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- PDB-6hga: Crystal Structure of the human IL-17RC D2-D3-D4 domains in comple... -

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Basic information

Entry
Database: PDB / ID: 6hga
TitleCrystal Structure of the human IL-17RC D2-D3-D4 domains in complex with an anti-APP tag Fab
Components
  • Interleukin-17 receptor C
  • anti-APP-tag Fab heavy-chain
  • anti-APP-tag Fab light-chain
KeywordsIMMUNE SYSTEM / FnIII domains / Fab complex
Function / homology
Function and homology information


interleukin-17 receptor activity / granulocyte chemotaxis / Interleukin-17 signaling / interleukin-17A-mediated signaling pathway / positive regulation of cytokine production involved in inflammatory response / defense response to fungus / coreceptor activity / positive regulation of interleukin-6 production / inflammatory response / signaling receptor binding ...interleukin-17 receptor activity / granulocyte chemotaxis / Interleukin-17 signaling / interleukin-17A-mediated signaling pathway / positive regulation of cytokine production involved in inflammatory response / defense response to fungus / coreceptor activity / positive regulation of interleukin-6 production / inflammatory response / signaling receptor binding / SARS-CoV-2 activates/modulates innate and adaptive immune responses / cell surface / plasma membrane
Similarity search - Function
Interleukin-17 receptor C/E, N-terminal / Interleukin-17 receptor extracellular region / Interleukin-17 receptor-like / SEFIR domain / SEFIR domain / SEFIR domain profile. / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Interleukin-17 receptor C
Similarity search - Component
Biological speciesHomo sapiens (human)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.6 Å
AuthorsRondeau, J.M. / Goepfert, A.
CitationJournal: Immunity / Year: 2020
Title: Structural Analysis Reveals that the Cytokine IL-17F Forms a Homodimeric Complex with Receptor IL-17RC to Drive IL-17RA-Independent Signaling.
Authors: Goepfert, A. / Lehmann, S. / Blank, J. / Kolbinger, F. / Rondeau, J.M.
History
DepositionAug 23, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 18, 2020Provider: repository / Type: Initial release
Revision 1.1Apr 1, 2020Group: Database references / Category: citation / citation_author
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 / _citation_author.identifier_ORCID
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 / _entity.pdbx_description ..._chem_comp.name / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_role
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: Interleukin-17 receptor C
H: anti-APP-tag Fab heavy-chain
L: anti-APP-tag Fab light-chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,9974
Polymers77,7763
Non-polymers2211
Water1,33374
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6020 Å2
ΔGint-24 kcal/mol
Surface area33870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)250.910, 250.910, 78.610
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number180
Space group name H-MP6222

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Components

#1: Protein Interleukin-17 receptor C / IL-17RC / Interleukin-17 receptor homolog / IL17Rhom / Interleukin-17 receptor-like protein / IL- ...IL-17RC / Interleukin-17 receptor homolog / IL17Rhom / Interleukin-17 receptor-like protein / IL-17RL / ZcytoR14


Mass: 29792.088 Da / Num. of mol.: 1 / Fragment: IL-17RC D2-D3-D4 domains / Mutation: N263Q,Q307R,N349Q,N372Q,N406Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IL17RC, UNQ6118/PRO20040/PRO38901 / Plasmid: pCI-derived / Cell line (production host): HEK-293S / Production host: Homo sapiens (human) / Variant (production host): GnTi- / References: UniProt: Q8NAC3
#2: Antibody anti-APP-tag Fab heavy-chain / 6E10A5 Fab


Mass: 23832.586 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Cell line (production host): Hybridoma / Production host: Mus musculus (house mouse)
#3: Antibody anti-APP-tag Fab light-chain / 6E10A5 Fab


Mass: 24150.826 Da / Num. of mol.: 1 / Fragment: anti-APP-tag Fab heavy-chain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Cell line (production host): Hybridoma / Production host: Mus musculus (house mouse)
#4: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose


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
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 74 / 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: 4.59 Å3/Da / Density % sol: 73.22 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 0.1M HEPES, 30% Jeffamine ED-2001

