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- PDB-4nn6: Cytokine receptor complex - Crystal form 1B -

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Basic information

Entry
Database: PDB / ID: 4nn6
TitleCytokine receptor complex - Crystal form 1B
Components
  • Cytokine receptor-like factor 2
  • Interleukin-7 receptor subunit alpha
  • Thymic stromal lymphopoietin
KeywordsCYTOKINE/CYTOKINE RECEPTOR / four helical bundle fold / CHR domains / TSLP cytokine signaling / TSLPR and IL-7Ralpha receptors / cell surface / CYTOKINE-CYTOKINE RECEPTOR complex
Function / homology
Function and homology information


positive regulation of chemokine (C-C motif) ligand 1 production / interleukin-7 receptor binding / positive regulation of granulocyte colony-stimulating factor production / positive regulation of mast cell activation / Interleukin-7 signaling / positive regulation of receptor signaling pathway via STAT / negative regulation of T cell mediated cytotoxicity / positive regulation of cytokine-mediated signaling pathway / positive regulation of T cell differentiation in thymus / Cargo recognition for clathrin-mediated endocytosis ...positive regulation of chemokine (C-C motif) ligand 1 production / interleukin-7 receptor binding / positive regulation of granulocyte colony-stimulating factor production / positive regulation of mast cell activation / Interleukin-7 signaling / positive regulation of receptor signaling pathway via STAT / negative regulation of T cell mediated cytotoxicity / positive regulation of cytokine-mediated signaling pathway / positive regulation of T cell differentiation in thymus / Cargo recognition for clathrin-mediated endocytosis / Clathrin-mediated endocytosis / positive regulation of interleukin-5 production / negative regulation of T cell apoptotic process / cytokine receptor activity / positive regulation of interleukin-13 production / regulation of cell size / B cell proliferation / T cell homeostasis / positive regulation of interleukin-10 production / B cell homeostasis / hemopoiesis / T cell differentiation / defense response to fungus / lymph node development / positive regulation of chemokine production / positive regulation of tyrosine phosphorylation of STAT protein / cytokine activity / positive regulation of receptor signaling pathway via JAK-STAT / cell morphogenesis / T cell mediated cytotoxicity / positive regulation of inflammatory response / positive regulation of interleukin-6 production / cytokine-mediated signaling pathway / antimicrobial humoral immune response mediated by antimicrobial peptide / T cell differentiation in thymus / gene expression / defense response to Gram-negative bacterium / defense response to Gram-positive bacterium / inflammatory response / external side of plasma membrane / positive regulation of cell population proliferation / positive regulation of gene expression / negative regulation of apoptotic process / extracellular space / extracellular region / nucleoplasm / plasma membrane / cytosol
Similarity search - Function
Thymic stromal lymphopoietin / Thymic stromal lymphopoietin / Thymic stromal lymphopoietin superfamily / Thymic stromal lymphopoietin / Immunoglobulin-like - #1870 / IL-7Ralpha, fibronectin type III domain / Fibronectin type III domain / : / : / Cytokine receptor-like factor 2-like, D1 domain ...Thymic stromal lymphopoietin / Thymic stromal lymphopoietin / Thymic stromal lymphopoietin superfamily / Thymic stromal lymphopoietin / Immunoglobulin-like - #1870 / IL-7Ralpha, fibronectin type III domain / Fibronectin type III domain / : / : / Cytokine receptor-like factor 2-like, D1 domain / Cytokine receptor-like factor 2-like, D2 domain / Short hematopoietin receptor family 1 signature. / Short hematopoietin receptor, family 1, conserved site / Growth Hormone; Chain: A; / Fibronectin type III domain / Fibronectin type 3 domain / Fibronectin type-III domain profile. / Fibronectin type III / Fibronectin type III superfamily / Immunoglobulins / Immunoglobulin-like fold / Up-down Bundle / Immunoglobulin-like / Sandwich / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
Interleukin-7 receptor subunit alpha / Cytokine receptor-like factor 2 / Thymic stromal lymphopoietin
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.545 Å
AuthorsVerstraete, K. / van Schie, L. / Savvides, S.N.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2014
Title: Structural basis of the proinflammatory signaling complex mediated by TSLP.
Authors: Verstraete, K. / van Schie, L. / Vyncke, L. / Bloch, Y. / Tavernier, J. / Pauwels, E. / Peelman, F. / Savvides, S.N.
History
DepositionNov 16, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 19, 2014Provider: repository / Type: Initial release
Revision 1.1Apr 2, 2014Group: Database references
Revision 1.2Apr 16, 2014Group: Database references
Revision 1.3Mar 7, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.4Sep 20, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Thymic stromal lymphopoietin
B: Interleukin-7 receptor subunit alpha
C: Cytokine receptor-like factor 2


