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- PDB-5n9b: Crystal Structure of unliganded human IL-17RA -

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Basic information

Entry
Database: PDB / ID: 5n9b
TitleCrystal Structure of unliganded human IL-17RA
ComponentsInterleukin-17 receptor A
KeywordsSIGNALING PROTEIN / Fibronectin type III
Function / homology
Function and homology information


interleukin-17 receptor activity / granulocyte chemotaxis / Interleukin-17 signaling / T-helper 17 type immune response / interleukin-17A-mediated signaling pathway / positive regulation of interleukin-23 production / positive regulation of chemokine (C-X-C motif) ligand 1 production / interleukin-17-mediated signaling pathway / positive regulation of interleukin-13 production / positive regulation of interleukin-5 production ...interleukin-17 receptor activity / granulocyte chemotaxis / Interleukin-17 signaling / T-helper 17 type immune response / interleukin-17A-mediated signaling pathway / positive regulation of interleukin-23 production / positive regulation of chemokine (C-X-C motif) ligand 1 production / interleukin-17-mediated signaling pathway / positive regulation of interleukin-13 production / positive regulation of interleukin-5 production / fibroblast activation / positive regulation of cytokine production involved in inflammatory response / defense response to fungus / protein catabolic process / response to virus / positive regulation of inflammatory response / positive regulation of interleukin-6 production / cell surface receptor signaling pathway / inflammatory response / innate immune response / signaling receptor binding / SARS-CoV-2 activates/modulates innate and adaptive immune responses / extracellular region / plasma membrane
Similarity search - Function
Interleukin-17 receptor A/B, fibronectin-III-like domain 2 / Interleukin-17 receptor A/B, fibronectin-III-like domain 1 / Interleukin 17 receptor D / Interleukin-17 receptor, fibronectin-III-like domain 1 / Interleukin-17 receptor A/B, FnIII-like domain 1 superfamily / Interleukin-17 receptor A/B, FnIII-like domain 2 superfamily / Interleukin-17 receptor, fibronectin-III-like domain 1 / Interleukin-17 receptor-like / SEFIR domain / SEFIR domain ...Interleukin-17 receptor A/B, fibronectin-III-like domain 2 / Interleukin-17 receptor A/B, fibronectin-III-like domain 1 / Interleukin 17 receptor D / Interleukin-17 receptor, fibronectin-III-like domain 1 / Interleukin-17 receptor A/B, FnIII-like domain 1 superfamily / Interleukin-17 receptor A/B, FnIII-like domain 2 superfamily / Interleukin-17 receptor, fibronectin-III-like domain 1 / Interleukin-17 receptor-like / SEFIR domain / SEFIR domain / SEFIR domain profile. / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Interleukin-17 receptor A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.9 Å
AuthorsRondeau, J.-M. / Goepfert, A.
CitationJournal: Cell Rep / Year: 2022
Title: IL-17-induced dimerization of IL-17RA drives the formation of the IL-17 signalosome to potentiate signaling.
Authors: Goepfert, A. / Barske, C. / Lehmann, S. / Wirth, E. / Willemsen, J. / Gudjonsson, J.E. / Ward, N.L. / Sarkar, M.K. / Hemmig, R. / Kolbinger, F. / Rondeau, J.M.
History
DepositionFeb 24, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 13, 2018Provider: repository / Type: Initial release
Revision 1.1Jun 12, 2019Group: Data collection / Database references / Category: citation_author / Item: _citation_author.name
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 1.3Nov 2, 2022Group: Database references / Structure summary
Category: chem_comp / citation ...chem_comp / citation / citation_author / database_2
Item: _chem_comp.pdbx_synonyms / _citation.country ..._chem_comp.pdbx_synonyms / _citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Jan 31, 2024Group: 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

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Assembly

Deposited unit
A: Interleukin-17 receptor A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,0845
Polymers33,2001
Non-polymers8854
Water3,405189
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area670 Å2
ΔGint9 kcal/mol
Surface area14860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)40.593, 71.685, 105.385
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Interleukin-17 receptor A / IL-17RA / CDw217


Mass: 33199.617 Da / Num. of mol.: 1 / Fragment: Extracellular domain, UNP rsidues 33-318
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IL17RA, IL17R / Plasmid: pRS5 / Cell line (production host): HEK293S GnTI- / Production host: Homo sapiens (human) / References: UniProt: Q96F46
#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


