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- PDB-5j12: Structure of human TSLP:TSLPR in complex with mouse IL-7Ralpha -

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Basic information

Entry
Database: PDB / ID: 5j12
TitleStructure of human TSLP:TSLPR in complex with mouse IL-7Ralpha
Components
  • Cytokine receptor-like factor 2
  • Interleukin-7 receptor subunit alpha
  • Thymic stromal lymphopoietin
KeywordsSIGNALING PROTEIN / cytokine inflammation TSLP signaling complex
Function / homology
Function and homology information


positive regulation of chemokine (C-C motif) ligand 1 production / positive regulation of granulocyte colony-stimulating factor production / interleukin-7 receptor binding / Interleukin-7 signaling / positive regulation of mast cell activation / 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 / positive regulation of granulocyte colony-stimulating factor production / interleukin-7 receptor binding / Interleukin-7 signaling / positive regulation of mast cell activation / 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-13 production / positive regulation of interleukin-5 production / negative regulation of T cell apoptotic process / cytokine receptor activity / regulation of cell size / cytokine binding / 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 / Interleukin-7 signaling / cytokine activity / positive regulation of receptor signaling pathway via JAK-STAT / cell morphogenesis / T cell mediated cytotoxicity / cytokine-mediated signaling pathway / positive regulation of inflammatory response / antimicrobial humoral immune response mediated by antimicrobial peptide / positive regulation of interleukin-6 production / gene expression / T cell differentiation in thymus / defense response to Gram-negative bacterium / receptor complex / defense response to Gram-positive bacterium / 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-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 / Thymic stromal lymphopoietin / Cytokine receptor-like factor 2
Similarity search - Component
Biological speciesHomo sapiens (human)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.55 Å
AuthorsVerstraete, K. / Savvides, S.N.
CitationJournal: To Be Published
Title: Structure of human TSLP:TSLPR in complex with mouse IL-7Ralpha
Authors: Verstraete, K. / Savvides, S.N.
History
DepositionMar 28, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0Apr 5, 2017Provider: repository / Type: Initial release
Revision 1.1Feb 28, 2018Group: Source and taxonomy / Category: entity_src_gen
Item: _entity_src_gen.host_org_common_name / _entity_src_gen.pdbx_host_org_strain / _entity_src_gen.pdbx_host_org_variant
Revision 1.2Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / 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_role
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.3Jan 10, 2024Group: 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: Thymic stromal lymphopoietin
B: Interleukin-7 receptor subunit alpha
C: Cytokine receptor-like factor 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,4669
Polymers70,5143
Non-polymers9526
Water905
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4320 Å2
ΔGint-31 kcal/mol
Surface area25490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)125.442, 125.442, 194.573
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522

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Components

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Protein , 3 types, 3 molecules ABC

#1: Protein Thymic stromal lymphopoietin


Mass: 18522.500 Da / Num. of mol.: 1 / Mutation: N64Q,K126S + residues 127-131 were deleted
Source method: isolated from a genetically manipulated source
Details: The signal peptide (residues 1 - 28) is removed from the mature protein.
Source: (gene. exp.) Homo sapiens (human) / Gene: TSLP / Plasmid: pHL-hTSLP-N64Q-K126S-delta127-131 / Details (production host): transient transfection / Cell line (production host): HEK293S MGAT1-/- / Production host: Homo sapiens (human) / References: UniProt: Q969D9
#2: Protein Interleukin-7 receptor subunit alpha / IL-7RA


Mass: 25431.809 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Before crystallisation, the N-terminal His-tag (residues 1 - 17, MGSSHHHHHHSSGLVPR) was removed by thrombin cleavage.
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Il7r / Plasmid: pET15b-mIL7alpha
Details (production host): ORF cloned between NdeI and BamHI sites
Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P16872
#3: Protein Cytokine receptor-like factor 2 / Cytokine receptor-like 2 / IL-XR / Thymic stromal lymphopoietin protein receptor / TSLP receptor


Mass: 26559.537 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CRLF2, CRL2, ILXR, TSLPR / Plasmid: pHL-hTSLPR / Details (production host): transient transfection / Cell line (production host): HEK293S MGAT1-/- / Production host: Homo sapiens (human) / References: UniProt: Q9HC73

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Sugars , 1 types, 3 molecules

#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.: 3
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, 8 molecules

