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- PDB-1iar: INTERLEUKIN-4 / RECEPTOR ALPHA CHAIN COMPLEX -

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Basic information

Entry
Database: PDB / ID: 1iar
TitleINTERLEUKIN-4 / RECEPTOR ALPHA CHAIN COMPLEX
Components
  • PROTEIN (INTERLEUKIN-4 RECEPTOR ALPHA CHAIN)
  • PROTEIN (INTERLEUKIN-4)
KeywordsCYTOKINE/RECEPTOR / CYTOKINE RECEPTOR / INTERLEUKIN-4 / CYTOKINE-RECEPTOR COMPLEX
Function / homology
Function and homology information


interleukin-4 receptor activity / interleukin-4 receptor binding / positive regulation of isotype switching to IgE isotypes / negative regulation of complement-dependent cytotoxicity / negative regulation of T-helper 1 cell differentiation / T-helper 1 cell differentiation / positive regulation of cellular respiration / production of molecular mediator involved in inflammatory response / Interleukin-18 signaling / regulation of isotype switching ...interleukin-4 receptor activity / interleukin-4 receptor binding / positive regulation of isotype switching to IgE isotypes / negative regulation of complement-dependent cytotoxicity / negative regulation of T-helper 1 cell differentiation / T-helper 1 cell differentiation / positive regulation of cellular respiration / production of molecular mediator involved in inflammatory response / Interleukin-18 signaling / regulation of isotype switching / negative regulation of neuroinflammatory response / negative regulation of epithelial cell migration / positive regulation of T-helper 2 cell differentiation / positive regulation of T-helper 2 cell cytokine production / dendritic cell differentiation / interleukin-4-mediated signaling pathway / neuroinflammatory response / positive regulation of mast cell degranulation / positive regulation of isotype switching to IgG isotypes / positive regulation of interleukin-13 production / macrophage activation / positive regulation of amyloid-beta clearance / myeloid dendritic cell differentiation / positive regulation of MHC class II biosynthetic process / positive regulation of macrophage activation / cytokine receptor activity / type 2 immune response / T-helper 2 cell differentiation / negative regulation of cellular response to transforming growth factor beta stimulus / positive regulation of myoblast fusion / positive regulation of immunoglobulin production / positive regulation of T cell differentiation / defense response to protozoan / negative regulation of osteoclast differentiation / positive regulation of ATP biosynthetic process / immunoglobulin mediated immune response / positive regulation of interleukin-10 production / positive regulation of macroautophagy / negative regulation of tumor necrosis factor production / cell surface receptor signaling pathway via JAK-STAT / regulation of immune response / negative regulation of endothelial cell apoptotic process / cholesterol metabolic process / positive regulation of chemokine production / positive regulation of B cell proliferation / positive regulation of T cell proliferation / T cell activation / B cell differentiation / cytokine activity / growth factor activity / positive regulation of receptor-mediated endocytosis / negative regulation of inflammatory response / centriolar satellite / cytokine-mediated signaling pathway / positive regulation of cold-induced thermogenesis / Interleukin-4 and Interleukin-13 signaling / receptor complex / immune response / positive regulation of cell migration / external side of plasma membrane / negative regulation of DNA-templated transcription / positive regulation of cell population proliferation / positive regulation of gene expression / negative regulation of apoptotic process / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / signal transduction / positive regulation of transcription by RNA polymerase II / extracellular space / extracellular region / nucleoplasm / plasma membrane
Similarity search - Function
Interleukin-4 receptor alpha, N-terminal / Interleukin-4 receptor alpha chain, N-terminal / Interleukin-4 / Interleukin 4 / 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. / Short hematopoietin receptor, family 1, conserved site ...Interleukin-4 receptor alpha, N-terminal / Interleukin-4 receptor alpha chain, N-terminal / Interleukin-4 / Interleukin 4 / 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. / 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 / Interleukin-4 receptor subunit alpha
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.3 Å
AuthorsHage, T. / Sebald, W. / Reinemer, P.
Citation
Journal: Cell(Cambridge,Mass.) / Year: 1999
Title: Crystal structure of the interleukin-4/receptor alpha chain complex reveals a mosaic binding interface.
Authors: Hage, T. / Sebald, W. / Reinemer, P.
#1: Journal: Eur.J.Biochem. / Year: 1998
Title: Crystals of a 1:1 complex between human interleukin-4 and the extracellular domain of its receptor alpha chain.
Authors: Hage, T. / Reinemer, P. / Sebald, W.
History
DepositionFeb 25, 1999Deposition site: BNL / Processing site: RCSB
Revision 1.0Mar 3, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Mar 14, 2018Group: Database references / Category: struct_ref_seq_dif / Item: _struct_ref_seq_dif.details
Revision 1.5Nov 6, 2019Group: Data collection / Database references / Category: citation / struct_ref_seq_dif
Item: _citation.page_last / _citation.pdbx_database_id_PubMed ..._citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _struct_ref_seq_dif.details
Revision 1.6Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_seq_id
Revision 1.7Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PROTEIN (INTERLEUKIN-4)
B: PROTEIN (INTERLEUKIN-4 RECEPTOR ALPHA CHAIN)


