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- PDB-4nn5: Cytokine receptor complex - Crystal form 1A -

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Basic information

Entry
Database: PDB / ID: 4nn5
TitleCytokine receptor complex - Crystal form 1A
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


interleukin-7 receptor activity / Interleukin-7 signaling / negative regulation of T cell mediated cytotoxicity / positive regulation of T cell differentiation in thymus / positive regulation of receptor signaling pathway via STAT / Cargo recognition for clathrin-mediated endocytosis / Clathrin-mediated endocytosis / negative regulation of T cell apoptotic process / cellular homeostasis / regulation of cell size ...interleukin-7 receptor activity / Interleukin-7 signaling / negative regulation of T cell mediated cytotoxicity / positive regulation of T cell differentiation in thymus / positive regulation of receptor signaling pathway via STAT / Cargo recognition for clathrin-mediated endocytosis / Clathrin-mediated endocytosis / negative regulation of T cell apoptotic process / cellular homeostasis / regulation of cell size / T cell homeostasis / B cell homeostasis / B cell proliferation / T cell differentiation / lymph node development / cytokine activity / T cell mediated cytotoxicity / cell morphogenesis / T cell differentiation in thymus / gene expression / defense response to Gram-positive bacterium / inflammatory response / external side of plasma membrane / positive regulation of cell population proliferation / positive regulation of gene expression / extracellular space / extracellular region / nucleoplasm / plasma membrane / cytosol
Similarity search - Function
Thymic stromal lymphopoietin / Immunoglobulin-like - #1870 / Thymic stromal lymphopoietin / Thymic stromal lymphopoietin superfamily / Thymic stromal lymphopoietin / IL-7Ralpha, fibronectin type III domain / Fibronectin type III domain / : / : / Cytokine receptor-like factor 2-like, D2 domain ...Thymic stromal lymphopoietin / Immunoglobulin-like - #1870 / Thymic stromal lymphopoietin / Thymic stromal lymphopoietin superfamily / Thymic stromal lymphopoietin / IL-7Ralpha, fibronectin type III domain / Fibronectin type III domain / : / : / Cytokine receptor-like factor 2-like, D2 domain / Cytokine receptor-like factor 2, domain 1 / 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 / Immunoglobulin-like fold / Immunoglobulins / Up-down Bundle / Immunoglobulin-like / Sandwich / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
ACETATE ION / 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: 1.898 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 1.4Jul 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 1.5Sep 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
Revision 1.6Nov 27, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,6345
Polymers63,3543
Non-polymers2802
Water5,945330
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)150.060, 79.756, 52.138
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

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Protein , 3 types, 3 molecules ABC

#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

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Sugars , 1 types, 1 molecules

#5: 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

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Non-polymers , 2 types, 331 molecules

#4: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 330 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.46 Å3/Da / Density % sol: 50.05 %
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, 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: 0.976293 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 12, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976293 Å / Relative weight: 1
ReflectionResolution: 1.898→49.25 Å / Num. all: 50432 / Num. obs: 50292 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Redundancy: 13.2 % / Biso Wilson estimate: 28.7 Å2 / Rmerge(I) obs: 0.086 / Net I/σ(I): 19.9
Reflection shellResolution: 1.898→2.01 Å / Redundancy: 13.5 % / Rmerge(I) obs: 0.67 / Mean I/σ(I) obs: 3.9 / Num. unique all: 7921 / % possible all: 98.4

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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 3DI2

