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- PDB-6oaz: Apo Structure of WT Lipoprotein Lipase in Complex with GPIHBP1 Mu... -

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Basic information

Entry
Database: PDB / ID: 6oaz
TitleApo Structure of WT Lipoprotein Lipase in Complex with GPIHBP1 Mutant N78D N82D produced in HEK293-F cells
Components
  • Glycosylphosphatidylinositol-anchored high density lipoprotein-binding protein 1
  • Lipoprotein lipase
KeywordsHYDROLASE/PROTEIN BINDING / Lipase / HYDROLASE-PROTEIN BINDING complex
Function / homology
Function and homology information


chylomicron binding / positive regulation of chylomicron remodeling / positive regulation of chylomicron remnant clearance / lipoprotein lipase / low-density lipoprotein particle mediated signaling / lipoprotein lipase activity / lipoprotein lipase activator activity / chylomicron remodeling / positive regulation of cholesterol storage / response to heparin ...chylomicron binding / positive regulation of chylomicron remodeling / positive regulation of chylomicron remnant clearance / lipoprotein lipase / low-density lipoprotein particle mediated signaling / lipoprotein lipase activity / lipoprotein lipase activator activity / chylomicron remodeling / positive regulation of cholesterol storage / response to heparin / phospholipase A1 / phospholipase activity / lipase binding / phospholipase A1 activity / Assembly of active LPL and LIPC lipase complexes / triglyceride catabolic process / Post-translational modification: synthesis of GPI-anchored proteins / protein transporter activity / transcytosis / very-low-density lipoprotein particle remodeling / Chylomicron remodeling / very-low-density lipoprotein particle clearance / positive regulation of lipid storage / chylomicron / positive regulation of fatty acid biosynthetic process / high-density lipoprotein particle remodeling / cellular response to nutrient / protein import / triacylglycerol lipase activity / very-low-density lipoprotein particle / heparan sulfate proteoglycan binding / cellular response to fatty acid / positive regulation of macrophage derived foam cell differentiation / positive regulation of chemokine (C-X-C motif) ligand 2 production / protein localization to cell surface / triglyceride homeostasis / triglyceride metabolic process / lipoprotein particle binding / apolipoprotein binding / catalytic complex / positive regulation of fat cell differentiation / response to glucose / retinoid metabolic process / Retinoid metabolism and transport / positive regulation of chemokine production / protein-membrane adaptor activity / phospholipid metabolic process / positive regulation of adipose tissue development / cholesterol homeostasis / positive regulation of interleukin-1 beta production / response to bacterium / intracellular protein transport / fatty acid metabolic process / Transcriptional regulation of white adipocyte differentiation / positive regulation of interleukin-6 production / positive regulation of inflammatory response / positive regulation of tumor necrosis factor production / fatty acid biosynthetic process / heparin binding / MLL4 and MLL3 complexes regulate expression of PPARG target genes in adipogenesis and hepatic steatosis / basolateral plasma membrane / protein stabilization / apical plasma membrane / signaling receptor binding / external side of plasma membrane / calcium ion binding / lipid binding / cell surface / protein homodimerization activity / extracellular space / extracellular region / plasma membrane
Similarity search - Function
