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- PDB-4hsa: Structure of interleukin 17a in complex with il17ra receptor -

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Basic information

Entry
Database: PDB / ID: 4hsa
TitleStructure of interleukin 17a in complex with il17ra receptor
Components
  • Interleukin-17 receptor A
  • Interleukin-17A
KeywordsIMMUNE SYSTEM/PROTEIN BINDING / cytokine receptor / glycosylation / IMMUNE SYSTEM-PROTEIN BINDING complex
Function / homology
Function and homology information


interleukin-17 receptor activity / positive regulation of interleukin-16 production / granulocyte migration / granulocyte chemotaxis / positive regulation of antimicrobial peptide production / Interleukin-17 signaling / T-helper 17 type immune response / intestinal epithelial structure maintenance / negative regulation of inflammatory response to wounding / interleukin-17A-mediated signaling pathway ...interleukin-17 receptor activity / positive regulation of interleukin-16 production / granulocyte migration / granulocyte chemotaxis / positive regulation of antimicrobial peptide production / Interleukin-17 signaling / T-helper 17 type immune response / intestinal epithelial structure maintenance / negative regulation of inflammatory response to wounding / interleukin-17A-mediated signaling pathway / positive regulation of interleukin-23 production / positive regulation of chemokine (C-X-C motif) ligand 1 production / cell death / interleukin-17-mediated signaling pathway / positive regulation of bicellular tight junction assembly / positive regulation of interleukin-5 production / fibroblast activation / positive regulation of cytokine production involved in inflammatory response / positive regulation of osteoclast differentiation / positive regulation of interleukin-13 production / keratinocyte proliferation / defense response to fungus / cellular response to interleukin-1 / keratinocyte differentiation / Notch signaling pathway / positive regulation of interleukin-12 production / positive regulation of interleukin-1 beta production / cytokine activity / protein catabolic process / response to virus / positive regulation of inflammatory response / response to wounding / positive regulation of interleukin-6 production / positive regulation of tumor necrosis factor production / cell-cell signaling / gene expression / Interleukin-4 and Interleukin-13 signaling / defense response to Gram-negative bacterium / adaptive immune response / cell surface receptor signaling pathway / defense response to Gram-positive bacterium / immune response / inflammatory response / protein heterodimerization activity / external side of plasma membrane / signaling receptor binding / innate immune response / 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 D / 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-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 D / 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-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
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.15 Å
AuthorsLiu, S.
CitationJournal: Nat Commun / Year: 2013
Title: Crystal structures of interleukin 17A and its complex with IL-17 receptor A.
Authors: Liu, S. / Song, X. / Chrunyk, B.A. / Shanker, S. / Hoth, L.R. / Marr, E.S. / Griffor, M.C.
History
DepositionOct 29, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 22, 2013Provider: repository / Type: Initial release
Revision 1.1Jun 5, 2013Group: Database references
Revision 1.2Jun 19, 2013Group: Database references
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / 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_ref_seq_dif / struct_site / struct_site_gen
Item: _atom_site.auth_asym_id / _atom_site.auth_seq_id ..._atom_site.auth_asym_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_entity_id / _atom_site_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_asym_id / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_comp_id / _struct_ref_seq_dif.details
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
A: Interleukin-17A
B: Interleukin-17A
C: Interleukin-17 receptor A
D: Interleukin-17A
E: Interleukin-17A
F: Interleukin-17 receptor A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)129,14511
Polymers126,1966
Non-polymers2,9495
Water905
1
A: Interleukin-17A
B: Interleukin-17A
C: Interleukin-17 receptor A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,9316
Polymers63,0983
Non-polymers1,8333
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11520 Å2
ΔGint1 kcal/mol
Surface area24560 Å2
MethodPISA
2
D: Interleukin-17A
E: Interleukin-17A
F: Interleukin-17 receptor A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,2145
Polymers63,0983
Non-polymers1,1162
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10570 Å2
ΔGint-17 kcal/mol
Surface area23840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)138.710, 138.710, 179.090
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

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Protein , 2 types, 6 molecules ABDECF

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


Mass: 14120.848 Da / Num. of mol.: 4 / Mutation: N45D, C106S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IL17A, CTLA8, IL17 / Cell line (production host): HEK293 / Production host: Homo sapiens (human) / References: UniProt: Q16552
#2: Protein Interleukin-17 receptor A / IL-17 receptor A / IL-17RA / CDw217


