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- PDB-5nan: Crystal Structure of human IL-17AF in complex with human IL-17RA -

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Basic information

Entry
Database: PDB / ID: 5nan
TitleCrystal Structure of human IL-17AF in complex with human IL-17RA
Components
  • Interleukin-17 receptor A
  • Interleukin-17A
  • Interleukin-17F
KeywordsCYTOKINE / Cystine-knot / Fibronectin type III
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 / positive regulation of interleukin-16 production / granulocyte migration / regulation of interleukin-8 production / positive regulation of antimicrobial peptide production / Interleukin-17 signaling ...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 / positive regulation of interleukin-16 production / granulocyte migration / regulation of interleukin-8 production / positive regulation of antimicrobial peptide production / Interleukin-17 signaling / T-helper 17 type immune response / cell death / interleukin-17A-mediated signaling pathway / regulation of transforming growth factor beta receptor 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 / cytokine receptor binding / fibroblast activation / positive regulation of bicellular tight junction assembly / positive regulation of osteoclast differentiation / positive regulation of cytokine production involved in inflammatory response / cartilage development / regulation of interleukin-6 production / cytokine binding / keratinocyte proliferation / cellular response to interleukin-1 / defense response to fungus / keratinocyte differentiation / Notch signaling pathway / positive regulation of interleukin-12 production / negative regulation of angiogenesis / positive regulation of cytokine production / positive regulation of interleukin-1 beta production / cytokine activity / 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 / protein homodimerization activity / positive regulation of transcription by RNA polymerase II / extracellular space / 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, 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 A/B, fibronectin-III-like domain 2 / Interleukin-17 receptor A/B, fibronectin-III-like domain 1 / 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 Cytokines, subunit B / Cystine-knot cytokines / Cystine-knot cytokine / Ribbon / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Interleukin-17A / Interleukin-17 receptor A / Interleukin-17F
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.3 Å
AuthorsRondeau, J.-M. / Goepfert, A.
CitationJournal: Sci Rep / Year: 2017
Title: The human IL-17A/F heterodimer: a two-faced cytokine with unique receptor recognition properties.
Authors: Goepfert, A. / Lehmann, S. / Wirth, E. / Rondeau, J.M.
History
DepositionFeb 28, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 6, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 13, 2017Group: Structure summary / Category: audit_author / Item: _audit_author.name
Revision 1.2Sep 20, 2017Group: Database references / Category: citation / citation_author
Item: _citation.page_last / _citation.pdbx_database_id_PubMed ..._citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.3Jan 24, 2018Group: Source and taxonomy / Category: entity_src_gen
Item: _entity_src_gen.pdbx_host_org_cell_line / _entity_src_gen.pdbx_host_org_strain
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_auth_comp_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_asym_id / _atom_site_anisotrop.pdbx_label_atom_id / _atom_site_anisotrop.pdbx_label_comp_id / _atom_site_anisotrop.type_symbol / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Jan 17, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag
Revision 2.2Oct 23, 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-17A
B: Interleukin-17 receptor A
C: Interleukin-17 receptor A
D: Interleukin-17A
E: Interleukin-17F
F: Interleukin-17F
hetero molecules


Theoretical massNumber of molelcules
Total (without water)135,77612
Polymers134,0846
Non-polymers1,6936
Water00
1
A: Interleukin-17A
B: Interleukin-17 receptor A
F: Interleukin-17F
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,8505
Polymers67,0423
Non-polymers8082
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10420 Å2
ΔGint-37 kcal/mol
Surface area23410 Å2
MethodPISA
2
C: Interleukin-17 receptor A
D: Interleukin-17A
E: Interleukin-17F
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,9277
Polymers67,0423
Non-polymers8854
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10850 Å2
ΔGint-37 kcal/mol
Surface area23830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)100.002, 66.103, 104.119
Angle α, β, γ (deg.)90.000, 90.130, 90.000
Int Tables number3
Space group name H-MP121

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Components

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


Mass: 15146.124 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IL17A, CTLA8, IL17 / Plasmid: pCI / Cell line (production host): HEK293S / Production host: Homo sapiens (human) / References: UniProt: Q16552
#2: Protein Interleukin-17 receptor A / IL-17RA / CDw217


Mass: 36199.848 Da / Num. of mol.: 2
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
#3: Protein Interleukin-17F / IL-17F / Cytokine ML-1