Theoretical massNumber of molelcules
Total (without water)63,3543
Polymers63,3543
Non-polymers00
Water543
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)147.949, 75.157, 51.439
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Thymic stromal lymphopoietin / / TSLP / Thymic stroma-derived lymphopoietin


Mass: 15109.947 Da / Num. of mol.: 1 / Fragment: UNP residues 20-140 / Mutation: N123Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Tslp / Cell line (production host): HEK293S GnTI- / Production host: Homo sapiens (human) / References: UniProt: Q9JIE6
#2: Protein Interleukin-7 receptor subunit alpha / / IL-7 receptor subunit alpha / IL-7R subunit alpha / IL-7R-alpha / IL-7RA


Mass: 25431.809 Da / Num. of mol.: 1 / Fragment: extracellular domain (UNP residues 21-239)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Il7r, IL7RA / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta-gami B(DE3) / References: UniProt: P16872
#3: Protein Cytokine receptor-like factor 2 / Cytokine receptor-like molecule 2 / CRLM-2 / Thymic stromal lymphopoietin protein receptor / TSLP ...Cytokine receptor-like molecule 2 / CRLM-2 / Thymic stromal lymphopoietin protein receptor / TSLP receptor / TSLPR / Type I cytokine receptor delta 1


Mass: 22812.354 Da / Num. of mol.: 1 / Fragment: extracellular domain (UNP residues 20-222) / Mutation: N122Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Crlf2, CRLF2 (TSLPR), Crlm2, Tpte2, Tslpr / Cell line (production host): HEK293S GnTI- / Production host: Homo sapiens (human) / References: UniProt: Q8CII9
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Formula: H2O

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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: 2.26 Å3/Da / Density % sol: 45.5 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.1
Details: 14% PEG4000, 0.3 M sodium acetate, pH 4.5, 0.3 M calcium acetate, soaked in 18% PEG4000, 0.1 M Tris-HCl, pH 7.5, 0.3 M calcium acetate for 1 hour prior to cryoprotection, VAPOR DIFFUSION, ...Details: 14% PEG4000, 0.3 M sodium acetate, pH 4.5, 0.3 M calcium acetate, soaked in 18% PEG4000, 0.1 M Tris-HCl, pH 7.5, 0.3 M calcium acetate for 1 hour prior to cryoprotection, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.9686 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 4, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9686 Å / Relative weight: 1
ReflectionResolution: 2.545→50 Å / Num. all: 19531 / Num. obs: 19440 / % possible obs: 99.5 % / Observed criterion σ(I): -3 / Redundancy: 6.5 % / Biso Wilson estimate: 59.4 Å2 / Rmerge(I) obs: 0.108 / Net I/σ(I): 11.2
Reflection shellResolution: 2.545→2.7 Å / Redundancy: 6.4 % / Rmerge(I) obs: 0.846 / Mean I/σ(I) obs: 1.87 / Num. unique all: 3031 / % possible all: 97.8

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Processing

Software
NameVersionClassification
MxCuBEdata collection
PHASERphasing
PHENIX(phenix.refine: 1.8.3_1479)refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4NN5

