num. of bins used: 15
RfactorNum. reflection% reflection
Rfree0.2609 143 4.96 %
Rwork0.2224 2738 -
all0.2244 2881 -
obs--99.17 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.3905-0.52080.06261.6206-0.23652.16390.04750.0852-0.0426-0.0594-0.11040.2295-0.0467-0.46110.063-0.05380.0579-0.0027-0.1134-0.0578-0.11629.896325.15840.8897
21.16710.23540.20812.10480.33322.15520.0162-0.0630.0647-0.037-0.0002-0.3498-0.23330.4357-0.016-0.0812-0.07970.0001-0.1294-0.0129-0.101364.454721.487-27.888
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* }A9 - 384
2X-RAY DIFFRACTION2{ B|* }B9 - 384

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