3di2


Resolution: 1.898→49.25 Å / SU ML: 0.19 / Isotropic thermal model: ISOTROPIC + TLS / Cross valid method: FREE R / σ(F): 1.99 / Phase error: 18.75 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2009 2513 5 %RANDOM
Rwork0.1698 ---
obs0.1713 50285 99.72 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 38.7 Å2
Refinement stepCycle: LAST / Resolution: 1.898→49.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3804 0 18 330 4152
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0113931
X-RAY DIFFRACTIONf_angle_d1.2185337
X-RAY DIFFRACTIONf_dihedral_angle_d13.5341394
X-RAY DIFFRACTIONf_chiral_restr0.053596
X-RAY DIFFRACTIONf_plane_restr0.007678
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.898-1.9340.25121330.21572521X-RAY DIFFRACTION95
1.934-1.97350.25691370.1942608X-RAY DIFFRACTION100
1.9735-2.01640.21771380.19322617X-RAY DIFFRACTION100
2.0164-2.06330.19111370.18162619X-RAY DIFFRACTION100
2.0633-2.11490.22031390.18192631X-RAY DIFFRACTION100
2.1149-2.17210.22431400.17222651X-RAY DIFFRACTION100
2.1721-2.2360.2081360.16662597X-RAY DIFFRACTION100
2.236-2.30820.19891390.16272645X-RAY DIFFRACTION100
2.3082-2.39070.22381390.16992629X-RAY DIFFRACTION100
2.3907-2.48640.19611390.17032648X-RAY DIFFRACTION100
2.4864-2.59950.21021400.1742648X-RAY DIFFRACTION100
2.5995-2.73660.23641400.18172664X-RAY DIFFRACTION100
2.7366-2.9080.24091390.18592644X-RAY DIFFRACTION100
2.908-3.13250.2451400.19152665X-RAY DIFFRACTION100
3.1325-3.44770.18341420.17732692X-RAY DIFFRACTION100
3.4477-3.94640.20231420.15282692X-RAY DIFFRACTION100
3.9464-4.97130.15051430.1342731X-RAY DIFFRACTION100
4.9713-49.26650.18651500.182870X-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)
10.1281-0.00280.14020.3504-0.09010.1008-0.09440.1358-0.1129-0.2590.14070.0930.13770.0515-00.2745-0.04830.0190.2845-0.0040.245117.333515.801-0.789
21.2032-0.00640.97240.05580.04790.94920.67990.2196-0.16650.09170.12330.24090.3529-0.05210.27360.4123-0.1082-0.05490.25220.08260.547110.87992.78835.0738
30.0105-0.030.01470.1108-0.00550.03190.13550.031-0.146-0.52410.09860.22180.26670.01590.08980.3756-0.0323-0.11080.2919-0.07740.389413.82147.1484-5.6926
40.00350.00550.00960.04750.0460.0560.03910.171-0.2327-0.0112-0.09080.21890.2055-0.0313-0.1075-0.1598-0.4067-0.57860.26580.04070.96660.073510.974-5.0564
50.46290.3677-0.0650.6783-0.03420.17970.11420.35560.1386-0.8040.09710.8526-0.02580.05740.05710.3894-0.0913-0.12510.34320.0580.282810.795317.1896-7.4579
60.03720.0688-0.01990.44680.35481.39480.04650.0233-0.2161-0.10060.14620.33520.14370.00960.13220.205-0.0465-0.06480.20.050.387511.28697.67853.3551
70.223-0.15910.09870.16280.09310.14580.0997-0.04070.13350.10810.15580.2776-0.17950.0026-0.00010.248-0.02260.00030.22430.04150.22111.983941.69080.2143
80.2556-0.1187-0.20520.0503-0.01720.48370.10230.1871-0.0432-0.04620.01950.2893-0.2028-0.24590.0260.27240.0246-0.05180.23350.01760.28429.212844.0496-8.3947
90.0975-0.0350.00770.06690.04380.09970.09720.0151-0.0359-0.06720.0220.3985-0.0510.0096-0.00010.2159-0.00150.01830.24050.03610.39276.702638.6053-2.8398
100.0669-0.007-0.10980.05450.08170.13570.03750.06420.03320.0074-0.0531-0.0786-0.0258-0.050600.20150.00350.00670.26630.03680.201614.002441.3323-11.264
110.0108-0.05970.0280.0735-0.03250.0119-0.2282-0.08090.0107-0.0368-0.16680.06120.001-0.2853-00.19740.0053-0.02160.2906-0.00560.17114.899638.185215.0616
120.0417-0.0321-0.05240.03960.01880.0479-0.189-0.101-0.19690.35040.0097-0.08560.28890.007-0.00110.30280.0226-0.01540.29610.03240.176623.503338.383537.1782
13-0.0032-0.0140.06780.01010.01180.01650.1042-0.101-0.0514-0.1916-0.02430.05350.0987-0.25650.00010.32-0.06250.00680.32620.01390.270713.632129.223115.5468
140.1032-0.08310.12580.05590.00620.17010.00740.0806-0.03110.0031-0.02580.0466-0.07620.1177-00.2240.01830.00240.23890.00840.18126.281643.20522.443
150.03170.0269-0.00920.0243-0.00710.06690.1441-0.0954-0.10980.1406-0.1646-0.44420.02510.1218-00.28960.0057-0.01820.3092-0.00750.314929.266543.34234.5979
160.32140.24580.0020.2209-0.0820.24790.0105-0.0344-0.05110.05080.0337-0.04180.0563-0.0359-00.24220.022-0.02730.24250.01470.180721.455341.345919.8159
170.7269-0.4616-0.2840.82650.26961.1784-0.0249-0.3053-0.2738-0.16270.24340.29180.4721-0.13910.53650.3951-0.0819-0.12510.3210.14840.435215.6757-8.277818.1889
180.3901-0.15980.34930.2122-0.27620.607-0.0752-0.12510.08220.01120.0092-0.0352-0.1547-0.112800.27510.0227-0.04790.247-0.03770.261532.503217.63222.9758
190.0030.00990.0208-0.00260.00450.0006-0.0745-0.09230.34290.2933-0.1347-0.5404-0.28050.2631-0.00020.4508-0.0164-0.1260.4228-0.01810.52444.328221.893735.216
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 20 through 46 )
2X-RAY DIFFRACTION2chain 'A' and (resid 47 through 59 )
3X-RAY DIFFRACTION3chain 'A' and (resid 60 through 72 )
4X-RAY DIFFRACTION4chain 'A' and (resid 73 through 84 )
5X-RAY DIFFRACTION5chain 'A' and (resid 85 through 117 )
6X-RAY DIFFRACTION6chain 'A' and (resid 118 through 140 )
7X-RAY DIFFRACTION7chain 'B' and (resid 36 through 59 )
8X-RAY DIFFRACTION8chain 'B' and (resid 60 through 81 )
9X-RAY DIFFRACTION9chain 'B' and (resid 82 through 104 )
10X-RAY DIFFRACTION10chain 'B' and (resid 105 through 125 )
11X-RAY DIFFRACTION11chain 'B' and (resid 126 through 135 )
12X-RAY DIFFRACTION12chain 'B' and (resid 136 through 149 )
13X-RAY DIFFRACTION13chain 'B' and (resid 150 through 162 )
14X-RAY DIFFRACTION14chain 'B' and (resid 163 through 186 )
15X-RAY DIFFRACTION15chain 'B' and (resid 187 through 199 )
16X-RAY DIFFRACTION16chain 'B' and (resid 200 through 232 )
17X-RAY DIFFRACTION17chain 'C' and (resid 28 through 114 )
18X-RAY DIFFRACTION18chain 'C' and (resid 115 through 207 )
19X-RAY DIFFRACTION19chain 'C' and (resid 208 through 219 )

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