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Basic information

Entry
Database: PDB / ID: 2gys
Title2.7 A structure of the extracellular domains of the human beta common receptor involved in IL-3, IL-5, and GM-CSF signalling
ComponentsCytokine receptor common beta chain
KeywordsSIGNALING PROTEIN / CYTOKINE / DIMER OF INTERLOCKING CHAINS OF FIBRONECTIN-III DOMAINS / FOUR FIBRONECTIN-III DOMAINS PER CHAIN
Function / homology
Function and homology information


Defective CSF2RB causes SMDP5 / Defective CSF2RA causes SMDP4 / respiratory gaseous exchange by respiratory system / Surfactant metabolism / granulocyte macrophage colony-stimulating factor receptor complex / granulocyte-macrophage colony-stimulating factor signaling pathway / interleukin-5-mediated signaling pathway / positive regulation of leukocyte proliferation / cellular response to interleukin-3 / interleukin-3-mediated signaling pathway ...Defective CSF2RB causes SMDP5 / Defective CSF2RA causes SMDP4 / respiratory gaseous exchange by respiratory system / Surfactant metabolism / granulocyte macrophage colony-stimulating factor receptor complex / granulocyte-macrophage colony-stimulating factor signaling pathway / interleukin-5-mediated signaling pathway / positive regulation of leukocyte proliferation / cellular response to interleukin-3 / interleukin-3-mediated signaling pathway / cytokine receptor activity / cell surface receptor signaling pathway via JAK-STAT / Interleukin-3, Interleukin-5 and GM-CSF signaling / immunoglobulin mediated immune response / Interleukin receptor SHC signaling / coreceptor activity / cytokine-mediated signaling pathway / signaling receptor activity / RAF/MAP kinase cascade / response to lipopolysaccharide / external side of plasma membrane / signal transduction / plasma membrane
Similarity search - Function
: / GM-CSF/IL-3/IL-5 receptor common beta subunit, N-terminal / Cytokine IL-3/IL-5/GM-CSF receptor common beta chain / Short hematopoietin receptor family 1 signature. / Short hematopoietin receptor, family 1, conserved site / Interferon-alpha/beta receptor, fibronectin type III / Fibronectin type 3 domain / Fibronectin type-III domain profile. / Fibronectin type III / Fibronectin type III superfamily ...: / GM-CSF/IL-3/IL-5 receptor common beta subunit, N-terminal / Cytokine IL-3/IL-5/GM-CSF receptor common beta chain / Short hematopoietin receptor family 1 signature. / Short hematopoietin receptor, family 1, conserved site / Interferon-alpha/beta receptor, fibronectin type III / Fibronectin type 3 domain / Fibronectin type-III domain profile. / Fibronectin type III / Fibronectin type III superfamily / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
: / Cytokine receptor common subunit beta
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.7 Å
AuthorsCarr, P.D. / Conlan, F. / Ford, S. / Ollis, D.L. / Young, I.G.
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2006
Title: An improved resolution structure of the human beta common receptor involved in IL-3, IL-5 and GM-CSF signalling which gives better definition of the high-affinity binding epitope.
Authors: Carr, P.D. / Conlan, F. / Ford, S. / Ollis, D.L. / Young, I.G.
History
DepositionMay 9, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 20, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / database_PDB_caveat / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_validate_chiral / pdbx_validate_close_contact / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_seq_id_2 / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_comp_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Oct 20, 2021Group: Database references / Structure summary / Category: chem_comp / database_2 / struct_ref_seq_dif
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 2.2Aug 30, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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
B: Cytokine receptor common beta chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,2316
Polymers95,6252
Non-polymers2,6064
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12610 Å2
ΔGint8 kcal/mol
Surface area42520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)184.909, 184.909, 101.047
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3

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Components

#1: Protein Cytokine receptor common beta chain / GM-CSF/IL-3/IL-5 receptor common beta-chain / CD131 antigen / CDw131


Mass: 47812.473 Da / Num. of mol.: 2 / Fragment: extracellular domain, residues 25-443 / Mutation: N328Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CSF2RB, IL3RB, IL5RB / Plasmid: PBACPAK8 / Production host: Trichoplusia ni (cabbage looper) / References: GenBank: 47678387, UniProt: P32927*PLUS
#2: Polysaccharide beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-3)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 732.682 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4[LFucpa1-3]DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,4,3/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5][a1122h-1b_1-5]/1-2-1-3/a3-b1_a4-c1_c4-d1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(3+1)][a-L-Fucp]{}[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}}LINUCSPDB-CARE
#3: Polysaccharide alpha-L-fucopyranose-(1-3)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)]2-acetamido-2-deoxy-beta- ...alpha-L-fucopyranose-(1-3)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 570.542 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
LFucpa1-3[DGlcpNAcb1-4]DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5]/1-2-1/a3-b1_a4-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(3+1)][a-L-Fucp]{}[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE

