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- PDB-4qqv: Extracellular domains of mouse IL-3 beta receptor -

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Basic information

Entry
Database: PDB / ID: 4qqv
TitleExtracellular domains of mouse IL-3 beta receptor
ComponentsInterleukin-3 receptor class 2 subunit beta
KeywordsSIGNALING PROTEIN / intertwined dimer / cytokine receptor / interleukin-3
Function / homology
Function and homology information


RAF/MAP kinase cascade / Interleukin receptor SHC signaling / Interleukin-3, Interleukin-5 and GM-CSF signaling / cytokine receptor activity / membrane => GO:0016020 / plasma membrane
Similarity search - Function
Cytokine IL-3/IL-5/GM-CSF receptor common beta chain / Growth hormone/erythropoietin receptor, ligand binding / Erythropoietin receptor, ligand binding / Short hematopoietin receptor family 1 signature. / Short hematopoietin receptor, family 1, conserved site / Interferon/interleukin receptor domain / Interferon-alpha/beta receptor, fibronectin type III / Fibronectin type 3 domain / Fibronectin type-III domain profile. / Fibronectin type III ...Cytokine IL-3/IL-5/GM-CSF receptor common beta chain / Growth hormone/erythropoietin receptor, ligand binding / Erythropoietin receptor, ligand binding / Short hematopoietin receptor family 1 signature. / Short hematopoietin receptor, family 1, conserved site / Interferon/interleukin receptor domain / 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
Interleukin-3 receptor class 2 subunit beta
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.45 Å
AuthorsJackson, C.J. / Young, I.G. / Murphy, J.M. / Carr, P.D. / Ewens, C.L. / Dai, J. / Ollis, D.L.
CitationJournal: Biochem.J. / Year: 2014
Title: Crystal structure of the mouse interleukin-3 beta-receptor: insights into interleukin-3 binding and receptor activation.
Authors: Carr, P.D. / Ewens, C.L. / Dai, J. / Ollis, D.L. / Murphy, J.M. / Jackson, C.J. / Young, I.G.
History
DepositionJun 30, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 3, 2014Provider: repository / Type: Initial release
Revision 1.1Oct 22, 2014Group: Database references
Revision 1.2Jul 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_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_label_asym_id / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.3Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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-3 receptor class 2 subunit beta
B: Interleukin-3 receptor class 2 subunit beta
C: Interleukin-3 receptor class 2 subunit beta
D: Interleukin-3 receptor class 2 subunit beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)192,6788
Polymers191,7944
Non-polymers8854
Water0
1
A: Interleukin-3 receptor class 2 subunit beta
B: Interleukin-3 receptor class 2 subunit beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,3394
Polymers95,8972
Non-polymers4422
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Interleukin-3 receptor class 2 subunit beta
D: Interleukin-3 receptor class 2 subunit beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,3394
Polymers95,8972
Non-polymers4422
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)197.150, 166.460, 128.000
Angle α, β, γ (deg.)90.00, 122.77, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
Interleukin-3 receptor class 2 subunit beta / IL-3 receptor class 2 subunit beta / IL-3R class 2 subunit beta / Colony-stimulating factor 2 ...IL-3 receptor class 2 subunit beta / IL-3R class 2 subunit beta / Colony-stimulating factor 2 receptor subunit beta-2 / Interleukin-3 receptor class II beta chain / Interleukin-3 cytokine receptor


Mass: 47948.391 Da / Num. of mol.: 4 / Fragment: extracellular domain (UNP residues 23-438) / Mutation: N328Q,K331A,R333A,D334A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Ai2ca, Csf2rb2, Il3r, Il3rb2 / Plasmid: pBacPak8 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P26954
#2: 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 / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 4
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

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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: 4.6 Å3/Da / Density % sol: 73.28 %
Crystal growTemperature: 297 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 36% Tacsimate, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 297K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 21, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 3.45→20 Å / Num. all: 45507 / Num. obs: 45275 / % possible obs: 99.49 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 1.96 % / Biso Wilson estimate: 96.7 Å2 / Rmerge(I) obs: 0.127 / Net I/σ(I): 8.6
Reflection shellHighest resolution: 3.45 Å

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERphasing
PHENIX(phenix.refine: dev_1558)refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2GYS