#5: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 5 / 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: 3.49 Å3/Da / Density % sol: 64.72 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 1.53 M ammonium sulfate 0.1 M sodium chloride 0.1 M BIS-TRIS pH 7.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.98 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 26, 2014
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 3.55→50 Å / Num. obs: 11341 / % possible obs: 98.4 % / Redundancy: 10.7 % / Biso Wilson estimate: 125.17 Å2 / CC1/2: 0.998 / Rrim(I) all: 0.177 / Net I/σ(I): 10.8
Reflection shellResolution: 3.55→3.76 Å / Redundancy: 10.5 % / Mean I/σ(I) obs: 2 / Rrim(I) all: 1.122 / % possible all: 97.9

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Processing

Software
NameVersionClassification
BUSTER2.10.2refinement
XDSVERSION January 10, 2014data reduction
PHASERphasing
Coot0.8.1model building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB 4NN5

4nn5


Resolution: 3.55→47.43 Å / Cor.coef. Fo:Fc: 0.9198 / Cor.coef. Fo:Fc free: 0.9287 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.467
Details: - rigid body refinement (single rigid body per domain) in Phenix - Iterative cycles of refinement in autoBuster, model (re)building and validation: xyz coordinate refinement individual B- ...Details: - rigid body refinement (single rigid body per domain) in Phenix - Iterative cycles of refinement in autoBuster, model (re)building and validation: xyz coordinate refinement individual B-factors TLS parameterisation with one TLS-group per domain target restraints: chain A,C --> chain A,C in the 2.55 Angstrom structure of the human ternary TSLP complex chain B --> chain B of pdb 2NN5 automatic X-ray weight optimisation structure validation in COOT, Phenix (Molprobity) and PDB_REDO
RfactorNum. reflection% reflectionSelection details
Rfree0.2253 567 5 %RANDOM
Rwork0.2139 ---
obs0.2145 11336 98.53 %-
Displacement parametersBiso mean: 152.37 Å2
Baniso -1Baniso -2Baniso -3
1-8.7301 Å20 Å20 Å2
2--8.7301 Å20 Å2
3----17.4602 Å2
Refine analyzeLuzzati coordinate error obs: 0.475 Å
Refinement stepCycle: LAST / Resolution: 3.55→47.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3757 0 57 5 3819
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0113921HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.195390HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1196SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes70HARMONIC2
X-RAY DIFFRACTIONt_gen_planes593HARMONIC5
X-RAY DIFFRACTIONt_it3921HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.86
X-RAY DIFFRACTIONt_other_torsion16.85
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion568SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact4185SEMIHARMONIC4
LS refinement shellResolution: 3.55→3.89 Å / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.2645 131 4.98 %
Rwork0.2188 2500 -
all0.221 2631 -
obs--98.58 %
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)
12.4312-1.7510.22853.54390.66013.405-0.1012-0.1277-0.02990.29460.2107-0.361-0.24910.6593-0.1096-0.23850.1247-0.0870.03350.081-0.0822-9.5352-37.0244-21.4558
25.1297-1.4518-1.176512.54861.88532.52550.07880.6451-0.2833-1.7896-0.00290.31971.53890.3029-0.07580.61460.6875-0.3381-0.5777-0.0354-0.6841-7.5029-67.7469-26.4044
36.20414.1026-4.08712.6692-3.81977.50590.2978-0.7045-0.38870.3275-0.04191.66091.1707-0.7436-0.25590.0911-0.02930.1034-0.77720.43980.5742-29.1279-67.4043-6.5947
410.40382.2788-0.49377.23692.14494.13610.1003-0.99160.80870.01290.1183-0.5228-1.24270.8426-0.2186-0.0240.0369-0.0918-0.1502-0.0414-0.2508-16.0846-19.245-1.5883
55.70962.0537-0.22247.89942.15057.7617-0.1167-1.0315-0.7610.7488-0.72891.44591.1574-1.11610.8457-0.26630.02450.187-0.32550.087-0.0054-35.6692-43.6683-2.7882
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{A|29 - 501}
2X-RAY DIFFRACTION2{B|38 - 125}
3X-RAY DIFFRACTION3{B|126 - 232}
4X-RAY DIFFRACTION4{C|30 - 116}
5X-RAY DIFFRACTION5{C|117 -501}

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