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- PDB-6ob0: Compound 2 bound structure of WT Lipoprotein Lipase in Complex wi... -

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Basic information

Entry
Database: PDB / ID: 6ob0
TitleCompound 2 bound 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 / very-low-density lipoprotein particle remodeling / transcytosis / 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 / phospholipid metabolic process / protein-membrane adaptor activity / 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
Chem-M3D / Lipoprotein lipase / Glycosylphosphatidylinositol-anchored high density lipoprotein-binding protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.81 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 / pdbx_struct_conn_angle / 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 / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _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: 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)267,06037
Polymers260,7728
Non-polymers6,28929
Water4,071226
1
A: Lipoprotein lipase
E: Glycosylphosphatidylinositol-anchored high density lipoprotein-binding protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,7359
Polymers65,1932
Non-polymers1,5427
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2710 Å2
ΔGint-11 kcal/mol
Surface area24750 Å2
MethodPISA
2
B: Lipoprotein lipase
F: Glycosylphosphatidylinositol-anchored high density lipoprotein-binding protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,85710
Polymers65,1932
Non-polymers1,6648
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2800 Å2
ΔGint-11 kcal/mol
Surface area24730 Å2
MethodPISA
3
C: Lipoprotein lipase
G: Glycosylphosphatidylinositol-anchored high density lipoprotein-binding protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,7359
Polymers65,1932
Non-polymers1,5427
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2730 Å2
ΔGint-10 kcal/mol
Surface area24610 Å2
MethodPISA
4
D: Lipoprotein lipase
H: Glycosylphosphatidylinositol-anchored high density lipoprotein-binding protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,7359
Polymers65,1932
Non-polymers1,5427
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2730 Å2
ΔGint-11 kcal/mol
Surface area24520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)153.430, 191.420, 97.180
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 , 5 types, 247 molecules

#4: Chemical
ChemComp-M3D / 7-(3-cyano-4-hydroxyphenyl)-N-[2-(morpholin-4-yl)ethyl]dibenzo[b,f]oxepine-10-carboxamide


Mass: 467.516 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C28H25N3O4 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


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


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#7: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 226 / 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: 2.74 Å3/Da / Density % sol: 55.05 %
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: Mar 7, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.81→37.1 Å / Num. obs: 70015 / % possible obs: 99.1 % / Redundancy: 6.4 % / CC1/2: 0.998 / Rmerge(I) obs: 0.148 / Rpim(I) all: 0.064 / Rrim(I) all: 0.162 / Net I/σ(I): 12
Reflection shell

Diffraction-ID: 1

Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
2.81-2.820.01452.36930.840.610.015799.7
13.03-119.7233.479397.3

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Processing

Software
NameVersionClassification
BUSTER2.11.7refinement
XSCALEdata scaling
PDB_EXTRACT3.24data extraction
XDSdata reduction
BUSTER2.11.7phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6OAZ

6oaz


Resolution: 2.81→37.15 Å / Cor.coef. Fo:Fc: 0.903 / Cor.coef. Fo:Fc free: 0.891 / SU R Cruickshank DPI: 2.176 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 1.927 / SU Rfree Blow DPI: 0.319 / SU Rfree Cruickshank DPI: 0.325
RfactorNum. reflection% reflectionSelection details
Rfree0.233 3465 4.95 %RANDOM
Rwork0.198 ---
obs0.2 69989 99.1 %-
Displacement parametersBiso max: 172.97 Å2 / Biso mean: 67.92 Å2 / Biso min: 29.32 Å2
Baniso -1Baniso -2Baniso -3
1--20.5373 Å20 Å20 Å2
2---10.1582 Å20 Å2
3---30.6955 Å2
Refine analyzeLuzzati coordinate error obs: 0.36 Å
Refinement stepCycle: final / Resolution: 2.81→37.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16511 0 436 226 17173
Biso mean--61.7 52.63 -
Num. residues----2094
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d6044SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes2923HARMONIC5
X-RAY DIFFRACTIONt_it17461HARMONIC20
X-RAY DIFFRACTIONt_nbd1SEMIHARMONIC5
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion2265SEMIHARMONIC5
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_contact19024SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d17461HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg23708HARMONIC21.16
X-RAY DIFFRACTIONt_omega_torsion3.01
X-RAY DIFFRACTIONt_other_torsion20.99
LS refinement shellResolution: 2.81→2.83 Å / Rfactor Rfree error: 0 / Total num. of bins used: 50
RfactorNum. reflection% reflection
Rfree0.2862 77 5.5 %
Rwork0.2293 1323 -
all0.2325 1400 -
obs--99.63 %

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