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- PDB-2xqb: Crystal Structure of anti-IL-15 Antibody in Complex with human IL-15 -

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Basic information

Entry
Database: PDB / ID: 2xqb
TitleCrystal Structure of anti-IL-15 Antibody in Complex with human IL-15
Components
  • (ANTI-IL-15 ANTIBODY) x 2
  • INTERLEUKIN 15
KeywordsIMMUNE SYSTEM / AFFINITY MATURATION
Function / homology
Function and homology information


extrathymic T cell selection / natural killer cell proliferation / positive regulation of natural killer cell differentiation / NK T cell proliferation / tyrosine phosphorylation of STAT protein / positive regulation of tissue remodeling / natural killer cell differentiation / cytokine receptor binding / neutrophil activation / regulation of defense response to virus by host ...extrathymic T cell selection / natural killer cell proliferation / positive regulation of natural killer cell differentiation / NK T cell proliferation / tyrosine phosphorylation of STAT protein / positive regulation of tissue remodeling / natural killer cell differentiation / cytokine receptor binding / neutrophil activation / regulation of defense response to virus by host / interleukin-15-mediated signaling pathway / Interleukin-15 signaling / negative regulation of cold-induced thermogenesis / regulation of T cell differentiation / positive regulation of peptidyl-tyrosine phosphorylation / positive regulation of interleukin-17 production / positive regulation of natural killer cell proliferation / macrophage differentiation / lymph node development / cell maturation / positive regulation of T cell proliferation / positive regulation of phagocytosis / positive regulation of cytokine production / cytokine activity / positive regulation of immune response / positive regulation of inflammatory response / cell-cell signaling / endosome / nuclear speck / immune response / positive regulation of cell population proliferation / Golgi apparatus / signal transduction / extracellular space / extracellular region / nucleoplasm / cytoplasm / cytosol
Similarity search - Function
Interleukin-15 / Interleukin-15, mammal / Interleukin-15/Interleukin-21 family / Interleukin 15 / Interleukin-15/Interleukin-21 / Four-helical cytokine-like, core / Growth Hormone; Chain: A; / Immunoglobulins / Up-down Bundle / Immunoglobulin-like ...Interleukin-15 / Interleukin-15, mammal / Interleukin-15/Interleukin-21 family / Interleukin 15 / Interleukin-15/Interleukin-21 / Four-helical cytokine-like, core / Growth Hormone; Chain: A; / Immunoglobulins / Up-down Bundle / Immunoglobulin-like / Sandwich / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsLowe, D.C. / Gerhardt, S. / Ward, A. / Hargreaves, D. / Anderson, M. / StGallay, S. / Vousden, K. / Ferraro, F. / Pauptit, R.A. / Cochrane, D. ...Lowe, D.C. / Gerhardt, S. / Ward, A. / Hargreaves, D. / Anderson, M. / StGallay, S. / Vousden, K. / Ferraro, F. / Pauptit, R.A. / Cochrane, D. / Pattison, D.V. / Buchanan, C. / Popovic, B. / Finch, D.K. / Wilkinson, T. / Sleeman, M. / Vaughan, T.J. / Cruwys, S. / Mallinder, P.R.
CitationJournal: J.Mol.Biol. / Year: 2011
Title: Engineering a High Affinity Anti-Il-15 Antibody: Crystal Structure Reveals an Alpha-Helix in Vh Cdr3 as Key Component of Paratope.
Authors: Lowe, D.C. / Gerhardt, S. / Ward, A. / Hargreaves, D. / Anderson, M. / Ferraro, F. / Pauptit, R.A. / Pattison, D.V. / Buchanan, C. / Popovic, B. / Finch, D.K. / Wilkinson, T. / Sleeman, M. / ...Authors: Lowe, D.C. / Gerhardt, S. / Ward, A. / Hargreaves, D. / Anderson, M. / Ferraro, F. / Pauptit, R.A. / Pattison, D.V. / Buchanan, C. / Popovic, B. / Finch, D.K. / Wilkinson, T. / Sleeman, M. / Vaughan, T.J. / Mallinder, P.R.
History
DepositionSep 1, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 29, 2010Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Apr 4, 2018Group: Data collection / Source and taxonomy / Category: diffrn_source / entity_src_gen
Item: _diffrn_source.type / _entity_src_gen.pdbx_gene_src_scientific_name ..._diffrn_source.type / _entity_src_gen.pdbx_gene_src_scientific_name / _entity_src_gen.pdbx_host_org_cell_line / _entity_src_gen.pdbx_host_org_scientific_name / _entity_src_gen.pdbx_host_org_strain
Revision 1.4Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Oct 23, 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: INTERLEUKIN 15
H: ANTI-IL-15 ANTIBODY
L: ANTI-IL-15 ANTIBODY
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,3796
Polymers61,0903
Non-polymers2883
Water1,18966
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6100 Å2
ΔGint-79.8 kcal/mol
Surface area23010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)185.186, 43.754, 70.087
Angle α, β, γ (deg.)90.00, 95.95, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein INTERLEUKIN 15


