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- PDB-1egj: DOMAIN 4 OF THE BETA COMMON CHAIN IN COMPLEX WITH AN ANTIBODY -

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Basic information

Entry
Database: PDB / ID: 1egj
TitleDOMAIN 4 OF THE BETA COMMON CHAIN IN COMPLEX WITH AN ANTIBODY
Components
  • ANTIBODY (HEAVY CHAIN)
  • ANTIBODY (LIGHT CHAIN)
  • CYTOKINE RECEPTOR COMMON BETA CHAIN PRECURSOR
KeywordsIMMUNE SYSTEM / cytokine receptor complexed to an antibody
Function / homology
Function and homology information


Defective CSF2RB causes SMDP5 / Defective CSF2RA causes SMDP4 / positive regulation of B cell activation / phagocytosis, recognition / early endosome to late endosome transport / humoral immune response mediated by circulating immunoglobulin / respiratory gaseous exchange by respiratory system / granulocyte macrophage colony-stimulating factor receptor complex / granulocyte-macrophage colony-stimulating factor signaling pathway / interleukin-5-mediated signaling pathway ...Defective CSF2RB causes SMDP5 / Defective CSF2RA causes SMDP4 / positive regulation of B cell activation / phagocytosis, recognition / early endosome to late endosome transport / humoral immune response mediated by circulating immunoglobulin / respiratory gaseous exchange by respiratory system / granulocyte macrophage colony-stimulating factor receptor complex / granulocyte-macrophage colony-stimulating factor signaling pathway / interleukin-5-mediated signaling pathway / positive regulation of leukocyte proliferation / Surfactant metabolism / positive regulation of type IIa hypersensitivity / positive regulation of type I hypersensitivity / cellular response to interleukin-3 / interleukin-3-mediated signaling pathway / cytokine receptor activity / antibody-dependent cellular cytotoxicity / immunoglobulin complex, circulating / phagocytosis, engulfment / endosome to lysosome transport / antigen processing and presentation / immunoglobulin mediated immune response / regulation of proteolysis / Interleukin-3, Interleukin-5 and GM-CSF signaling / positive regulation of endocytosis / immunoglobulin complex / complement activation, classical pathway / Interleukin receptor SHC signaling / cell surface receptor signaling pathway via JAK-STAT / antigen binding / coreceptor activity / multivesicular body / positive regulation of phagocytosis / response to bacterium / positive regulation of immune response / cytokine-mediated signaling pathway / signaling receptor activity / RAF/MAP kinase cascade / response to lipopolysaccharide / adaptive immune response / immune response / external side of plasma membrane / signal transduction / plasma membrane
Similarity search - Function
Cytokine IL-3/IL-5/GM-CSF receptor common beta chain / : / GM-CSF/IL-3/IL-5 receptor common beta subunit, N-terminal / Short hematopoietin receptor family 1 signature. / Short hematopoietin receptor, family 1, conserved site / : / : / Fibronectin type 3 domain / Immunoglobulin V-Type / Fibronectin type-III domain profile. ...Cytokine IL-3/IL-5/GM-CSF receptor common beta chain / : / GM-CSF/IL-3/IL-5 receptor common beta subunit, N-terminal / Short hematopoietin receptor family 1 signature. / Short hematopoietin receptor, family 1, conserved site / : / : / Fibronectin type 3 domain / Immunoglobulin V-Type / Fibronectin type-III domain profile. / Fibronectin type III / Fibronectin type III superfamily / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin subtype / Immunoglobulin / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
: / Ig kappa chain V-III region MOPC 63 / Immunoglobulin heavy constant gamma 2A / Cytokine receptor common subunit beta
Similarity search - Component
Biological speciesHomo sapiens (human)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.8 Å
AuthorsRossjohn, J. / McKinstry, W.J. / Woodcock, J.M. / McClure, B.J. / Hercus, T.R. / Parker, M.W. / Lopez, A.F. / Bagley, C.J.
CitationJournal: Blood / Year: 2000
Title: Structure of the activation domain of the GM-CSF/IL-3/IL-5 receptor common beta-chain bound to an antagonist.
Authors: Rossjohn, J. / McKinstry, W.J. / Woodcock, J.M. / McClure, B.J. / Hercus, T.R. / Parker, M.W. / Lopez, A.F. / Bagley, C.J.
History
DepositionFeb 15, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 15, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Jan 31, 2018Group: Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.temp
Revision 1.4Jul 29, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_ref_seq_dif / 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 / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.5Oct 9, 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: CYTOKINE RECEPTOR COMMON BETA CHAIN PRECURSOR
L: ANTIBODY (LIGHT CHAIN)
H: ANTIBODY (HEAVY CHAIN)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,1834
Polymers58,9613
Non-polymers2211
Water2,594144
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5160 Å2
ΔGint-26 kcal/mol
Surface area24800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.610, 77.610, 296.250
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein CYTOKINE RECEPTOR COMMON BETA CHAIN PRECURSOR


Mass: 11991.282 Da / Num. of mol.: 1 / Fragment: DOMAIN 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: PCDNA3 (INVITROGEN) / Production host: Escherichia coli (E. coli) / References: UniProt: P32927
#2: Antibody ANTIBODY (LIGHT CHAIN)


Mass: 23589.877 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: MONOCLONAL ANTIBODY / Source: (natural) Mus musculus (house mouse) / References: EMBL: 7024437, UniProt: P01661*PLUS
#3: Antibody ANTIBODY (HEAVY CHAIN)


Mass: 23380.188 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: MONOCLONAL ANTIBODY / Source: (natural) Mus musculus (house mouse) / References: UniProt: P01865
#4: 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.: 1
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
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 144 / 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: 3.78 Å3/Da / Density % sol: 67.47 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 12% peg 4000, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 22K
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
12.9-4 mg/mlprotein1drop
20.043 Mcitrate1drop
35.1 %(w/v)PEG40001drop
40.100 Mcitrate1reservoir
512 %(w/v)PEG40001reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-BM-C / Wavelength: 1
DetectorType: OTHER / Detector: CCD / Date: May 1, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.8→30 Å / Num. all: 21211 / Num. obs: 21211 / % possible obs: 88.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.8 % / Biso Wilson estimate: 85.6 Å2 / Rmerge(I) obs: 0.098 / Net I/σ(I): 11.4
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 2 % / Rmerge(I) obs: 0.62 / Num. unique all: 2058 / % possible all: 87.9
Reflection
*PLUS
Num. measured all: 58732

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNSrefinement
RefinementResolution: 2.8→30 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.288 1087 random
Rwork0.228 --
all0.22 21211 -
obs0.22 21211 -
Refinement stepCycle: LAST / Resolution: 2.8→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4146 0 14 144 4304
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_angle_deg1.5
Software
*PLUS
Name: CNS / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.8 Å / Lowest resolution: 30 Å / σ(F): 0 / % reflection Rfree: 6 % / Rfactor obs: 0.228
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg27.1
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.95

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