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- PDB-6hg4: Crystal Structure of the human IL-17RC ECD in complex with human ... -

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Basic information

Entry
Database: PDB / ID: 6hg4
TitleCrystal Structure of the human IL-17RC ECD in complex with human IL-17F
Components
  • Interleukin-17 receptor C
  • Interleukin-17F
KeywordsIMMUNE SYSTEM / Cystine-knot / FnIII domains / receptor-cytokine complex
Function / homology
Function and homology information


regulation of granulocyte macrophage colony-stimulating factor production / regulation of interleukin-2 production / interleukin-17 receptor activity / positive regulation of lymphotoxin A production / granulocyte chemotaxis / regulation of interleukin-8 production / positive regulation of antimicrobial peptide production / Interleukin-17 signaling / interleukin-17A-mediated signaling pathway / regulation of transforming growth factor beta receptor signaling pathway ...regulation of granulocyte macrophage colony-stimulating factor production / regulation of interleukin-2 production / interleukin-17 receptor activity / positive regulation of lymphotoxin A production / granulocyte chemotaxis / regulation of interleukin-8 production / positive regulation of antimicrobial peptide production / Interleukin-17 signaling / interleukin-17A-mediated signaling pathway / regulation of transforming growth factor beta receptor signaling pathway / positive regulation of chemokine (C-X-C motif) ligand 1 production / interleukin-17-mediated signaling pathway / cytokine receptor binding / positive regulation of cytokine production involved in inflammatory response / cartilage development / regulation of interleukin-6 production / cytokine binding / defense response to fungus / coreceptor activity / negative regulation of angiogenesis / positive regulation of cytokine production / cytokine activity / positive regulation of interleukin-6 production / Interleukin-4 and Interleukin-13 signaling / defense response to Gram-negative bacterium / adaptive immune response / defense response to Gram-positive bacterium / inflammatory response / protein heterodimerization activity / signaling receptor binding / innate immune response / 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-like / SEFIR domain / SEFIR domain / SEFIR domain profile. / Interleukin-17, chordata / Interleukin-17 family / Interleukin-17 / Cystine Knot Cytokines, subunit B ...Interleukin-17 receptor C/E, N-terminal / Interleukin-17 receptor extracellular region / Interleukin-17 receptor-like / SEFIR domain / SEFIR domain / SEFIR domain profile. / Interleukin-17, chordata / Interleukin-17 family / Interleukin-17 / Cystine Knot Cytokines, subunit B / Cystine-knot cytokines / Cystine-knot cytokine / Ribbon / Mainly Beta
Similarity search - Domain/homology
Interleukin-17 receptor C / Interleukin-17F
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.32 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 22, 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 1.2Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Nov 20, 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: Interleukin-17F
B: Interleukin-17 receptor C


Theoretical massNumber of molelcules
Total (without water)66,1502
Polymers66,1502
Non-polymers00
Water00
1
A: Interleukin-17F
B: Interleukin-17 receptor C

A: Interleukin-17F
B: Interleukin-17 receptor C


Theoretical massNumber of molelcules
Total (without water)132,3004
Polymers132,3004
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_676x-y+1,-y+2,-z+11
Buried area12470 Å2
ΔGint-53 kcal/mol
Surface area52160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)154.322, 154.322, 78.792
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number150
Space group name H-MP321

