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- PDB-5e4e: Engineered Interleukin-13 bound to receptor -

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Basic information

Entry
Database: PDB / ID: 5e4e
TitleEngineered Interleukin-13 bound to receptor
Components
  • Interleukin-13
  • Interleukin-13 receptor subunit alpha-1
  • Interleukin-4 receptor subunit alpha
KeywordsSIGNALING PROTEIN / agonist-receptor complex / protein engineering
Function / homology
Function and homology information


interleukin-13 receptor complex / interleukin-4 receptor activity / interleukin-13 receptor binding / negative regulation of lung ciliated cell differentiation / positive regulation of lung goblet cell differentiation / positive regulation of pancreatic stellate cell proliferation / interleukin-13-mediated signaling pathway / regulation of proton transport / production of molecular mediator involved in inflammatory response / negative regulation of complement-dependent cytotoxicity ...interleukin-13 receptor complex / interleukin-4 receptor activity / interleukin-13 receptor binding / negative regulation of lung ciliated cell differentiation / positive regulation of lung goblet cell differentiation / positive regulation of pancreatic stellate cell proliferation / interleukin-13-mediated signaling pathway / regulation of proton transport / production of molecular mediator involved in inflammatory response / negative regulation of complement-dependent cytotoxicity / negative regulation of T-helper 1 cell differentiation / T-helper 1 cell differentiation / Interleukin-18 signaling / negative regulation of transforming growth factor beta production / positive regulation of T-helper 2 cell differentiation / interleukin-4-mediated signaling pathway / positive regulation of mast cell degranulation / macrophage activation / response to selenium ion / positive regulation of macrophage activation / response to nematode / cytokine receptor activity / T-helper 2 cell differentiation / positive regulation of immunoglobulin production / positive regulation of myoblast fusion / defense response to protozoan / cytokine binding / immunoglobulin mediated immune response / positive regulation of interleukin-10 production / negative regulation of endothelial cell apoptotic process / positive regulation of chemokine production / positive regulation of B cell proliferation / positive regulation of release of sequestered calcium ion into cytosol / cytokine activity / positive regulation of protein secretion / response to nicotine / positive regulation of smooth muscle cell proliferation / microglial cell activation / cytokine-mediated signaling pathway / centriolar satellite / negative regulation of inflammatory response / cellular response to mechanical stimulus / positive regulation of cold-induced thermogenesis / Interleukin-4 and Interleukin-13 signaling / response to lipopolysaccharide / response to ethanol / receptor complex / cell surface receptor signaling pathway / immune response / inflammatory response / external side of plasma membrane / positive regulation of gene expression / signal transduction / positive regulation of transcription by RNA polymerase II / extracellular space / extracellular region / nucleoplasm / plasma membrane / cytoplasm
Similarity search - Function
Interleukin-13 receptor subunit alpha-1, Ig-like domain / Interleukin-13 receptor subunit alpha Ig-like domain / Interleukin-4 receptor alpha, N-terminal / Interleukin-4 receptor alpha chain, N-terminal / Interleukin-13 / Interleukin-13 / Short hematopoietin receptor, family 2, conserved site / Short hematopoietin receptor family 2 signature. / Interleukin-4/interleukin-13 / Interleukin-4/interleukin-13, conserved site ...Interleukin-13 receptor subunit alpha-1, Ig-like domain / Interleukin-13 receptor subunit alpha Ig-like domain / Interleukin-4 receptor alpha, N-terminal / Interleukin-4 receptor alpha chain, N-terminal / Interleukin-13 / Interleukin-13 / Short hematopoietin receptor, family 2, conserved site / Short hematopoietin receptor family 2 signature. / Interleukin-4/interleukin-13 / Interleukin-4/interleukin-13, conserved site / Interleukins -4 and -13 signature. / Interleukins 4 and 13 / Short hematopoietin receptor family 1 signature. / Type I cytokine receptor, cytokine-binding domain / Interleukin-6 receptor alpha chain, binding / Short hematopoietin receptor, family 1, conserved site / Growth Hormone; Chain: A; - #10 / Four-helical cytokine-like, core / Growth Hormone; Chain: A; / Fibronectin type-III domain profile. / Fibronectin type III / Fibronectin type III superfamily / Immunoglobulin-like fold / Immunoglobulins / Up-down Bundle / Immunoglobulin-like / Sandwich / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
Interleukin-4 receptor subunit alpha / Interleukin-13 / Interleukin-13 receptor subunit alpha-1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 3 Å
AuthorsMoraga, I. / Thomas, C. / Jude, K.M. / Garcia, K.C.
CitationJournal: Sci.Signal. / Year: 2015
Title: Instructive roles for cytokine-receptor binding parameters in determining signaling and functional potency.
Authors: Moraga, I. / Richter, D. / Wilmes, S. / Winkelmann, H. / Jude, K. / Thomas, C. / Suhoski, M.M. / Engleman, E.G. / Piehler, J. / Garcia, K.C.
History
DepositionOct 5, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 2, 2015Provider: repository / Type: Initial release
Revision 1.1Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_struct_oper_list / 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_oper_list.symmetry_operation / _struct_conn.pdbx_role
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.2Nov 20, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _chem_comp.pdbx_synonyms / _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: Interleukin-13
B: Interleukin-4 receptor subunit alpha
C: Interleukin-13 receptor subunit alpha-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,36112
Polymers72,2463
Non-polymers1,1159
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6540 Å2
ΔGint-113 kcal/mol
Surface area28950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.590, 69.370, 186.800
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21221