Theoretical massNumber of molelcules
Total (without water)38,7282
Polymers38,7282
Non-polymers00
Water4,143230
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1550 Å2
ΔGint-3 kcal/mol
Surface area16850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.720, 67.980, 108.460
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein PROTEIN (INTERLEUKIN-4)


Mass: 14989.248 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Description: RECOMBINANT; / Production host: Escherichia coli (E. coli) / References: UniProt: P05112
#2: Protein PROTEIN (INTERLEUKIN-4 RECEPTOR ALPHA CHAIN)


Mass: 23738.562 Da / Num. of mol.: 1 / Fragment: EXTRACELLULAR DOMAIN / Mutation: M1F, C182A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Description: RECOMBINANT / Production host: Escherichia coli (E. coli) / References: UniProt: P24394
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 230 / 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: 2.4 Å3/Da / Density % sol: 49 %
Crystal growpH: 8 / Details: pH 8.0
Crystal grow
*PLUS
pH: 5 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
110 mg/mlprotein1drop
225 mMsodium acetate1drop
3120 mM1dropNaCl
420 %(v/v)ethanol1reservoir
55 %(v/v)methylpentanediol1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MPG/DESY, HAMBURG / Beamline: BW6 / Wavelength: 1.2
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Nov 1, 1997 / Details: DOUBLE-FOCUSSING TOROIDAL MIRROR
RadiationMonochromator: SI(111) DOUBLE MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.2 Å / Relative weight: 1
ReflectionResolution: 2.3→25 Å / Num. obs: 16897 / % possible obs: 99.7 % / Redundancy: 5.8 % / Rsym value: 0.038 / Net I/σ(I): 52
Reflection shellResolution: 2.3→2.4 Å / Redundancy: 5.2 % / Mean I/σ(I) obs: 20 / Rsym value: 0.067 / % possible all: 99.2
Reflection
*PLUS
Rmerge(I) obs: 0.038
Reflection shell
*PLUS
% possible obs: 99.2 % / Rmerge(I) obs: 0.067

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
ROTAVATA/AGROVATAdata reduction
MLPHAREphasing
X-PLOR3.8refinement
CCP4(AGROVATAdata scaling
ROTAVATAdata scaling
RefinementMethod to determine structure: MAD / Resolution: 2.3→25 Å / Cross valid method: THROUGHOUT / σ(F): 3
RfactorNum. reflection% reflectionSelection details
Rfree0.289 797 4.7 %RANDOM
Rwork0.218 ---
obs-16652 98.2 %-
Displacement parametersBiso mean: 20.5 Å2
Refinement stepCycle: LAST / Resolution: 2.3→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2565 0 0 230 2795
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.012
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.7
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d25.3
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d0.9
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
LS refinement shellResolution: 2.3→2.35 Å / Total num. of bins used: 15
RfactorNum. reflection% reflection
Rfree0.344 41 3.7 %
Rwork0.284 1028 -
obs--96.1 %
Xplor fileSerial no: 1 / Param file: PAR_CSD (ENGH & HUBER) / Topol file: TOP_CSD (ENGH & HUBER)
Software
*PLUS
Name: X-PLOR / Version: 3.8 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg25.3
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg0.9

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