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- PDB-3jvf: Crystal structure of an Interleukin-17 receptor complex -

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Basic information

Entry
Database: PDB / ID: 3jvf
TitleCrystal structure of an Interleukin-17 receptor complex
Components
  • Interleukin-17 receptor A
  • Interleukin-17F
KeywordsSIGNALING PROTEIN / CYTOKINE / cytokine / interleukin / cysteine-knot growth factor / receptor-cytokine complex / Disulfide bond / Glycoprotein / Secreted / Membrane / Receptor / Transmembrane / SIGNALING PROTEIN / SIGNALING PROTEIN - 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 / T-helper 17 type immune response / interleukin-17A-mediated 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 / T-helper 17 type immune response / interleukin-17A-mediated signaling pathway / positive regulation of interleukin-23 production / positive regulation of chemokine (C-X-C motif) ligand 1 production / interleukin-17-mediated signaling pathway / regulation of transforming growth factor beta receptor signaling pathway / cytokine receptor binding / positive regulation of interleukin-13 production / positive regulation of interleukin-5 production / fibroblast activation / positive regulation of cytokine production involved in inflammatory response / cartilage development / regulation of interleukin-6 production / cytokine binding / defense response to fungus / negative regulation of angiogenesis / positive regulation of cytokine production / cytokine activity / protein catabolic process / response to virus / positive regulation of inflammatory response / positive regulation of interleukin-6 production / 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 / inflammatory response / protein heterodimerization activity / innate immune response / signaling receptor binding / 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-17 receptor A / Interleukin-17F
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 3.3 Å
AuthorsEly, L.K. / Garcia, K.C.
CitationJournal: Nat.Immunol. / Year: 2009
Title: Structural basis of receptor sharing by interleukin 17 cytokines.
Authors: Ely, L.K. / Fischer, S. / Garcia, K.C.
History
DepositionSep 16, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 20, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / database_PDB_caveat / 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 / pdbx_struct_conn_angle / pdbx_validate_close_contact / struct_asym / struct_conn / 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 / _chem_comp.name / _chem_comp.type / _pdbx_entity_nonpoly.comp_id / _pdbx_entity_nonpoly.entity_id / _pdbx_entity_nonpoly.name / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_seq_id_2 / _struct_conn.conn_type_id / _struct_conn.id / _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_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id
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-17F
B: Interleukin-17F
C: Interleukin-17 receptor A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,63110
Polymers63,0613
Non-polymers1,5717
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10710 Å2
ΔGint-45 kcal/mol
Surface area23710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)170.730, 170.730, 81.900
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein Interleukin-17F / IL-17F / Interleukin-24 / IL-24 / Cytokine ML-1


Mass: 14922.104 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IL17F, IL24 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q96PD4
#2: Protein Interleukin-17 receptor A / IL-17 receptor / CDw217


Mass: 33216.629 Da / Num. of mol.: 1 / Fragment: extracellular domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IL17RA, IL17R / Cell (production host): bacmam 293 cells / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q96F46
#3: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#5: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose


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

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 4

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Sample preparation

CrystalDensity Matthews: 4.73 Å3/Da / Density % sol: 74.01 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 9.2
Details: PEG6000, 0.1M CAPSO, calcium chloride, pH 9.2, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
31001
41001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONSSRL BL9-211
SYNCHROTRONSSRL BL11-121.07
SYNCHROTRONSSRL BL11-130.978
SYNCHROTRONAPS 23-ID-D41.03
Detector
IDDate
1Apr 16, 2008
2Apr 16, 2009
3Jul 17, 2008
4Dec 10, 2008
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2x-ray1
3x-ray1
4x-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
111
21.071
30.9781
41.031
ReflectionHighest resolution: 3.3 Å / Num. obs: 18749

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Processing

Software
NameVersionClassification
Blu-Icedata collection
SHARPphasing
PHENIX(phenix.refine)refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: SIRAS / Resolution: 3.3→39.821 Å / SU ML: 0.3 / σ(F): 1.34 / Phase error: 27.68 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2557 948 5.13 %
Rwork0.2292 --
obs0.2305 18479 98.57 %
all-19427 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 72.062 Å2 / ksol: 0.309 e/Å3
Refinement stepCycle: LAST / Resolution: 3.3→39.821 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3779 0 99 0 3878
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0093987
X-RAY DIFFRACTIONf_angle_d1.3335428
X-RAY DIFFRACTIONf_dihedral_angle_d19.8921456
X-RAY DIFFRACTIONf_chiral_restr0.079631
X-RAY DIFFRACTIONf_plane_restr0.005695
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.3003-3.47420.33361510.29992465X-RAY DIFFRACTION100
3.4742-3.69180.32331520.27152456X-RAY DIFFRACTION99
3.6918-3.97660.30541240.2432481X-RAY DIFFRACTION99
3.9766-4.37630.26111470.2182492X-RAY DIFFRACTION99
4.3763-5.00850.23091290.18632509X-RAY DIFFRACTION99
5.0085-6.30610.22361290.20942547X-RAY DIFFRACTION99
6.3061-39.82350.22511160.23582581X-RAY DIFFRACTION95

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