: / Snake toxin/toxin-like / Lipoprotein lipase / Lipase, LIPH-type / Lipase, N-terminal / Triacylglycerol lipase family / Lipase / Lipase / Snake toxin and toxin-like protein / u-PAR/Ly-6 domain ...: / Snake toxin/toxin-like / Lipoprotein lipase / Lipase, LIPH-type / Lipase, N-terminal / Triacylglycerol lipase family / Lipase / Lipase / Snake toxin and toxin-like protein / u-PAR/Ly-6 domain / PLAT/LH2 domain / Lipoxygenase-1 / Lipoxygenase homology 2 (beta barrel) domain / PLAT/LH2 domain / PLAT/LH2 domain superfamily / PLAT/LH2 domain / PLAT domain profile. / Lipases, serine active site. / Snake toxin-like superfamily / Alpha/Beta hydrolase fold, catalytic domain / Alpha/Beta hydrolase fold / Sandwich / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Lipoprotein lipase / Glycosylphosphatidylinositol-anchored high density lipoprotein-binding protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.04 Å
AuthorsArora, R. / Horton, P.A. / Benson, T.E. / Romanowski, M.J.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2019
Title: Structure of lipoprotein lipase in complex with GPIHBP1.
Authors: Arora, R. / Nimonkar, A.V. / Baird, D. / Wang, C. / Chiu, C.H. / Horton, P.A. / Hanrahan, S. / Cubbon, R. / Weldon, S. / Tschantz, W.R. / Mueller, S. / Brunner, R. / Lehr, P. / Meier, P. / ...Authors: Arora, R. / Nimonkar, A.V. / Baird, D. / Wang, C. / Chiu, C.H. / Horton, P.A. / Hanrahan, S. / Cubbon, R. / Weldon, S. / Tschantz, W.R. / Mueller, S. / Brunner, R. / Lehr, P. / Meier, P. / Ottl, J. / Voznesensky, A. / Pandey, P. / Smith, T.M. / Stojanovic, A. / Flyer, A. / Benson, T.E. / Romanowski, M.J. / Trauger, J.W.
History
DepositionMar 19, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 8, 2019Provider: repository / Type: Initial release
Revision 1.1May 22, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation.title ..._citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Jun 5, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Oct 11, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.5Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Lipoprotein lipase
B: Lipoprotein lipase
C: Lipoprotein lipase
D: Lipoprotein lipase
E: Glycosylphosphatidylinositol-anchored high density lipoprotein-binding protein 1
F: Glycosylphosphatidylinositol-anchored high density lipoprotein-binding protein 1
G: Glycosylphosphatidylinositol-anchored high density lipoprotein-binding protein 1
H: Glycosylphosphatidylinositol-anchored high density lipoprotein-binding protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)263,35832
Polymers260,7728
Non-polymers2,58724
Water37821
1
A: Lipoprotein lipase
E: Glycosylphosphatidylinositol-anchored high density lipoprotein-binding protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,8408
Polymers65,1932
Non-polymers6476
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2990 Å2
ΔGint-11 kcal/mol
Surface area22850 Å2
MethodPISA
2
B: Lipoprotein lipase
F: Glycosylphosphatidylinositol-anchored high density lipoprotein-binding protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,8408
Polymers65,1932
Non-polymers6476
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2980 Å2
ΔGint-14 kcal/mol
Surface area22700 Å2
MethodPISA
3
C: Lipoprotein lipase
G: Glycosylphosphatidylinositol-anchored high density lipoprotein-binding protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,8408
Polymers65,1932
Non-polymers6476
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3020 Å2
ΔGint-13 kcal/mol
Surface area22550 Å2
MethodPISA
4
D: Lipoprotein lipase
H: Glycosylphosphatidylinositol-anchored high density lipoprotein-binding protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,8408
Polymers65,1932
Non-polymers6476
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2940 Å2
ΔGint-15 kcal/mol
Surface area22670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)157.000, 191.940, 96.060
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212

