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- PDB-7zan: Crystal Structure of human IL-17A in complex with IL-17RA and IL-17RC -

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Basic information

Entry
Database: PDB / ID: 7zan
TitleCrystal Structure of human IL-17A in complex with IL-17RA and IL-17RC
Components
  • Interleukin-17 receptor A
  • Interleukin-17A
  • Isoform 2 of Interleukin-17 receptor C
KeywordsCYTOKINE / Immune system
Function / homology
Function and homology information


interleukin-17 receptor activity / granulocyte chemotaxis / positive regulation of interleukin-16 production / granulocyte migration / positive regulation of antimicrobial peptide production / Interleukin-17 signaling / T-helper 17 type immune response / cell death / interleukin-17A-mediated signaling pathway / positive regulation of interleukin-23 production ...interleukin-17 receptor activity / granulocyte chemotaxis / positive regulation of interleukin-16 production / granulocyte migration / positive regulation of antimicrobial peptide production / Interleukin-17 signaling / T-helper 17 type immune response / cell death / interleukin-17A-mediated signaling pathway / positive regulation of interleukin-23 production / negative regulation of inflammatory response to wounding / positive regulation of chemokine (C-X-C motif) ligand 1 production / interleukin-17-mediated signaling pathway / intestinal epithelial structure maintenance / positive regulation of interleukin-13 production / positive regulation of interleukin-5 production / fibroblast activation / positive regulation of bicellular tight junction assembly / positive regulation of osteoclast differentiation / positive regulation of cytokine production involved in inflammatory response / keratinocyte proliferation / cellular response to interleukin-1 / defense response to fungus / coreceptor activity / keratinocyte differentiation / Notch signaling pathway / positive regulation of interleukin-12 production / cytokine activity / positive regulation of interleukin-1 beta production / protein catabolic process / positive regulation of interleukin-6 production / response to wounding / response to virus / positive regulation of inflammatory response / positive regulation of tumor necrosis factor production / cell-cell signaling / Interleukin-4 and Interleukin-13 signaling / defense response to Gram-negative bacterium / gene expression / adaptive immune response / cell surface receptor signaling pathway / defense response to Gram-positive bacterium / immune response / inflammatory response / protein heterodimerization activity / signaling receptor binding / innate immune response / external side of plasma membrane / apoptotic process / SARS-CoV-2 activates/modulates innate and adaptive immune responses / cell surface / protein homodimerization activity / positive regulation of transcription by RNA polymerase II / extracellular space / extracellular region / plasma membrane
Similarity search - Function
Interleukin-17 receptor C/E, N-terminal / Interleukin-17 receptor extracellular region / 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 D / Interleukin-17 receptor-like / SEFIR domain / SEFIR domain ...Interleukin-17 receptor C/E, N-terminal / Interleukin-17 receptor extracellular region / 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 D / Interleukin-17 receptor-like / SEFIR domain / SEFIR domain / SEFIR domain profile. / Interleukin-17, chordata / Interleukin-17 family / Interleukin-17 / Cystine-knot cytokine
Similarity search - Domain/homology
Interleukin-17A / Interleukin-17 receptor C / Interleukin-17 receptor A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 5.061 Å
Model detailsasymmetric unit contains one half complex
AuthorsRondeau, J.M. / Goepfert, A.
Funding support1items
OrganizationGrant numberCountry
Not funded
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
DepositionMar 22, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 12, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 2, 2022Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Interleukin-17A
B: Interleukin-17A
C: Interleukin-17 receptor A
D: Isoform 2 of Interleukin-17 receptor C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)113,8728
Polymers112,9884
Non-polymers8854
Water00
1
A: Interleukin-17A
B: Interleukin-17A
C: Interleukin-17 receptor A
D: Isoform 2 of Interleukin-17 receptor C
hetero molecules

A: Interleukin-17A
B: Interleukin-17A
C: Interleukin-17 receptor A
D: Isoform 2 of Interleukin-17 receptor C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)227,74516
Polymers225,9758
Non-polymers1,7708
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation1
Unit cell
Length a, b, c (Å)186.305, 186.305, 238.305
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number179
Space group name H-MP6522

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Components

#1: Protein Interleukin-17A / IL-17 / IL-17A / Cytotoxic T-lymphocyte-associated antigen 8 / CTLA-8


Mass: 14177.899 Da / Num. of mol.: 2 / Fragment: IL-17A / Mutation: N68D,C129S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IL17A, CTLA8, IL17 / Plasmid: pCI-derived / Production host: Homo sapiens (human) / Strain (production host): HEK293-6E / References: UniProt: Q16552
#2: Protein Interleukin-17 receptor A / IL-17 receptor A / IL-17RA / CDw217


