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- PDB-5fb8: Structure of Interleukin-16 bound to the 14.1 antibody -

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Basic information

Entry
Database: PDB / ID: 5fb8
TitleStructure of Interleukin-16 bound to the 14.1 antibody
Components
  • (Anti-IL-16 antibody 14.1 Fab domain ...) x 2
  • Pro-interleukin-16
KeywordsIMMUNE SYSTEM / Cytokine / Interleukin / Antibody / Complex
Function / homology
Function and homology information


positive regulation of interleukin-1 alpha production / induction of positive chemotaxis / CD4 receptor binding / Flemming body / leukocyte chemotaxis / Other interleukin signaling / regulation of calcium ion transport / positive regulation of interleukin-12 production / cytokine activity / positive regulation of inflammatory response ...positive regulation of interleukin-1 alpha production / induction of positive chemotaxis / CD4 receptor binding / Flemming body / leukocyte chemotaxis / Other interleukin signaling / regulation of calcium ion transport / positive regulation of interleukin-12 production / cytokine activity / positive regulation of inflammatory response / positive regulation of interleukin-6 production / nuclear speck / immune response / focal adhesion / extracellular space / extracellular region / plasma membrane / cytosol
Similarity search - Function
Interleukin-16 / PDZ domain / Pdz3 Domain / PDZ domain / PDZ domain profile. / Domain present in PSD-95, Dlg, and ZO-1/2. / PDZ domain / PDZ superfamily / Roll / Immunoglobulins ...Interleukin-16 / PDZ domain / Pdz3 Domain / PDZ domain / PDZ domain profile. / Domain present in PSD-95, Dlg, and ZO-1/2. / PDZ domain / PDZ superfamily / Roll / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesMus musculus (house mouse)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.07 Å
AuthorsHall, G. / Cowan, R. / Bayliss, R. / Carr, M.
CitationJournal: J.Biol.Chem. / Year: 2016
Title: Structure of a Potential Therapeutic Antibody Bound to Interleukin-16 (IL-16): MECHANISTIC INSIGHTS AND NEW THERAPEUTIC OPPORTUNITIES.
Authors: Hall, G. / Cullen, E. / Sawmynaden, K. / Arnold, J. / Fox, S. / Cowan, R. / Muskett, F.W. / Matthews, D. / Merritt, A. / Kettleborough, C. / Cruikshank, W. / Taylor, D. / Bayliss, R. / Carr, M.D.
History
DepositionDec 14, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jun 8, 2016Provider: repository / Type: Initial release
Revision 1.1Aug 17, 2016Group: Database references
Revision 1.2Jan 10, 2024Group: 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: Anti-IL-16 antibody 14.1 Fab domain Kappa Chain
B: Anti-IL-16 antibody 14.1 Fab domain Heavy Chain
C: Pro-interleukin-16
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,63114
Polymers58,7863
Non-polymers84511
Water5,242291
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8120 Å2
ΔGint-37 kcal/mol
Surface area22750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.690, 65.950, 196.440
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 1 molecules C

#3: Protein Pro-interleukin-16


Mass: 10785.303 Da / Num. of mol.: 1 / Fragment: UNP residues 1224-1323
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IL16 / Plasmid: pLEICS-01 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q14005

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Antibody , 2 types, 2 molecules AB

#1: Antibody Anti-IL-16 antibody 14.1 Fab domain Kappa Chain


Mass: 23818.469 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Plasmid: pCMV / Cell line (production host): Expi293F / Production host: Homo sapiens (human)
#2: Antibody Anti-IL-16 antibody 14.1 Fab domain Heavy Chain


Mass: 24181.986 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Plasmid: pCMV / Cell line (production host): Expi293F / Production host: Homo sapiens (human)

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Non-polymers , 4 types, 302 molecules

#4: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER / Tris


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


Mass: 18.015 Da / Num. of mol.: 291 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.29 Å3/Da / Density % sol: 62.6 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 16% PEG3350, 0.1 M Bis-Tris-Propane, pH 6.5 and 0.2 M sodium sulphate.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97626 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: May 3, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97626 Å / Relative weight: 1
ReflectionResolution: 2.07→29.45 Å / Num. obs: 48100 / % possible obs: 99.81 % / Redundancy: 6.3 % / Rmerge(I) obs: 0.055 / Net I/σ(I): 17.79
Reflection shellResolution: 2.07→2.144 Å / Redundancy: 6.5 % / Rmerge(I) obs: 0.695 / Mean I/σ(I) obs: 3.44 / % possible all: 99.85

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1I7Z for chain A, 4F33 for chain B, and 1I16 for chain C

1i7z

4f33

1i16


Resolution: 2.07→29.45 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.67 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2053 2434 5.06 %
Rwork0.1718 --
obs0.1735 48095 99.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.07→29.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3997 0 51 291 4339
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0084130
X-RAY DIFFRACTIONf_angle_d1.155589
X-RAY DIFFRACTIONf_dihedral_angle_d13.8641488
X-RAY DIFFRACTIONf_chiral_restr0.044627
X-RAY DIFFRACTIONf_plane_restr0.006707
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.07-2.11230.26811380.23552627X-RAY DIFFRACTION100
2.1123-2.15820.27281550.23192624X-RAY DIFFRACTION100
2.1582-2.20840.25161470.21942660X-RAY DIFFRACTION100
2.2084-2.26360.24731280.21282645X-RAY DIFFRACTION100
2.2636-2.32470.2441390.20972654X-RAY DIFFRACTION100
2.3247-2.39310.25961320.20882674X-RAY DIFFRACTION100
2.3931-2.47030.27951560.212639X-RAY DIFFRACTION100
2.4703-2.55860.2351410.19982641X-RAY DIFFRACTION100
2.5586-2.6610.21091560.2062649X-RAY DIFFRACTION100
2.661-2.7820.27541420.19812690X-RAY DIFFRACTION100
2.782-2.92850.21721350.19942658X-RAY DIFFRACTION100
2.9285-3.11180.23141540.20142695X-RAY DIFFRACTION100
3.1118-3.35180.21521560.19192679X-RAY DIFFRACTION100
3.3518-3.68850.20691300.16732732X-RAY DIFFRACTION100
3.6885-4.22090.18721280.14842741X-RAY DIFFRACTION100
4.2209-5.31280.14361430.12282761X-RAY DIFFRACTION100
5.3128-29.45430.17191540.14882892X-RAY DIFFRACTION100

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