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Components

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Protein , 2 types, 8 molecules ABCDEFGH

#1: Protein
Lipoprotein lipase / LPL


Mass: 50465.133 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GPIHBP1, HBP1 / Cell line (production host): HEK293-F / Production host: Homo sapiens (human) / References: UniProt: P06858, lipoprotein lipase
#2: Protein
Glycosylphosphatidylinositol-anchored high density lipoprotein-binding protein 1 / GPI-anchored HDL-binding protein 1 / High density lipoprotein-binding protein 1


Mass: 14727.757 Da / Num. of mol.: 4 / Fragment: residues 21-151 / Mutation: N78D, N82D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GPIHBP1, HBP1 / Cell line (production host): HEK293-F / Production host: Homo sapiens (human) / References: UniProt: Q8IV16

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Sugars , 1 types, 8 molecules

#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.: 8
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

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Non-polymers , 3 types, 37 molecules

#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Ca
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 21 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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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: 2.78 Å3/Da / Density % sol: 55.68 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / Details: 0.15M calcium acetate, 18% PEG3350

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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 PILATUS 6M / Detector: PIXEL / Date: Dec 7, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.04→191.94 Å / Num. obs: 55090 / % possible obs: 97.2 % / Redundancy: 5.5 % / Biso Wilson estimate: 85.06 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.105 / Rpim(I) all: 0.049 / Rrim(I) all: 0.117 / Net I/σ(I): 10.6 / Num. measured all: 303821
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
3.04-3.25.80.9224772181900.8750.4221.0172.299.9
9.61-191.944.90.042963819540.9970.020.04630.699

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Processing

Software
NameVersionClassification
BUSTER2.11.7refinement
Aimless0.5.29data scaling
PDB_EXTRACT3.24data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1LPA, 2J8B

1lpa

2j8b


Resolution: 3.04→121.52 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.92 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.393
RfactorNum. reflection% reflectionSelection details
Rfree0.245 2738 4.98 %RANDOM
Rwork0.203 ---
obs0.205 54997 97 %-
Displacement parametersBiso max: 230.6 Å2 / Biso mean: 113.11 Å2 / Biso min: 16.12 Å2
Baniso -1Baniso -2Baniso -3
1--9.7007 Å20 Å20 Å2
2---0.8881 Å20 Å2
3---10.5888 Å2
Refine analyzeLuzzati coordinate error obs: 0.45 Å
Refinement stepCycle: final / Resolution: 3.04→121.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15670 0 152 21 15843
Biso mean--128.7 46.98 -
Num. residues----1987
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d5590SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes2706HARMONIC5
X-RAY DIFFRACTIONt_it16230HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion2148SEMIHARMONIC5
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_contact17732SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d16230HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg22012HARMONIC21.16
X-RAY DIFFRACTIONt_omega_torsion2.82
X-RAY DIFFRACTIONt_other_torsion21.09
LS refinement shellResolution: 3.04→3.06 Å / Rfactor Rfree error: 0 / Total num. of bins used: 50
RfactorNum. reflection% reflection
Rfree0.3013 52 4.73 %
Rwork0.2441 1048 -
all0.2469 1100 -
obs--96.86 %
Refinement TLS params.

T11: 0.6079 Å2 / 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 °)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.141-0.5478-1.70541.81180.73316.3289-0.1637-0.0782-0.0626-0.2890.0623-0.16540.18640.05910.10130.07880.0669-0.5561-0.0641-0.607920.4758-14.913393.471
20.97030.27211.09673.8082-0.912710.1035-0.237-0.06620.18770.6253-0.0696-0.3187-1.08850.24080.3066-0.0115-0.1635-0.5949-0.0993-0.607913.957920.974355.3524
30.8926-0.44790.88691.7178-0.2415.4158-0.1499-0.0360.1318-0.2827-0.01210.2269-0.4939-0.29250.1620.0996-0.144-0.60790.0718-0.607958.976315.990984.5933
40.69140.3097-1.03051.8432-0.52565.8583-0.1999-0.0424-0.06850.02920.1439-0.00260.32170.10190.0560.04070.0368-0.55460.1015-0.582363.5849-20.229746.5742
56.2793-0.7114-1.126710.65792.10335.0861-0.04420.1075-0.8412-0.8125-0.41420.1750.8665-0.80490.4584-0.11740.2175-0.6079-0.1775-0.605231.6341-38.592963.1811
66.04630.10671.962613.05125.82087.5077-0.10170.37951.00320.88280.0892-0.5404-0.76210.67130.0126-0.0111-0.0565-0.6079-0.304-0.607916.011246.083686.5418
78.2228-2.11931.299113.5165-2.58638.91030.107-0.19060.80840.21810.05060.4435-1.0122-0.759-0.15760.2296-0.0582-0.60790.2656-0.607950.154540.106753.9767
811.81361.38-0.12614.7747-3.24417.91870.02750.0485-0.58290.7004-0.2451-0.11721.08850.86280.21760.3040.0293-0.60790.3039-0.607960.7082-45.556977.3554
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* }A30 - 471
2X-RAY DIFFRACTION2{ B|* }B30 - 471
3X-RAY DIFFRACTION3{ C|* }C30 - 471
4X-RAY DIFFRACTION4{ D|* }D30 - 471
5X-RAY DIFFRACTION5{ E|* }E61 - 143
6X-RAY DIFFRACTION6{ F|* }F65 - 143
7X-RAY DIFFRACTION7{ G|* }G63 - 143
8X-RAY DIFFRACTION8{ H|* }H63 - 142

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