4nn5


Resolution: 2.545→42.449 Å / SU ML: 0.39 / Isotropic thermal model: ISOTROPIC + TLS / Cross valid method: FREE R / σ(F): 2.01 / Phase error: 32.55 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2966 979 5.04 %RANDOM
Rwork0.2587 ---
obs0.2606 19427 99.49 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 87.7 Å2
Refinement stepCycle: LAST / Resolution: 2.545→42.449 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3362 0 0 3 3365
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0033457
X-RAY DIFFRACTIONf_angle_d0.864723
X-RAY DIFFRACTIONf_dihedral_angle_d12.3671150
X-RAY DIFFRACTIONf_chiral_restr0.034551
X-RAY DIFFRACTIONf_plane_restr0.004600
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.545-2.67880.31681400.35072537X-RAY DIFFRACTION98
2.6788-2.84660.37331360.32962601X-RAY DIFFRACTION100
2.8466-3.06630.3031370.3062587X-RAY DIFFRACTION100
3.0663-3.37480.31441410.27742623X-RAY DIFFRACTION100
3.3748-3.86290.27581330.26232632X-RAY DIFFRACTION100
3.8629-4.86570.271460.22132661X-RAY DIFFRACTION100
4.8657-42.45470.30441460.24492807X-RAY DIFFRACTION100
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)
11.90294.10232.24628.83094.82252.6568-0.46880.5994-1.116-1.56720.5843-0.85520.67131.1792-0.35641.09440.2140.1051.5511-0.30291.261323.599111.374-10.5308
27.39094.5358-3.66778.3269-0.32615.37940.724-1.4654-0.99730.4975-0.55950.33950.4225-0.7118-0.11010.4371-0.2115-0.11740.99890.27510.653915.076816.88452.3721
33.8161-0.124.25320.18750.61397.98931.0476-0.329-1.61470.02760.54510.95352.8206-1.1826-0.81020.9558-0.5058-0.45581.29160.21341.6688.287.0305-3.9875
44.4243.4643-0.2027.8048-0.25134.7388-0.23591.09830.073-1.75920.76280.93110.7466-0.46690.38690.5107-0.2952-0.20660.8960.06230.627612.556317.8336-7.7996
53.87011.84221.78054.0255.55127.90160.02170.8175-1.24420.6260.894-0.15332.43910.1898-0.42370.9873-0.2523-0.45810.81140.35271.059211.25497.34351.8357
65.75381.1330.44736.95331.7615.0440.4371-0.49570.6514-1.4024-0.64031.8548-1.7492-1.4912-0.08971.01580.4239-0.15951.0557-0.1760.730310.790240.623-3.2179
71.9197-1.69890.2431.5308-0.1061.0813-0.5106-1.21911.00550.0449-0.33480.667-1.3198-1.72430.16620.45730.5536-0.49041.8345-0.44341.0236.87838.4686-2.7239
80.440.20930.85316.22533.42635.08690.0909-0.04970.05160.1167-0.2760.4252-0.2089-1.17360.10110.4165-0.07530.05620.63370.01950.459218.618837.088812.6949
92.9789-0.0366-0.44436.89421.44385.0678-0.03480.37450.25471.02160.2461-0.8689-0.1228-0.5216-0.23410.6941-0.0946-0.04450.44880.06460.560527.233943.47425.4321
101.47571.1047-0.68247.6076.7257.61110.02650.35390.18370.72920.1989-0.12460.5319-0.1459-0.29210.5830.02-0.02870.6170.11460.49921.989739.562318.1331
114.9967-0.38340.82313.6972.09432.32050.5571-0.575-1.7925-0.91750.23930.19411.639-0.6086-0.68661.9075-0.138-0.49510.90880.23981.468218.6654-9.599917.3701
123.12350.26920.87153.65220.94035.1670.3161-0.0861-0.1818-0.16920.0329-0.036-0.0971-0.8365-0.3770.73060.0328-0.12530.53530.18020.703427.21614.701521.7192
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 22 through 26 )
2X-RAY DIFFRACTION2chain 'A' and (resid 27 through 46 )
3X-RAY DIFFRACTION3chain 'A' and (resid 47 through 84 )
4X-RAY DIFFRACTION4chain 'A' and (resid 85 through 117 )
5X-RAY DIFFRACTION5chain 'A' and (resid 118 through 139 )
6X-RAY DIFFRACTION6chain 'B' and (resid 37 through 81 )
7X-RAY DIFFRACTION7chain 'B' and (resid 82 through 103 )
8X-RAY DIFFRACTION8chain 'B' and (resid 104 through 171 )
9X-RAY DIFFRACTION9chain 'B' and (resid 172 through 209 )
10X-RAY DIFFRACTION10chain 'B' and (resid 210 through 232 )
11X-RAY DIFFRACTION11chain 'C' and (resid 30 through 90 )
12X-RAY DIFFRACTION12chain 'C' and (resid 91 through 211 )

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