Mass: 34856.297 Da / Num. of mol.: 2 / Mutation: N175D, N234D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IL17RA, IL17R / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q96F46

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Sugars , 4 types, 5 molecules

#3: Polysaccharide alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 894.823 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3DManpa1-4DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,5,4/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1a_1-5][a1221m-1a_1-5]/1-1-2-2-3/a4-b1_a6-e1_b4-c1_c3-d1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][a-D-Manp]{[(3+1)][a-D-Manp]{}}}[(6+1)][a-L-Fucp]{}}}LINUCSPDB-CARE
#4: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 570.542 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5]/1-1-2/a4-b1_a6-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}[(6+1)][a-L-Fucp]{}}}LINUCSPDB-CARE
#5: Polysaccharide alpha-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 367.349 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
LFucpa1-6DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5]/1-2/a6-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(6+1)][a-L-Fucp]{}}}LINUCSPDB-CARE
#6: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-Acetylglucosamine


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

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Non-polymers , 1 types, 5 molecules

#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.95 Å3/Da / Density % sol: 68.83 %

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorDetector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.15→100 Å / Num. obs: 34990 / % possible obs: 92.7 % / Observed criterion σ(I): 2 / Redundancy: 14.6 % / Biso Wilson estimate: 97.66 Å2

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Processing

SoftwareName: BUSTER / Version: 2.11.2 / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.15→43.14 Å / Cor.coef. Fo:Fc: 0.9205 / Cor.coef. Fo:Fc free: 0.8877 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2315 1774 5.07 %RANDOM
Rwork0.1869 ---
obs0.1891 32406 99.94 %-
Displacement parametersBiso mean: 106.31 Å2
Baniso -1Baniso -2Baniso -3
1--11.2764 Å20 Å20 Å2
2---11.2764 Å20 Å2
3---22.5527 Å2
Refine analyzeLuzzati coordinate error obs: 0.674 Å
Refinement stepCycle: LAST / Resolution: 3.15→43.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7830 0 196 5 8031
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.018289HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.3111345HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d2842SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes201HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1186HARMONIC5
X-RAY DIFFRACTIONt_it8289HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.19
X-RAY DIFFRACTIONt_other_torsion24
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion1125SEMIHARMONIC5
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_contact8885SEMIHARMONIC4
LS refinement shellResolution: 3.15→3.24 Å / Total num. of bins used: 18
RfactorNum. reflection% reflection
Rfree0.3115 154 5.47 %
Rwork0.2323 2662 -
all0.2366 2816 -
obs--99.94 %
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)
11.80960.1365-0.59912.62761.17134.08120.2538-0.0419-0.36030.3029-0.18440.28010.5105-0.3158-0.0694-0.3285-0.126-0.021-0.06780.0041-0.392-58.373442.9358-33.2586
21.56271.01021.02263.45872.05875.11660.31210.1821-0.0394-0.1338-0.15960.145-0.1462-0.3417-0.1525-0.41740.00680.0675-0.07320.0155-0.429-52.946552.394-35.6823
31.10560.79280.61933.16031.54092.69690.35650.0243-0.42650.45230.0003-0.45260.5770.3635-0.3568-0.54080.1002-0.1562-0.2621-0.053-0.5712-36.214642.0479-34.7152
43.03650.4268-0.08293.21580.27857.4173-0.0946-0.30190.0430.12840.15830.73580.0695-1.1046-0.0637-0.31210.05040.05280.15840.16520.1288-80.779258.709-64.8682
52.7884-0.1431-0.50042.3805-0.54757.38980.1568-0.15520.12130.01390.33760.25090.1031-0.1988-0.4944-0.35540.0102-0.0124-0.13320.0563-0.0691-70.458.3355-68.9809
62.51550.1594-1.48751.6543-0.66785.1270.3642-0.14610.96420.39030.29070.4405-1.2441-0.3766-0.6549-0.43650.1540.1656-0.71390.0422-0.3677-70.237478.0096-68.0738
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A17 - 131
2X-RAY DIFFRACTION2B19 - 127
3X-RAY DIFFRACTION3C2 - 273
4X-RAY DIFFRACTION4D20 - 131
5X-RAY DIFFRACTION5E19 - 127
6X-RAY DIFFRACTION6F2 - 272

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