Mass: 12784.453 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: PT7#3.3 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): STAR / References: UniProt: P40933
#2: Antibody ANTI-IL-15 ANTIBODY


Mass: 25390.467 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK293/EBNA / Production host: Homo sapiens (human)
#3: Antibody ANTI-IL-15 ANTIBODY


Mass: 22915.441 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK293/EBNA / Production host: Homo sapiens (human)
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 66 / Source method: isolated from a natural source / Formula: H2O
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: 1.8 Å3/Da / Density % sol: 32 % / Description: NONE
Crystal growpH: 9.5
Details: PCTP 100MM, PH 9.5, 25 %W/V PEG-3350, 200MM AMMONIUM SULPHATE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E / Wavelength: 1.5418
DetectorType: RIGAKU CCD / Detector: CCD / Date: Feb 26, 2008 / Details: OSMIC
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.6→69.7 Å / Num. obs: 17425 / % possible obs: 99.1 % / Observed criterion σ(I): 0 / Redundancy: 3 % / Rmerge(I) obs: 0.13 / Net I/σ(I): 4.4
Reflection shellResolution: 2.6→2.69 Å / Redundancy: 3 % / Rmerge(I) obs: 0.36 / Mean I/σ(I) obs: 2 / % possible all: 98.8

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Processing

Software
NameVersionClassification
REFMAC5.4.0069refinement
d*TREKdata reduction
d*TREKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1AQK

1aqk


Resolution: 2.6→69.71 Å / Cor.coef. Fo:Fc: 0.922 / Cor.coef. Fo:Fc free: 0.859 / SU B: 31.94 / SU ML: 0.339 / Cross valid method: THROUGHOUT / ESU R: 2.527 / ESU R Free: 0.419 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS.
RfactorNum. reflection% reflectionSelection details
Rfree0.31811 883 5.1 %RANDOM
Rwork0.24441 ---
obs0.24809 16532 99.03 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 51.224 Å2
Baniso -1Baniso -2Baniso -3
1-0.35 Å20 Å20.36 Å2
2--1.52 Å20 Å2
3----1.79 Å2
Refinement stepCycle: LAST / Resolution: 2.6→69.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3982 0 15 66 4063
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0224094
X-RAY DIFFRACTIONr_bond_other_d0.0010.022659
X-RAY DIFFRACTIONr_angle_refined_deg1.6051.9565592
X-RAY DIFFRACTIONr_angle_other_deg1.8513.0046521
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1585527
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.17524.762147
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.72515620
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.3991511
X-RAY DIFFRACTIONr_chiral_restr0.0680.2643
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0214537
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02777
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.2551.52660
X-RAY DIFFRACTIONr_mcbond_other0.0391.51069
X-RAY DIFFRACTIONr_mcangle_it0.47224283
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it0.71431434
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it1.2164.51309
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.6→2.667 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.43 56 -
Rwork0.342 1218 -
obs--98.91 %
Refinement TLS params.

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 °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.9163-0.4074-0.09731.57320.00131.92490.15720.18330.0602-0.053-0.1520.0680.0983-0.2237-0.0052-0.1108-0.0190.0174-0.211-0.0112-0.142534.99971.634128.9464
24.45871.6971.8572.5461.38433.58540.04780.5957-0.1265-0.3496-0.02830.04870.06540.0872-0.0195-0.00020.0937-0.00210.0617-0.0186-0.189534.646-2.47447.5739
33.02911.29211.0533.07840.98843.84510.06760.2081-0.107-0.32550.13120.13570.38460.1443-0.1988-0.04810.0238-0.05690.0479-0.044-0.0001-0.6445-10.038623.8519
43.6758-0.7226-1.31230.89-0.56144.48520.26860.22950.1568-0.14410.11850.0422-0.11560.0137-0.3871-0.0161-0.03840.03650.0893-0.03520.12160.89890.865212.6323
52.53750.32450.41195.7358-1.55274.91510.17520.4717-0.0558-0.3124-0.3262-0.44970.11530.55770.151-0.11780.04150.09130.11740.02050.051660.6301-1.089319.4312
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1H1 - 114
2X-RAY DIFFRACTION2L5 - 108
3X-RAY DIFFRACTION3H115 - 215
4X-RAY DIFFRACTION4L109 - 209
5X-RAY DIFFRACTION5A1 - 113

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