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
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 189 / 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: 2.31 Å3/Da / Density % sol: 46.74 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 7 / Details: Tris-HCl, PEG 2000 MME, lithium sulfate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1.00001 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Oct 25, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00001 Å / Relative weight: 1
ReflectionResolution: 1.9→59.27 Å / Num. obs: 24921 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Redundancy: 6.263 % / Biso Wilson estimate: 31.43 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.104 / Rrim(I) all: 0.115 / Χ2: 0.931 / Net I/σ(I): 11.8 / Num. measured all: 156084 / Scaling rejects: 1
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
1.9-1.956.5311.1251.7318070.6841.22399.9
1.95-26.4980.872.3617580.8140.94899.8
2-2.066.3910.7362.7817350.8370.802100
2.06-2.126.2680.5943.517000.8950.649100
2.12-2.195.9870.4744.2115940.9030.52199.9
2.19-2.276.2110.4035.0815660.9330.44199.9
2.27-2.366.60.3516.1415440.9470.38399.9
2.36-2.456.5510.2966.9614490.9550.322100
2.45-2.566.4130.2438.3614230.9660.26599.8
2.56-2.696.3560.19610.6713390.9770.21599.6
2.69-2.836.0110.15812.8412870.9860.17499.8
2.83-36.2790.12415.8612090.9890.13699.8
3-3.216.5980.08820.7211570.9950.09699.9
3.21-3.476.3470.07324.4310730.9950.07999.9
3.47-3.86.0850.0627.1910010.9960.06699.3
3.8-4.255.5670.05328.799010.9970.05999.3
4.25-4.916.0270.04433.298170.9970.04899.8
4.91-6.015.9990.04631.526950.9970.05199.4
6.01-8.55.3410.04829.55400.9960.05397.6
8.5-59.275.1290.04235.113260.9980.04897

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
XSCALEdata scaling
BUSTER2.11.6refinement
PDB_EXTRACT3.22data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4HSA

4hsa


Resolution: 1.9→59.27 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.92 / Rfactor Rfree error: 0 / SU R Cruickshank DPI: 0.135 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.144 / SU Rfree Blow DPI: 0.138 / SU Rfree Cruickshank DPI: 0.133
RfactorNum. reflection% reflectionSelection details
Rfree0.234 1246 5 %RANDOM
Rwork0.19 ---
obs0.192 24918 99.7 %-
Displacement parametersBiso max: 145.08 Å2 / Biso mean: 38.76 Å2 / Biso min: 18.49 Å2
Baniso -1Baniso -2Baniso -3
1--8.4562 Å20 Å20 Å2
2--6.132 Å20 Å2
3---2.3242 Å2
Refine analyzeLuzzati coordinate error obs: 0.24 Å
Refinement stepCycle: final / Resolution: 1.9→59.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1989 0 56 189 2234
Biso mean--59.44 45.98 -
Num. residues----244
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d730SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes51HARMONIC2
X-RAY DIFFRACTIONt_gen_planes306HARMONIC5
X-RAY DIFFRACTIONt_it2109HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion284SEMIHARMONIC5
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_contact2304SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d2109HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg2877HARMONIC21.1
X-RAY DIFFRACTIONt_omega_torsion3.71
X-RAY DIFFRACTIONt_other_torsion17.3
LS refinement shellResolution: 1.9→1.98 Å / Rfactor Rfree error: 0 / Total num. of bins used: 13
RfactorNum. reflection% reflection
Rfree0.231 137 4.97 %
Rwork0.227 2618 -
all0.228 2755 -
obs--99.82 %
Refinement TLS params.Method: refined / Origin x: -5.9972 Å / Origin y: -19.7529 Å / Origin z: 17.5814 Å
111213212223313233
T-0.0475 Å2-0.0038 Å2-0.0243 Å2--0.0188 Å2-0.0109 Å2---0.1011 Å2
L0.3594 °20.3473 °2-0.2233 °2-1.6146 °2-0.7511 °2--0.607 °2
S-0.0198 Å °0.059 Å °0.0053 Å °-0.1848 Å °-0.0109 Å °0.0561 Å °0.0673 Å °0.0139 Å °0.0307 Å °
Refinement TLS groupSelection details: { A|* }

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