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- PDB-6hg9: Crystal Structure of the human IL-17RC ECD in complex with human ... -

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Basic information

Entry
Database: PDB / ID: 6hg9
TitleCrystal Structure of the human IL-17RC ECD in complex with human IL-17F, Crystal form II
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 / molecular replacement / Resolution: 3.62 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 1.2Jan 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 1.3Oct 16, 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)66,1642
Polymers66,1642
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)132,3284
Polymers132,3284
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation16_544y+1/3,x-1/3,-z-1/31
Buried area12790 Å2
ΔGint-51 kcal/mol
Surface area53290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)160.312, 160.312, 197.983
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number155
Space group name H-MH32

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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 / Production host: Homo sapiens (human) / Variant (production host): GnTi- / 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: 50468.336 Da / Num. of mol.: 1
Mutation: N118Q, N186Q, N213Q, N226Q, N263Q, N349Q, Q307R, N372Q, N406Q
Source method: isolated from a genetically manipulated source
Details: Q307R variant,with the following N-glycosylation site mutations: N118Q, N186Q, N213Q, N226Q, N263Q, N349Q, N372Q, N406Q
Source: (gene. exp.) Homo sapiens (human) / Gene: IL17RC, UNQ6118/PRO20040/PRO38901 / Plasmid: pCI-derived / Cell line (production host): HEK293S / Production host: Homo sapiens (human) / Variant (production host): GnTi- / 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: 3.7 Å3/Da / Density % sol: 66.76 % / Mosaicity: 0.1 °
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 200mM ammonium formate, 20.0% PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.99996 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Mar 18, 2017 / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99996 Å / Relative weight: 1
ReflectionResolution: 3.62→80.6 Å / Num. obs: 11380 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 10.2 % / Biso Wilson estimate: 165.32 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.099 / Rpim(I) all: 0.033 / Rrim(I) all: 0.105 / Net I/σ(I): 16.9
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
3.62-3.8210.62.14616420.5150.6892.25599.9
11.45-80.68.80.02439710.0080.02599.6

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
XDSdata reduction
Aimless0.7.2data scaling
PHASERphasing
PHENIX1.13_2998refinement
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1JPY

1jpy


Resolution: 3.62→56.836 Å / SU ML: 0.65 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 31.75
RfactorNum. reflection% reflection
Rfree0.2577 558 4.91 %
Rwork0.2256 --
obs0.2272 11371 99.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 446.25 Å2 / Biso mean: 193.8146 Å2 / Biso min: 83.49 Å2
Refinement stepCycle: final / Resolution: 3.62→56.836 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4169 0 0 0 4169
Num. residues----532
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 4 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
3.6204-3.98470.40091300.325526692799
3.9847-4.5610.27941490.27326792828
4.561-5.74560.27161430.235926762819
5.7456-56.84250.22331360.192627892925
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)
19.0711.03652.02964.02550.73845.05990.0196-0.3047-0.3021-0.34870.3030.23170.2745-0.0067-0.33741.1668-0.101-0.05860.9620.1110.888320.3759-63.2106-8.9584
26.45111.854-0.76425.79740.31025.1822-0.252-1.31030.5192-0.81680.1688-0.6062-0.26810.76270.11451.55870.053-0.34411.8475-0.57052.058555.5914-36.027-19.9494
30.4811.6837-0.62814.1992-1.56414.06110.07660.9314-0.76380.7502-0.2345-1.2826-0.6308-0.56930.17941.85560.2374-0.14061.9304-0.60612.186958.5294-3.8074-18.0365
43.4064-1.5882-0.99765.99851.79113.9683-0.12170.7506-0.05890.14991.1928-1.9420.79480.2182-1.00752.15770.2015-0.02571.8778-0.27111.621363.134620.3434-15.4519
51.94040.7169-2.34667.6885-1.64815.22860.3001-0.70870.41740.7645-0.1943-0.2795-0.63110.3429-0.12921.7038-0.37510.00211.4173-0.00361.13720.4022-48.2923-30.2459
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'B' and (resid 21 through 207 )B21 - 207
2X-RAY DIFFRACTION2chain 'B' and (resid 208 through 292 )B208 - 292
3X-RAY DIFFRACTION3chain 'B' and (resid 293 through 387 )B293 - 387
4X-RAY DIFFRACTION4chain 'B' and (resid 388 through 464 )B388 - 464
5X-RAY DIFFRACTION5chain 'A' and (resid 54 through 162 )A54 - 162

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