2gys


Resolution: 3.45→19.912 Å / SU ML: 0.46 / σ(F): 2 / Phase error: 26.51 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2485 2269 5.01 %RANDOM
Rwork0.2033 ---
obs0.2056 45275 99.49 %-
all-45507 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.45→19.912 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12218 0 56 0 12274
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01212669
X-RAY DIFFRACTIONf_angle_d1.70517236
X-RAY DIFFRACTIONf_dihedral_angle_d21.7184665
X-RAY DIFFRACTIONf_chiral_restr0.0681822
X-RAY DIFFRACTIONf_plane_restr0.012235
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.45-3.52460.34341390.30362676X-RAY DIFFRACTION100
3.5246-3.60610.34931480.28622703X-RAY DIFFRACTION100
3.6061-3.69570.30011390.27942630X-RAY DIFFRACTION98
3.6957-3.7950.28841400.25472700X-RAY DIFFRACTION100
3.795-3.90580.29461250.23522610X-RAY DIFFRACTION97
3.9058-4.03090.30141360.22932699X-RAY DIFFRACTION100
4.0309-4.17370.27071490.21632669X-RAY DIFFRACTION100
4.1737-4.33920.26061460.19792704X-RAY DIFFRACTION100
4.3392-4.53440.24041170.18382696X-RAY DIFFRACTION100
4.5344-4.77040.19881310.17112753X-RAY DIFFRACTION100
4.7704-5.06470.23571340.15912676X-RAY DIFFRACTION100
5.0647-5.44830.18531430.16122694X-RAY DIFFRACTION100
5.4483-5.9830.21561360.18612721X-RAY DIFFRACTION100
5.983-6.81820.26091830.21532674X-RAY DIFFRACTION100
6.8182-8.47840.24521380.19912718X-RAY DIFFRACTION99
8.4784-19.91260.21841650.1842683X-RAY DIFFRACTION98
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)
11.2415-0.4046-0.22094.1591.17254.7451-0.2008-0.30030.58490.83070.13470.7237-0.8505-0.3466-0.08090.98260.12160.14530.68070.12461.053241.222747.788416.3736
24.13282.6159-1.28429.9655-0.40362.3184-0.02630.8748-0.0264-2.11140.3845-0.1082-0.30090.1106-0.07761.4104-0.1155-0.02330.8156-0.08020.6441.629712.2115-14.1536
31.98660.04780.75654.0881-0.97941.6798-0.18270.0641-0.1584-0.2430.3197-0.52520.01540.1581-0.13630.66710.00150.15550.4339-0.1550.6544.2178-12.3677-1.0131
45.02210.3617-1.77571.1699-0.47912.4333-0.7999-0.0901-1.56240.30070.69860.62360.2447-0.98680.26121.00290.04220.37451.3410.48352.18735.7772-55.714315.8209
54.2692-1.5891-0.1327.0018-0.2664.1117-0.5639-0.3086-1.23460.37780.19981.22630.5523-0.59530.21760.6632-0.06710.17620.56110.02251.087424.3726-36.03913.0687
65.14443.0820.21526.56230.59551.3052-0.23680.3943-1.3336-0.28850.2946-1.41260.2869-0.09990.01840.71470.11560.13780.5209-0.07530.828143.4899-27.57381.0198
76.0748-1.2593-1.46638.11621.50026.03130.0051-0.1-0.7620.42230.3-2.07190.410.7583-0.33790.8125-0.1103-0.22430.5135-0.11081.109161.51077.281710.0499
82.20861.1535-0.27244.4077-0.7760.5279-0.08520.2821-0.1154-0.17170.3262-0.3711-0.04660.0339-0.20620.6843-0.0608-0.01970.44650.00380.506954.157717.08287.0473
94.6461.25340.4475.1882-1.12946.201-0.39990.29780.6388-0.30990.40980.39950.0172-0.5143-0.040.5601-0.01890.11240.46080.11220.94244.219536.84842.2888
102.1875-1.2638-0.57592.23970.45720.48110.6532-1.01090.86960.67780.3956-0.1109-1.3864-0.4292-0.87892.09620.25660.47831.2897-0.06481.186831.22463.499327.1964
117.2211-0.8237-2.36063.04122.13812.9482-0.8862-1.4663-0.2701-0.06310.5712-0.2602-0.4688-0.09430.46582.57680.48290.68721.49190.17122.01524.578675.715133.9206
122.941-0.33221.97335.3762-1.23471.48480.1751-0.4018-0.178-0.2091-0.0717-0.1178-0.3623-0.0725-0.12542.11990.41860.72861.45530.13742.014418.248470.807637.2998
135.05331.56562.21382.22761.32643.11380.03690.1724-0.0708-0.3331-0.24910.2926-0.1967-0.59140.27330.5850.1227-0.05030.69320.04010.541817.47122.29255.5
144.3681-0.95441.02331.71890.21580.82970.2118-0.42980.4005-0.0518-0.2067-0.64260.3720.23210.01950.85190.0075-0.04530.96660.19750.644879.23047.353733.9811
156.69821.17060.86673.5042-0.3735-0.1401-0.01430.31850.8861-0.12230.0555-0.79460.3168-0.1819-0.03240.6838-0.07430.02531.1970.07870.536575.444712.604738.1438
164.11960.4851.52072.25130.10624.41190.3192-0.1455-0.3235-0.0479-0.27860.30520.2373-0.4622-0.0350.4259-0.0409-0.08180.5891-0.10760.684220.1314-4.097617.0385
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 7:129)
2X-RAY DIFFRACTION2(chain A and resid 130:179)
3X-RAY DIFFRACTION3(chain A and resid 180:317)
4X-RAY DIFFRACTION4(chain A and resid 318:412)
5X-RAY DIFFRACTION5(chain B and resid 7:81)
6X-RAY DIFFRACTION6(chain B and resid 82:121)
7X-RAY DIFFRACTION7(chain B and resid 122:178)
8X-RAY DIFFRACTION8(chain B and resid 179:239)
9X-RAY DIFFRACTION9(chain B and resid 240:300)
10X-RAY DIFFRACTION10(chain B and resid 301:337)
11X-RAY DIFFRACTION11(chain B and resid 338:357)
12X-RAY DIFFRACTION12(chain B and resid 358:411)
13X-RAY DIFFRACTION13(chain C and resid 7:202)
14X-RAY DIFFRACTION14(chain C and resid 203:412)
15X-RAY DIFFRACTION15(chain D and resid 7:121)
16X-RAY DIFFRACTION16(chain D and resid 122:322)

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