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.99998 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Oct 8, 2017 / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99998 Å / Relative weight: 1
ReflectionResolution: 2.6→82.13 Å / Num. obs: 45204 / % possible obs: 100 % / Redundancy: 19.973 % / Biso Wilson estimate: 79.44 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.168 / Rrim(I) all: 0.173 / Χ2: 0.947 / Net I/σ(I): 17.99
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
2.6-2.6718.7483.364133000.5283.458100
2.67-2.7419.4992.6311.3632040.6612.70199.9
2.74-2.8221.0031.9081.9531200.7941.955100
2.82-2.9120.9351.4282.5830180.8641.463100
2.91-320.7261.063.4529440.9361.086100
3-3.1120.6110.8264.3928370.9520.847100
3.11-3.2220.4320.5716.3527560.9740.585100
3.22-3.3619.940.418.5126540.9870.42199.9
3.36-3.5118.6390.31210.725680.990.321100
3.51-3.6820.2290.25913.3624180.9930.265100
3.68-3.8821.0660.19617.523470.9970.201100
3.88-4.1120.770.13524.4722200.9980.139100
4.11-4.3920.4110.09133.8420870.9990.093100
4.39-4.7519.8980.07738.8819390.9990.079100
4.75-5.218.0960.06542.8218060.9990.067100
5.2-5.8119.9680.06544.9416460.9990.066100
5.81-6.7120.2320.06744.9414700.9990.069100
6.71-8.2219.2970.04857.9112610.9990.049100
8.22-11.6317.0860.02979.71100110.03100
11.63-82.1317.840.02594.6660810.02699.2

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
XDSOct. 15, 2015data reduction
XSCALEOct. 15, 2015data scaling
PHASERphasing
BUSTER2.11.7refinement
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.6→82.13 Å / Cor.coef. Fo:Fc: 0.928 / Cor.coef. Fo:Fc free: 0.918 / SU R Cruickshank DPI: 0.261 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.259 / SU Rfree Blow DPI: 0.208 / SU Rfree Cruickshank DPI: 0.211
RfactorNum. reflection% reflectionSelection details
Rfree0.232 2261 5 %RANDOM
Rwork0.205 ---
obs0.206 45204 100 %-
Displacement parametersBiso max: 205.76 Å2 / Biso mean: 87.62 Å2 / Biso min: 34.46 Å2
Baniso -1Baniso -2Baniso -3
1--10.3042 Å20 Å20 Å2
2---10.3042 Å20 Å2
3---20.6083 Å2
Refine analyzeLuzzati coordinate error obs: 0.38 Å
Refinement stepCycle: final / Resolution: 2.6→82.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5463 0 14 74 5551
Biso mean--157.37 63.8 -
Num. residues----704
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d1863SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes131HARMONIC2
X-RAY DIFFRACTIONt_gen_planes807HARMONIC5
X-RAY DIFFRACTIONt_it5640HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion740SEMIHARMONIC5
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_contact5908SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d5640HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg7723HARMONIC21.19
X-RAY DIFFRACTIONt_omega_torsion3.52
X-RAY DIFFRACTIONt_other_torsion17.5
LS refinement shellResolution: 2.6→2.67 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.277 165 5 %
Rwork0.2655 3133 -
all0.266 3298 -
obs--99.97 %
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)
11.84380.6772-1.11665.0527-3.66823.4276-0.0060.0174-0.1147-0.149-0.1936-0.54260.00960.62880.1995-0.2836-0.1872-0.03810.2836-0.1461-0.2196-25.6907106.8625-12.0953
23.3129-0.3463-0.15541.79960.16362.35050.15260.2739-0.4282-0.02970.0025-0.20310.37240.3145-0.1551-0.1312-0.1696-0.10620.2532-0.1012-0.1056-41.551194.4354-3.6764
38.5242-1.3792.94513.3952-0.69216.0116-0.09760.08510.07280.3345-0.26490.17820.1579-0.16990.3626-0.2836-0.1872-0.16110.28360.0825-0.1016.467994.049827.8835
43.1494-0.6848-2.35791.69261.99935.07180.1190.05360.48090.13450.19870.0015-0.41260.3722-0.3177-0.0204-0.33920.10610.0204-0.0356-0.1967-47.0189135.2449-3.9856
51.7704-0.36650.0352.52620.51912.4540.22090.28790.2578-0.08540.05080.2579-0.5799-0.082-0.2717-0.092-0.27120.10750.12280.0125-0.1418-59.152127.5748-10.3628
67.63220.42751.88677.2880.39820.9051-0.05340.0844-0.4059-0.0214-0.13350.30490.3464-0.29840.187-0.2357-0.0175-0.20760.13550.0556-0.10631.959276.686141.5258
73.4747-0.64832.5589-0.8192-0.02773.40620.2759-0.13290.4031-0.228-0.5296-0.3879-0.25620.11480.2537-0.2796-0.1333-0.16480.2253-0.01850.0683-7.8674102.440312.8058
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1L1 - 112
2X-RAY DIFFRACTION2H1 - 119
3X-RAY DIFFRACTION3B300 - 392
4X-RAY DIFFRACTION4L113 - 219
5X-RAY DIFFRACTION5H120 - 222
6X-RAY DIFFRACTION6B209 - 299
7X-RAY DIFFRACTION7B393 - 501

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