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- PDB-6wn4: Structural basis for the binding of monoclonal antibody 5D2 to th... -

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Basic information

Entry
Database: PDB / ID: 6wn4
TitleStructural basis for the binding of monoclonal antibody 5D2 to the tryptophan-rich lipid-binding loop in lipoprotein lipase
Components
  • 5D2 FAB HEAVY CHAIN
  • 5D2 FAB LIGHT CHAIN
  • Lipoprotein lipase peptide
KeywordsIMMUNE SYSTEM / 5D2 / LIPOPROTEIN LIPASE
Function / homology
Function and homology information


lipoprotein lipase / lipoprotein lipase activity / positive regulation of sequestering of triglyceride / low-density lipoprotein particle mediated signaling / chylomicron remodeling / positive regulation of cholesterol storage / phospholipase A1 / phosphatidylserine 1-acylhydrolase activity / 1-acyl-2-lysophosphatidylserine acylhydrolase activity / phospholipase A1 activity ...lipoprotein lipase / lipoprotein lipase activity / positive regulation of sequestering of triglyceride / low-density lipoprotein particle mediated signaling / chylomicron remodeling / positive regulation of cholesterol storage / 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 / very-low-density lipoprotein particle remodeling / positive regulation of macrophage derived foam cell differentiation / Chylomicron remodeling / positive regulation of lipid storage / cellular response to nutrient / chylomicron / high-density lipoprotein particle remodeling / very-low-density lipoprotein particle / triglyceride lipase activity / heparan sulfate proteoglycan binding / positive regulation of chemokine (C-X-C motif) ligand 2 production / 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 / 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 / signaling receptor 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 / Lipoxygenase homology 2 (beta barrel) domain / PLAT/LH2 domain / PLAT/LH2 domain superfamily / PLAT/LH2 domain ...Lipoprotein lipase / Lipase, LIPH-type / Lipase, N-terminal / Triacylglycerol lipase family / Lipase / Lipase / Lipoxygenase homology 2 (beta barrel) domain / PLAT/LH2 domain / PLAT/LH2 domain superfamily / PLAT/LH2 domain / PLAT domain profile. / Lipases, serine active site. / Alpha/Beta hydrolase fold
Similarity search - Domain/homology
Biological speciesMus musculus (house mouse)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsLuz, J.G. / Birrane, G. / Young, S.G. / Meiyappan, M. / Ploug, M.
Funding support United States, France, 4items
OrganizationGrant numberCountry
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)HL090553 United States
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)HL087228 United States
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)HL125335 United States
Leducq Foundation12CVD04 France
CitationJournal: J.Lipid Res. / Year: 2020
Title: The structural basis for monoclonal antibody 5D2 binding to the tryptophan-rich loop of lipoprotein lipase.
Authors: Luz, J.G. / Beigneux, A.P. / Asamoto, D.K. / He, C. / Song, W. / Allan, C.M. / Morales, J. / Tu, Y. / Kwok, A. / Cottle, T. / Meiyappan, M. / Fong, L.G. / Kim, J.E. / Ploug, M. / Young, S.G. / Birrane, G.
History
DepositionApr 22, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 29, 2020Provider: repository / Type: Initial release
Revision 1.1Dec 2, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _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 1.2Oct 18, 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: 5D2 FAB HEAVY CHAIN
B: 5D2 FAB LIGHT CHAIN
C: Lipoprotein lipase peptide
D: Lipoprotein lipase peptide
H: 5D2 FAB HEAVY CHAIN
L: 5D2 FAB LIGHT CHAIN


Theoretical massNumber of molelcules
Total (without water)98,8686
Polymers98,8686
Non-polymers00
Water52229
1
A: 5D2 FAB HEAVY CHAIN
B: 5D2 FAB LIGHT CHAIN
C: Lipoprotein lipase peptide


Theoretical massNumber of molelcules
Total (without water)49,4343
Polymers49,4343
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
D: Lipoprotein lipase peptide
H: 5D2 FAB HEAVY CHAIN
L: 5D2 FAB LIGHT CHAIN


Theoretical massNumber of molelcules
Total (without water)49,4343
Polymers49,4343
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)51.624, 67.745, 130.073
Angle α, β, γ (deg.)90.000, 94.369, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Antibody 5D2 FAB HEAVY CHAIN


Mass: 24296.217 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / Plasmid details: 5D2 HYBRIDOMA
#2: Antibody 5D2 FAB LIGHT CHAIN


Mass: 23368.805 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / Plasmid details: 5D2 HYBRIDOMA
#3: Protein/peptide Lipoprotein lipase peptide / LPL


Mass: 1768.814 Da / Num. of mol.: 2 / Fragment: tryptophan-rich lipid-binding loop / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P06858
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 29 / 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: 2.31 Å3/Da / Density % sol: 46.71 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: 16-22% PEG 3350, 250mM Sodium Thiocyanate / Temp details: NULL