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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: 3.47 Å3/Da / Density % sol: 64.6 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.4
Details: 10% polyethylene glycol 5000 mono-methyl ether in phosphate buffer, pH 6.4, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-ID-B / Wavelength: 1.117 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Nov 7, 2004
RadiationMonochromator: Diamond (111) double-crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.117 Å / Relative weight: 1
ReflectionResolution: 2.7→50 Å / Num. all: 35381 / Num. obs: 32327 / % possible obs: 91.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.96 % / Biso Wilson estimate: 45.3 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 19.2
Reflection shellResolution: 2.7→2.8 Å / Rmerge(I) obs: 0.153 / Mean I/σ(I) obs: 2.4 / % possible all: 40.2

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
DENZOdata reduction
SCALEPACKdata scaling
CCP4phasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: pdb entry 1gh7

1gh7


Resolution: 2.7→50 Å / Cor.coef. Fo:Fc: 0.915 / Cor.coef. Fo:Fc free: 0.873 / SU B: 26.835 / SU ML: 0.27 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.671 / ESU R Free: 0.347 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.26913 1392 4.3 %RANDOM
Rwork0.21169 ---
all0.21426 35381 --
obs0.21426 30934 91.36 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 51.114 Å2
Baniso -1Baniso -2Baniso -3
1--1.16 Å2-0.58 Å20 Å2
2---1.16 Å20 Å2
3---1.74 Å2
Refine analyzeLuzzati coordinate error obs: 0.459 Å
Refinement stepCycle: LAST / Resolution: 2.7→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6280 0 174 0 6454
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.0216656
X-RAY DIFFRACTIONr_angle_refined_deg2.2171.9639141
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.2995795
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.83222.852298
X-RAY DIFFRACTIONr_dihedral_angle_3_deg22.32115945
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.0651558
X-RAY DIFFRACTIONr_chiral_restr0.1670.21043
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.025076
X-RAY DIFFRACTIONr_nbd_refined0.2540.22722
X-RAY DIFFRACTIONr_nbtor_refined0.330.24457
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1640.2220
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2180.234
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.310.27
X-RAY DIFFRACTIONr_mcbond_it0.751.54109
X-RAY DIFFRACTIONr_mcangle_it1.3526529
X-RAY DIFFRACTIONr_scbond_it2.17132903
X-RAY DIFFRACTIONr_scangle_it3.5574.52612
LS refinement shellResolution: 2.7→2.77 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.541 46 -
Rwork0.394 873 -
obs-1431 34.98 %
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)
19.1155-1.0110.69380.8462-0.22.3907-0.05860.5109-0.4543-0.3549-0.13170.09480.03190.26410.1904-0.2152-0.0394-0.0149-0.2986-0.022-0.1403-21.5591-20.261-33.2171
21.34611.37262.01324.80783.59495.1981-0.0052-0.0199-0.15010.24360.2070.005-0.16940.4323-0.2018-0.1135-0.0296-0.01-0.19440.0813-0.09410.1119-31.708611.4699
32.227-2.7301-4.21714.64274.71718.14380.2888-0.00530.22270.19330.0267-0.34320.12320.5212-0.31550.0372-0.1162-0.1611-0.03890.00810.135733.6766-9.953415.8708
41.563-3.3257-2.07828.5672.64834.87370.26180.42070.52980.17410.09290.7918-0.5861-0.6604-0.35470.3951-0.00440.15310.1413-0.00530.322422.29340.655537.7761
51.27890.3642-0.15649.8212-0.38923.3543-0.0004-0.2357-0.13210.8715-0.0045-0.23120.2696-0.03660.00490.073-0.08050.02410.0729-0.0467-0.143929.487511.828532.8835
66.85360.03795.24220.99790.0957.8950.1386-0.33420.04410.26430.0184-0.26090.4138-0.0808-0.157-0.2838-0.00080.0704-0.292-0.0422-0.00125.1704-22.2292-10.766
71.5821-1.21061.57476.0149-5.64025.43320.1190.0852-0.18950.2473-0.00530.20420.03890.0032-0.1137-0.3369-0.0006-0.0245-0.2443-0.0047-0.0463-4.2762-33.8789-15.6066
83.7481-0.13160.63283.6637-1.70614.0982-0.16780.59740.5906-0.19860.16770.2874-0.8813-0.528200.01970.0739-0.1348-0.05460.00550.0102-45.1186-3.7271-39.1486
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA1 - 911 - 91
2X-RAY DIFFRACTION1BB310 - 317310 - 317
3X-RAY DIFFRACTION2AA106 - 215106 - 215
4X-RAY DIFFRACTION3AA220 - 300220 - 300
5X-RAY DIFFRACTION3BB94 - 10394 - 103
6X-RAY DIFFRACTION4AA320 - 418320 - 418
7X-RAY DIFFRACTION5BB1 - 911 - 91
8X-RAY DIFFRACTION5AA310 - 317310 - 317
9X-RAY DIFFRACTION6BB106 - 215106 - 215
10X-RAY DIFFRACTION7BB220 - 307220 - 307
11X-RAY DIFFRACTION7AA94 - 10394 - 103
12X-RAY DIFFRACTION8BB320 - 418320 - 418

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