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

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Basic information

Entry
Database: PDB / ID: 6oau
TitleApo Structure of WT Lipoprotein Lipase in Complex with GPIHBP1 Mutant N78D N82D produced in GnTI-deficient 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 remnant clearance / lipoprotein lipase / lipoprotein lipase activity / positive regulation of sequestering of triglyceride / low-density lipoprotein particle mediated signaling / chylomicron remodeling / response to heparin / positive regulation of cholesterol storage / lipoprotein lipase activator activity ...chylomicron binding / positive regulation of chylomicron remnant clearance / lipoprotein lipase / lipoprotein lipase activity / positive regulation of sequestering of triglyceride / low-density lipoprotein particle mediated signaling / chylomicron remodeling / response to heparin / positive regulation of cholesterol storage / lipoprotein lipase activator activity / lipase binding / phospholipase A1 / phosphatidylserine 1-acylhydrolase activity / 1-acyl-2-lysophosphatidylserine acylhydrolase activity / phospholipase A1 activity / triglyceride catabolic process / phospholipase activity / Assembly of active LPL and LIPC lipase complexes / Post-translational modification: synthesis of GPI-anchored proteins / positive regulation of lipoprotein lipase activity / protein transporter activity / very-low-density lipoprotein particle remodeling / positive regulation of macrophage derived foam cell differentiation / Chylomicron remodeling / positive regulation of lipid storage / acetylcholine receptor inhibitor activity / cellular response to nutrient / chylomicron / high-density lipoprotein particle remodeling / very-low-density lipoprotein particle / transcytosis / protein import / triglyceride lipase activity / heparan sulfate proteoglycan binding / positive regulation of chemokine (C-X-C motif) ligand 2 production / protein localization to cell surface / triglyceride homeostasis / cellular response to fatty acid / triglyceride metabolic process / lipoprotein particle binding / apolipoprotein binding / catalytic complex / positive regulation of fat cell differentiation / phospholipid metabolic process / response to glucose / positive regulation of chemokine production / Retinoid metabolism and transport / protein-membrane adaptor activity / positive regulation of adipose tissue development / fatty acid metabolic process / positive regulation of interleukin-1 beta production / cholesterol homeostasis / response to bacterium / intracellular protein transport / fatty acid biosynthetic process / Transcriptional regulation of white adipocyte differentiation / positive regulation of inflammatory response / positive regulation of interleukin-6 production / positive regulation of tumor necrosis factor production / heparin binding / basolateral plasma membrane / protein stabilization / apical plasma membrane / external side of plasma membrane / signaling receptor binding / lipid binding / calcium ion binding / cell surface / protein homodimerization activity / extracellular space / extracellular region / plasma membrane
Similarity search - Function
Lipoprotein lipase / Lipase, LIPH-type / Lipase, N-terminal / Triacylglycerol lipase family / Lipase / Lipase / u-PAR/Ly-6 domain / Ly-6 antigen/uPA receptor-like / Lipoxygenase homology 2 (beta barrel) domain / PLAT/LH2 domain ...Lipoprotein lipase / Lipase, LIPH-type / Lipase, N-terminal / Triacylglycerol lipase family / Lipase / Lipase / u-PAR/Ly-6 domain / Ly-6 antigen/uPA receptor-like / 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
Similarity search - Domain/homology
MALONATE ION / Lipoprotein lipase / Glycosylphosphatidylinositol-anchored high density lipoprotein-binding protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.48 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 18, 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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Oct 11, 2023Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms
Item: _chem_comp.pdbx_synonyms / _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: Lipoprotein lipase
B: Lipoprotein lipase
C: Glycosylphosphatidylinositol-anchored high density lipoprotein-binding protein 1
D: Glycosylphosphatidylinositol-anchored high density lipoprotein-binding protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)131,45311
Polymers130,3864
Non-polymers1,0677
Water1,49583
1
A: Lipoprotein lipase
C: Glycosylphosphatidylinositol-anchored high density lipoprotein-binding protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,7776
Polymers65,1932
Non-polymers5854
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2720 Å2
ΔGint-9 kcal/mol
Surface area23060 Å2
MethodPISA
2
B: Lipoprotein lipase
D: Glycosylphosphatidylinositol-anchored high density lipoprotein-binding protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,6755
Polymers65,1932
Non-polymers4823
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2440 Å2
ΔGint-13 kcal/mol
Surface area23370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)177.480, 97.250, 77.210
Angle α, β, γ (deg.)90.000, 93.470, 90.000
Int Tables number5
Space group name H-MC121

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Components

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Protein , 2 types, 4 molecules ABCD

#1: Protein Lipoprotein lipase / LPL


Mass: 50465.133 Da / Num. of mol.: 2
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.: 2 / 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, 4 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.: 4
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, 86 molecules

#4: Chemical ChemComp-MLI / MALONATE ION


Mass: 102.046 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H2O4
#5: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 83 / Source method: isolated from a natural source / Formula: H2O

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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: 2.55 Å3/Da / Density % sol: 51.77 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / Details: 0.2M Sodium Malonate, 20% PEG3350, 4% 2-propanol

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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: Jul 5, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.48→88.58 Å / Num. obs: 45839 / % possible obs: 98.8 % / Redundancy: 3.4 % / Biso Wilson estimate: 60.97 Å2 / CC1/2: 0.978 / Rmerge(I) obs: 0.125 / Rpim(I) all: 0.08 / Rrim(I) all: 0.148 / Net I/σ(I): 6.5 / Num. measured all: 154530
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
2.48-2.623.30.54667060.8150.3520.65199.9
7.85-88.583.20.10514590.9630.0690.12695.1

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Processing

Software
NameVersionClassification
BUSTER2.11.7refinement
Aimlessdata scaling
PDB_EXTRACT3.24data extraction
XDSdata reduction
BUSTER2.11.7phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1lpa

1lpa


Resolution: 2.48→35.5 Å / Cor.coef. Fo:Fc: 0.86 / Cor.coef. Fo:Fc free: 0.846 / SU R Cruickshank DPI: 0.41 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.379 / SU Rfree Blow DPI: 0.247 / SU Rfree Cruickshank DPI: 0.257
RfactorNum. reflection% reflectionSelection details
Rfree0.246 2308 5.04 %RANDOM
Rwork0.213 ---
obs0.215 45819 98.8 %-
Displacement parametersBiso max: 149.7 Å2 / Biso mean: 52 Å2 / Biso min: 21.23 Å2
Baniso -1Baniso -2Baniso -3
1-3.2668 Å20 Å21.34 Å2
2--19.5375 Å20 Å2
3----22.8043 Å2
Refine analyzeLuzzati coordinate error obs: 0.38 Å
Refinement stepCycle: final / Resolution: 2.48→35.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7934 0 60 83 8077
Biso mean--64.87 47.46 -
Num. residues----1007
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d2834SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes1378HARMONIC5
X-RAY DIFFRACTIONt_it8220HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion1088SEMIHARMONIC5
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_contact8780SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d8220HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg11157HARMONIC21.2
X-RAY DIFFRACTIONt_omega_torsion3.15
X-RAY DIFFRACTIONt_other_torsion20.4
LS refinement shellResolution: 2.48→2.5 Å / Rfactor Rfree error: 0 / Total num. of bins used: 50
RfactorNum. reflection% reflection
Rfree0.2616 41 4.47 %
Rwork0.2412 876 -
all0.2421 917 -
obs--100 %

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