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Components

#1: Protein Interleukin-13 / IL-13


Mass: 12463.391 Da / Num. of mol.: 1 / Fragment: UNP residues 34-146 / Mutation: L10V, V18I, L39R, D87S, T88S, L101F, K104R, K105T
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IL13, NC30 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P35225
#2: Protein Interleukin-4 receptor subunit alpha / IL-4RA


Mass: 23212.086 Da / Num. of mol.: 1 / Fragment: UNP residues 26-228
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IL4R, IL4RA, 582J2.1 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P24394
#3: Protein Interleukin-13 receptor subunit alpha-1 / IL-13RA1 / Cancer/testis antigen 19 / CT19


Mass: 36570.961 Da / Num. of mol.: 1 / Fragment: UNP residues 23-340
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IL13RA1, IL13R, IL13RA / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P78552
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: SO4
#5: 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.: 2
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
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: 2.81 Å3/Da / Density % sol: 56.17 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 4.2
Details: lithium sulfate, phosphate/citrate pH 4.2, PEG 1000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 21, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3→38.74 Å / Num. obs: 16583 / % possible obs: 99.2 % / Redundancy: 4.2 % / Net I/σ(I): 15.6

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementResolution: 3→38.74 Å / SU ML: 0.46 / Cross valid method: FREE R-VALUE / σ(F): 1.99 / Phase error: 31.27 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2885 829 5 %
Rwork0.2338 --
obs0.2366 16583 97.73 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3→38.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4660 0 63 0 4723
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0024855
X-RAY DIFFRACTIONf_angle_d0.5266623
X-RAY DIFFRACTIONf_dihedral_angle_d10.4451694
X-RAY DIFFRACTIONf_chiral_restr0.023737
X-RAY DIFFRACTIONf_plane_restr0.003842
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.0002-3.18810.37741310.30182491X-RAY DIFFRACTION95
3.1881-3.43410.29931360.25962588X-RAY DIFFRACTION98
3.4341-3.77950.35191360.23912581X-RAY DIFFRACTION98
3.7795-4.32570.25351380.21782637X-RAY DIFFRACTION98
4.3257-5.44760.22461400.19682657X-RAY DIFFRACTION99
5.4476-38.74270.31141480.24452800X-RAY DIFFRACTION98

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