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- PDB-6wt3: Structural basis for the binding of monoclonal antibody 5D2 to th... -

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Basic information

Entry
Database: PDB / ID: 6wt3
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
KeywordsIMMUNE SYSTEM / 5D2 / LIPOPROTEIN LIPASE
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.85 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
DepositionMay 1, 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
H: 5D2 FAB HEAVY CHAIN
L: 5D2 FAB LIGHT CHAIN


Theoretical massNumber of molelcules
Total (without water)47,7802
Polymers47,7802
Non-polymers00
Water1267
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3760 Å2
ΔGint-25 kcal/mol
Surface area19840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)138.790, 37.070, 107.960
Angle α, β, γ (deg.)90.00, 126.19, 90.00
Int Tables number5
Space group name H-MC121
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z

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Components

#1: Antibody 5D2 FAB HEAVY CHAIN


Mass: 24411.305 Da / Num. of mol.: 1 / 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.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 7 / 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: 2.39 Å3/Da / Density % sol: 48.46 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 100mM 2-(N-morpholino)ethanesulfonic acid, 150mM ammonium sulfate, 24% PEG 4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9686 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jan 21, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9686 Å / Relative weight: 1
ReflectionResolution: 2.848→43.57 Å / Num. obs: 10111 / % possible obs: 97.7 % / Redundancy: 2.8 % / Biso Wilson estimate: 39.05 Å2 / CC1/2: 0.976 / Rmerge(I) obs: 0.164 / Rpim(I) all: 0.116 / Net I/σ(I): 4.9
Reflection shellResolution: 2.848→2.91 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.515 / Mean I/σ(I) obs: 1.6 / Num. unique obs: 525 / CC1/2: 0.617 / Rpim(I) all: 0.407 / % possible all: 80.3

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Processing

Software
NameVersionClassification
PHENIX(1.18_3855: ???)refinement
Coot0.8.9.2model building
XDS20200131data reduction
STARANISO2.3.28data scaling
PHASER2.8.3phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6WN4

6wn4


Resolution: 2.85→43.57 Å / SU ML: 0.48 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 30.89 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3076 498 4.93 %
Rwork0.2533 --
obs0.256 10110 94.84 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.85→43.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3301 0 0 7 3308
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0033402
X-RAY DIFFRACTIONf_angle_d0.6894637
X-RAY DIFFRACTIONf_dihedral_angle_d5.518460
X-RAY DIFFRACTIONf_chiral_restr0.045514
X-RAY DIFFRACTIONf_plane_restr0.004582
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.85-3.140.37921000.32342035X-RAY DIFFRACTION82
3.14-3.60.32551250.28732509X-RAY DIFFRACTION100
3.6-4.530.29391470.22932483X-RAY DIFFRACTION99
4.53-43.570.28561260.22762585X-RAY DIFFRACTION98

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