Mass: 15695.895 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IL17F / Plasmid: pCI / Cell line (production host): HEK293S / Production host: Homo sapiens (human) / References: UniProt: Q96PD4
#4: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[beta-D-galactopyranose-(1-6)]2-acetamido-2-deoxy- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[beta-D-galactopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 586.542 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4[DGalpb1-6]DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a2112h-1b_1-5]/1-1-2/a4-b1_a6-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}[(6+1)][b-D-Galp]{}}}LINUCSPDB-CARE
#5: 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.: 5
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
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: 2.57 Å3/Da / Density % sol: 52.08 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 7.5
Details: 0.1M HEPES, 15% PEG MME 5,000, 0.05M Ammonium Acetate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.99992 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Feb 6, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99992 Å / Relative weight: 1
ReflectionResolution: 3.3→66.1 Å / Num. obs: 20621 / % possible obs: 99.1 % / Observed criterion σ(I): -3 / Redundancy: 3.368 % / Biso Wilson estimate: 145.29 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.149 / Rrim(I) all: 0.178 / Χ2: 0.97 / Net I/σ(I): 5.71 / Num. measured all: 69444 / Scaling rejects: 33
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
3.3-3.393.3373.4830.3214940.1844.15199.5
3.39-3.483.2042.360.4614770.3122.84398.9
3.48-3.583.3371.6220.7114340.4291.93299.3
3.58-3.693.4031.3510.914070.5641.60399.1
3.69-3.813.5390.8891.3513310.8761.04799.6
3.81-3.943.5290.6431.8413150.8640.75899.4
3.94-4.093.4970.4572.5512820.9250.54199.5
4.09-4.263.4620.3463.3512160.9370.41199.1
4.26-4.453.280.2554.3611770.960.30699.5
4.45-4.673.3180.1745.8711110.9810.20999.6
4.67-4.923.3090.1437.0510760.9880.17199.4
4.92-5.223.5250.1318.3110130.990.15599.2
5.22-5.583.4560.1258.69610.9850.14899.5
5.58-6.023.4280.1159.148810.9880.13798.8
6.02-6.63.180.1049.768210.9860.12699.2
6.6-7.383.1930.07712.997360.9910.09399.2
7.38-8.523.4080.0617.316550.9950.07298.1
8.52-10.443.2710.04322.435580.9950.05298.2
10.44-14.763.0070.03625.024350.9960.04496
14.76-66.13.170.02927.232410.9990.03492

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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: pdbid 4HSA

4hsa


Resolution: 3.3→66.1 Å / Cor.coef. Fo:Fc: 0.929 / Cor.coef. Fo:Fc free: 0.911 / Rfactor Rfree error: 0 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.491
RfactorNum. reflection% reflectionSelection details
Rfree0.243 1009 5.01 %RANDOM
Rwork0.186 ---
obs0.189 20143 96.8 %-
Displacement parametersBiso max: 281.49 Å2 / Biso mean: 169.11 Å2 / Biso min: 97.76 Å2
Baniso -1Baniso -2Baniso -3
1-36.3656 Å20 Å224.9616 Å2
2---38.0106 Å20 Å2
3---1.645 Å2
Refine analyzeLuzzati coordinate error obs: 0.54 Å
Refinement stepCycle: final / Resolution: 3.3→66.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7814 0 109 0 7923
Biso mean--225.81 --
Num. residues----972
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d2811SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes204HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1175HARMONIC5
X-RAY DIFFRACTIONt_it8161HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion1086SEMIHARMONIC5
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_contact8618SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d8161HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg11144HARMONIC21.34
X-RAY DIFFRACTIONt_omega_torsion3.31
X-RAY DIFFRACTIONt_other_torsion23.18
LS refinement shellResolution: 3.3→3.48 Å / Rfactor Rfree error: 0 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.273 129 5.12 %
Rwork0.257 2391 -
all0.258 2520 -
obs--84.22 %
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)
13.32241.02861.21794.62972.9344.6022-0.0524-0.13330.08140.10110.1675-0.48910.17850.4678-0.1151-0.328-0.2959-0.30450.06090.2017-0.076213.7063-6.967932.9451
23.2094-1.9235-0.2796.08170.84841.25050.07590.49880.1658-0.0698-0.0286-0.6275-0.18840.5083-0.0473-0.34-0.2828-0.03260.09650.2705-0.29622.6648-7.675513.9743
36.35272.4113-0.06352.9901-1.6923.1540.152-0.42820.0208-0.05770.00860.0175-0.1168-0.6126-0.1606-0.24870.0835-0.0384-0.2464-0.1952-0.3559-52.2768-1.329337.9313
43.71661.3524-1.4586.0816-3.02292.96190.03970.6630.3233-0.15540.11610.25770.2141-1.0776-0.1557-0.3472-0.1152-0.24590.34020.026-0.3017-62.89020.079718.6009
55.72594.0968-0.57919.5049-2.21644.7337-0.17490.906-0.0595-0.4672-0.3274-0.33420.3029-0.03720.5023-0.2656-0.0825-0.04030.1423-0.0966-0.3936-51.5893-0.113217.0697
65.1933-2.0655-0.07596.861-0.12822.053-0.0766-0.4665-0.08040.43340.0226-0.1239-0.0099-0.08620.0539-0.1475-0.2391-0.14190.03560.2568-0.35351.7399-4.705134.3514
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* }A44 - 154
2X-RAY DIFFRACTION2{ B|* }B33 - 303
3X-RAY DIFFRACTION3{ C|* }C33 - 303
4X-RAY DIFFRACTION4{ D|* }D43 - 154
5X-RAY DIFFRACTION5{ E|* }E46 - 158
6X-RAY DIFFRACTION6{ F|* }F46 - 158

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