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Components

#1: Protein Interleukin-17F / IL-17F / Cytokine ML-1


Mass: 15695.895 Da / Num. of mol.: 1 / Fragment: IL-17F
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IL17F / Plasmid: pCI-derived / Cell line (production host): HEK293S GnTi- / Production host: Homo sapiens (human) / References: UniProt: Q96PD4
#2: 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: 50454.312 Da / Num. of mol.: 1 / Mutation: N186Q, N226Q, N253Q, N263Q, N349Q, N372Q, N406Q
Source method: isolated from a genetically manipulated source
Details: Q307R variant with the following N-glycosylation site mutations: ,N186Q, N226Q, N253Q, N263Q, N349Q, N372Q, N406Q
Source: (gene. exp.) Homo sapiens (human) / Gene: IL17RC, UNQ6118/PRO20040/PRO38901 / Plasmid: pCI-derived / Cell line (production host): HEK293S GnTi- / Production host: Homo sapiens (human) / References: UniProt: Q8NAC3
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: 4.09 Å3/Da / Density % sol: 69.96 % / Mosaicity: 0.21 °
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 200mM ammonium citrate tribasic, 20.0% PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.99994 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Dec 12, 2016 / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99994 Å / Relative weight: 1
ReflectionResolution: 3.32→133.66 Å / Num. obs: 16301 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 23.5 % / Biso Wilson estimate: 125.14 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.181 / Rpim(I) all: 0.038 / Rrim(I) all: 0.185 / Net I/σ(I): 18
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
3.32-3.518.23.75723480.4540.8993.865100
10.49-133.6621.50.0515710.9990.0120.05399.9

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Processing

Software
NameVersionClassification
Aimless0.7.1data scaling
BUSTERrefinement
PDB_EXTRACT3.24data extraction
XDSAutoprocdata reduction
BUSTERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1jpy

1jpy


Resolution: 3.32→78.79 Å / Cor.coef. Fo:Fc: 0.921 / Cor.coef. Fo:Fc free: 0.853 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.391
RfactorNum. reflection% reflectionSelection details
Rfree0.239 815 5 %RANDOM
Rwork0.198 ---
obs0.2 16293 99.9 %-
Displacement parametersBiso max: 273.63 Å2 / Biso mean: 164.64 Å2 / Biso min: 78.74 Å2
Baniso -1Baniso -2Baniso -3
1-20.8557 Å20 Å20 Å2
2--20.8557 Å20 Å2
3----41.7114 Å2
Refine analyzeLuzzati coordinate error obs: 0.44 Å
Refinement stepCycle: final / Resolution: 3.32→78.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4176 0 0 0 4176
Num. residues----531
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d1444SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes720HARMONIC5
X-RAY DIFFRACTIONt_it4294HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion545SEMIHARMONIC5
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_contact4498SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d4294HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg5881HARMONIC21.26
X-RAY DIFFRACTIONt_omega_torsion2.94
X-RAY DIFFRACTIONt_other_torsion22.49
LS refinement shellResolution: 3.32→3.55 Å / Rfactor Rfree error: 0 / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.3039 146 5.01 %
Rwork0.2429 2767 -
all0.2459 2913 -
obs--99.69 %
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)
17.62740.64510.94133.25040.94994.2405-0.07040.3684-0.1411-0.28960.2387-1.18510.13250.8974-0.1683-0.25640.00260.1060.1190.0299-0.4616-32.0443129.350536.7455
27.21732.38221.32785.3442-0.05254.3237-0.10850.1510.708-0.77960.0011-0.4841-0.51940.49110.10730.00820.04620.1941-0.00480.0555-0.5519-45.5992134.83614.8126
32.69381.22820.01566.5483-0.987811.4292-0.24640.44640.7157-0.3741-0.0541-0.1758-0.73660.16580.3004-0.7769-0.17260.2270.2580.55240.6963-6.3266154.230724.7676
423.7908-11.1412-1.62038.5783-3.00240-0.0007-0.10951.10980.27060.79221.14660.2877-0.9466-0.7915-0.6243-0.04010.14390.13040.00930.351523.7437142.553423.9632
58.8282-1.55310.411511.30495.33857.9938-0.0012-0.62440.98420.3248-0.03440.1151-0.26140.11880.0356-0.29610.080.0562-0.0937-0.0631-0.264546.8678136.162522.3616
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A54 - 161
2X-RAY DIFFRACTION2B21 - 207
3X-RAY DIFFRACTION3B208 - 292
4X-RAY DIFFRACTION4B293 - 387
5X-RAY DIFFRACTION5B388 - 465

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