Mass: 34073.570 Da / Num. of mol.: 1 / Mutation: N49D, N206D, N265D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IL17RA, IL17R / Plasmid: pCI-derived / Production host: Homo sapiens (human) / Strain (production host): HEK293S GnTI- / References: UniProt: Q96F46
#3: Protein Isoform 2 of Interleukin-17 receptor C / IL-17 receptor C / IL-17RC / Interleukin-17 receptor homolog / IL17Rhom / Interleukin-17 receptor- ...IL-17 receptor C / IL-17RC / Interleukin-17 receptor homolog / IL17Rhom / Interleukin-17 receptor-like protein / IL-17RL / ZcytoR14


Mass: 50558.285 Da / Num. of mol.: 1 / Fragment: Extracellular domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IL17RC, UNQ6118/PRO20040/PRO38901 / Plasmid: pCI-derived / Production host: Homo sapiens (human) / Strain (production host): HEK293S GnTI- / References: UniProt: Q8NAC3
#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.: 4 / Source method: obtained synthetically / 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
Has ligand of interestN
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: 5.28 Å3/Da / Density % sol: 76.72 % / Description: Hexagonal rods
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: 0.1M MES, 10.0% PEG DME 500

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1.00003 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Dec 12, 2015 / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00003 Å / Relative weight: 1
ReflectionResolution: 5.061→133.601 Å / Num. obs: 10707 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 19.2 % / Biso Wilson estimate: 378.5 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.103 / Rpim(I) all: 0.025 / Rrim(I) all: 0.106 / Net I/σ(I): 15.8
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
5.061-5.078206.2721940970.4041.4376.4360.5100
23.449-133.60113.90.02718721350.9990.0090.02881.896.4

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
BUSTER2.11.8refinement
XDSVersion Feb. 5, 2021data reduction
Aimless0.7.7data scaling
PHASER2.8.3phasing
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4hsa, 6hg4

4hsa

6hg4


Resolution: 5.061→37.55 Å / Cor.coef. Fo:Fc: 0.858 / Cor.coef. Fo:Fc free: 0.812 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 1.503
Details: HYDROGENS WERE FULLY REFINED WITH ZERO OCCUPANCY AT NUCLEAR POSITION.
RfactorNum. reflection% reflectionSelection details
Rfree0.3531 530 5.04 %RANDOM
Rwork0.294 ---
obs0.2969 10524 98.6 %-
Displacement parametersBiso max: 300 Å2 / Biso mean: 268.1 Å2 / Biso min: 139.46 Å2
Baniso -1Baniso -2Baniso -3
1-26.0729 Å20 Å20 Å2
2--26.0729 Å20 Å2
3----52.1458 Å2
Refine analyzeLuzzati coordinate error obs: 0.88 Å
Refinement stepCycle: final / Resolution: 5.061→37.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7361 0 56 0 7417
Biso mean--277.77 --
Num. residues----921
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d4263SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes2433HARMONIC5
X-RAY DIFFRACTIONt_it7587HARMONIC10
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion986SEMIHARMONIC5
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_contact9455SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d14753HARMONIC20.007
X-RAY DIFFRACTIONt_angle_deg26692HARMONIC20.85
X-RAY DIFFRACTIONt_omega_torsion2.38
X-RAY DIFFRACTIONt_other_torsion14.39
LS refinement shellResolution: 5.061→5.15 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.5173 25 6.17 %
Rwork0.3997 380 -
obs--75.56 %
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)
121.1716-2.044-3.771710.08924.543713.3829-0.492-0.5498-0.19690.58750.27430.7488-1.0505-0.30460.21770.04420.03110.4152-0.6936-0.11130.015746.0354-45.54931.7004
28.2257.38373.641113.14165.00620-0.3670.1835-0.04550.12730.51570.4163-1.0354-0.0587-0.14870.3388-0.1660.4152-0.1715-0.1113-0.209446.4578-51.6448-6.3766
34.0464-3.5553-1.12246.34332.512514.76440.2802-1.4655-0.84140.71140.71560.7711-0.3984-1.4869-0.99590.4083-0.39060.33470.15740.0283-0.607953.1534-66.14027.9045
419.4695-2.8067-6.754712.44382.82153.67720.24280.65611.4869-1.51550.7328-0.3984-1.2149-0.0727-0.97570.39170.28460.2975-0.26120.09260.60797.4581-49.3616-4.6004
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* }A37 - 155
2X-RAY DIFFRACTION2{ B|* }B43 - 153
3X-RAY DIFFRACTION3{ C|* }C33 - 306
4X-RAY DIFFRACTION4{ D|* }D21 - 464

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