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Data collection

DiffractionMean temperature: 100 K / Ambient temp details: NULL / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-1 / Wavelength: 0.9201 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Apr 25, 2019 / Details: NULL
RadiationMonochromator: Si(III) SILICON CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9201 Å / Relative weight: 1
ReflectionResolution: 2.74→29.264 Å / Num. obs: 23348 / % possible obs: 99.29 % / Redundancy: 5.1 % / CC1/2: 0.995 / Rmerge(I) obs: 0.12 / Rpim(I) all: 0.057 / Rrim(I) all: 0.133 / Net I/σ(I): 10.4
Reflection shellResolution: 2.74→2.84 Å / Redundancy: 5.08 % / Rmerge(I) obs: 0.692 / Mean I/σ(I) obs: 1.9 / Num. unique obs: 2178 / CC1/2: 0.729 / Rpim(I) all: 0.33 / Rrim(I) all: 0.769 / % possible all: 93.72

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
Coot0.8.9.2model building
HKL-2000v720data scaling
HKL-2000v720data reduction
PHASER2.8.3phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5D8J

5d8j


Resolution: 2.8→29.264 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.919 / WRfactor Rfree: 0.216 / WRfactor Rwork: 0.184 / SU B: 18.187 / SU ML: 0.321 / Average fsc free: 0.8774 / Average fsc work: 0.8927 / Cross valid method: FREE R-VALUE / ESU R Free: 0.392
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflectionSelection details
Rfree0.2427 1066 4.782 %Random selection
Rwork0.2079 21225 --
all0.21 ---
obs-22291 99.816 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 54.434 Å2
Baniso -1Baniso -2Baniso -3
1-1.721 Å20 Å2-2.888 Å2
2--2.905 Å20 Å2
3----4.136 Å2
Refinement stepCycle: LAST / Resolution: 2.8→29.264 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6797 0 0 29 6826
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0030.0136993
X-RAY DIFFRACTIONr_bond_other_d0.0010.0176093
X-RAY DIFFRACTIONr_angle_refined_deg1.2631.6459541
X-RAY DIFFRACTIONr_angle_other_deg1.0731.5714259
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9175869
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.76623.402291
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.146151099
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.2471519
X-RAY DIFFRACTIONr_chiral_restr0.0390.2932
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.027773
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021440
X-RAY DIFFRACTIONr_nbd_refined0.1640.2946
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1650.25129
X-RAY DIFFRACTIONr_nbtor_refined0.160.23190
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0710.22997
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1530.2121
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1430.221
X-RAY DIFFRACTIONr_nbd_other0.1760.269
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1610.29
X-RAY DIFFRACTIONr_mcbond_it1.0765.9753500
X-RAY DIFFRACTIONr_mcbond_other1.0765.9743499
X-RAY DIFFRACTIONr_mcangle_it1.9168.9574361
X-RAY DIFFRACTIONr_mcangle_other1.9168.9584362
X-RAY DIFFRACTIONr_scbond_it0.8655.9163493
X-RAY DIFFRACTIONr_scbond_other0.8645.9143491
X-RAY DIFFRACTIONr_scangle_it1.5318.8575180
X-RAY DIFFRACTIONr_scangle_other1.5318.8575180
X-RAY DIFFRACTIONr_lrange_it4.519110.53226643
X-RAY DIFFRACTIONr_lrange_other4.519110.53426640
X-RAY DIFFRACTIONr_ncsr_local_group_10.1040.056190
X-RAY DIFFRACTIONr_ncsr_local_group_20.1220.055828
X-RAY DIFFRACTIONr_ncsr_local_group_30.1350.05353
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8-2.8720.344820.331592X-RAY DIFFRACTION100
2.872-2.9510.428660.3181514X-RAY DIFFRACTION99.8736
2.951-3.0370.399860.2961478X-RAY DIFFRACTION99.6178
3.037-3.130.361720.2881400X-RAY DIFFRACTION100
3.13-3.2330.331620.2751425X-RAY DIFFRACTION100
3.233-3.3460.238740.2681307X-RAY DIFFRACTION99.8554
3.346-3.4720.304700.241298X-RAY DIFFRACTION99.927
3.472-3.6140.265700.2271263X-RAY DIFFRACTION99.925
3.614-3.7740.266740.2131173X-RAY DIFFRACTION99.9199
3.774-3.9590.238490.1971187X-RAY DIFFRACTION100
3.959-4.1720.171650.1921057X-RAY DIFFRACTION99.9109
4.172-4.4250.18540.1611037X-RAY DIFFRACTION100
4.425-4.730.18530.153993X-RAY DIFFRACTION99.9045
4.73-5.1090.175390.15923X-RAY DIFFRACTION100
5.109-5.5960.282420.164829X-RAY DIFFRACTION99.8853
5.596-6.2550.141300.2774X-RAY DIFFRACTION99.8758
6.255-7.2190.193300.187691X-RAY DIFFRACTION100
7.219-8.8350.159210.153578X-RAY DIFFRACTION99.8333
8.835-12.4660.17100.135467X-RAY DIFFRACTION100
12.466-29.2640.224170.216239X-RAY DIFFRACTION91.7563

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