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- PDB-6df3: Crystal structure of ternary complex of IL-24 with soluble recept... -

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Basic information

Entry
Database: PDB / ID: 6df3
TitleCrystal structure of ternary complex of IL-24 with soluble receptors IL-22RA and IL-20RB
Components
  • Interleukin-20 receptor subunit beta
  • Interleukin-22 receptor subunit alpha-1
  • Interleukin-24
KeywordsCYTOKINE / ternary complex / cell signaling / JAK-STAT pathway
Function / homology
Function and homology information


serine phosphorylation of STAT protein / negative regulation of type IV hypersensitivity / interleukin-20 binding / interferon receptor activity / immune response-inhibiting signal transduction / interleukin-22 receptor activity / inflammatory response to antigenic stimulus / cytokine receptor activity / negative regulation of interleukin-2 production / Interleukin-20 family signaling ...serine phosphorylation of STAT protein / negative regulation of type IV hypersensitivity / interleukin-20 binding / interferon receptor activity / immune response-inhibiting signal transduction / interleukin-22 receptor activity / inflammatory response to antigenic stimulus / cytokine receptor activity / negative regulation of interleukin-2 production / Interleukin-20 family signaling / positive regulation of interleukin-4 production / T cell homeostasis / positive regulation of interleukin-10 production / negative regulation of type II interferon production / cellular response to interleukin-4 / T cell proliferation / negative regulation of T cell proliferation / positive regulation of tyrosine phosphorylation of STAT protein / homeostasis of number of cells within a tissue / negative regulation of cell migration / cytokine activity / wound healing / cytokine-mediated signaling pathway / negative regulation of inflammatory response / cellular response to lipopolysaccharide / defense response to Gram-negative bacterium / negative regulation of cell population proliferation / apoptotic process / positive regulation of cell population proliferation / extracellular space / extracellular region / plasma membrane
Similarity search - Function
Interleukin-24 / Interleukin-10, conserved site / Interleukin-10 family signature. / Interferon/interleukin receptor domain / Interferon-alpha/beta receptor, fibronectin type III / Tissue factor / Four-helical cytokine-like, core / Fibronectin type-III domain profile. / Fibronectin type III / Fibronectin type III superfamily ...Interleukin-24 / Interleukin-10, conserved site / Interleukin-10 family signature. / Interferon/interleukin receptor domain / Interferon-alpha/beta receptor, fibronectin type III / Tissue factor / Four-helical cytokine-like, core / Fibronectin type-III domain profile. / Fibronectin type III / Fibronectin type III superfamily / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Interleukin-24 / Interleukin-20 receptor subunit beta / Interleukin-22 receptor subunit alpha-1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.15 Å
AuthorsLubkowski, J. / Wlodawer, A.
CitationJournal: J. Immunol. / Year: 2018
Title: Crystal Structure of the Labile Complex of IL-24 with the Extracellular Domains of IL-22R1 and IL-20R2.
Authors: Lubkowski, J. / Sonmez, C. / Smirnov, S.V. / Anishkin, A. / Kotenko, S.V. / Wlodawer, A.
History
DepositionMay 14, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 15, 2018Provider: repository / Type: Initial release
Revision 1.1Aug 29, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.pdbx_database_id_DOI ..._citation.journal_abbrev / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Oct 3, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
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.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_entity_nonpoly.entity_id / _pdbx_entity_nonpoly.name / _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.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Oct 11, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
L: Interleukin-22 receptor subunit alpha-1
C: Interleukin-24
H: Interleukin-20 receptor subunit beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,9587
Polymers63,1283
Non-polymers8304
Water1,44180
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration, Additional support from: SDS-PAGE, native SDS, mass spectroscopy, Western blot
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6090 Å2
ΔGint-1 kcal/mol
Surface area26730 Å2
Unit cell
Length a, b, c (Å)77.702, 77.702, 124.785
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number78
Space group name H-MP43

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Components

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Protein , 3 types, 3 molecules LCH

#1: Protein Interleukin-22 receptor subunit alpha-1 / IL-22RA1 / Cytokine receptor class-II member 9 / Cytokine receptor family 2 member 9 / CRF2-9 / ZcytoR11


Mass: 23560.807 Da / Num. of mol.: 1 / Fragment: UNP residues 24-228
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IL22RA1, IL22R / Production host: Drosophila melanogaster (fruit fly) / References: UniProt: Q8N6P7
#2: Protein Interleukin-24 / IL-24 / Melanoma differentiation-associated gene 7 protein / MDA-7 / Suppression of tumorigenicity 16 protein


Mass: 18201.967 Da / Num. of mol.: 1 / Fragment: UNP residues 52-206 / Mutation: N85Q, N99Q, N126Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IL24, MDA7, ST16 / Production host: Drosophila melanogaster (fruit fly) / References: UniProt: Q13007
#3: Protein Interleukin-20 receptor subunit beta / IL-20RB / Fibronectin type III domain containing 6 / FNDC6 / IL-20R2


Mass: 21365.219 Da / Num. of mol.: 1 / Fragment: UNP residues 35-224 / Mutation: N134Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IL20RB, DIRS1, UNQ557/PRO1114 / Production host: Drosophila melanogaster (fruit fly) / References: UniProt: Q6UXL0

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Sugars , 2 types, 2 molecules

#4: 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
#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.: 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 , 2 types, 82 molecules

#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 80 / Source method: isolated from a natural source / Formula: H2O

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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: 2.98 Å3/Da / Density % sol: 58.78 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 8 mg/mL protein in 0.2 M sodium chloride, 0.05 M HEPES against 215 w/v MEPEG2000, 0.05 M Tris, pH 8.5, 0.05 M trimethylamine N-oxide dihydrate
PH range: 7.5 - 8.0

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Data collection

DiffractionMean temperature: 100 K / Ambient temp details: STREAM OF VAPOURIZED NITROGEN
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jul 1, 2017
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.15→99 Å / Num. obs: 39903 / % possible obs: 99.7 % / Redundancy: 8 % / CC1/2: 0.97 / Rmerge(I) obs: 0.072 / Rpim(I) all: 0.034 / Net I/σ(I): 29.7
Reflection shellResolution: 2.15→2.23 Å / Redundancy: 7.1 % / Rmerge(I) obs: 1.416 / Mean I/σ(I) obs: 1.62 / Num. unique obs: 3987 / CC1/2: 0.7 / Rpim(I) all: 0.62 / % possible all: 100

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
REFMAC5.8.0189refinement
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 4DOH

4doh


Resolution: 2.15→30 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.953 / SU B: 13.072 / SU ML: 0.155 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.191 / ESU R Free: 0.17 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2246 1978 5 %RANDOM
Rwork0.1816 ---
obs0.1838 37897 99.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 180.36 Å2 / Biso mean: 74.672 Å2 / Biso min: 34.86 Å2
Baniso -1Baniso -2Baniso -3
1-1.75 Å2-0 Å2-0 Å2
2--1.75 Å2-0 Å2
3----3.49 Å2
Refinement stepCycle: final / Resolution: 2.15→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4395 0 54 80 4529
Biso mean--110.93 62.45 -
Num. residues----544
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0194563
X-RAY DIFFRACTIONr_bond_other_d0.0020.024172
X-RAY DIFFRACTIONr_angle_refined_deg2.0181.9576200
X-RAY DIFFRACTIONr_angle_other_deg1.0839684
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.8995539
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.47823.575207
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.22415769
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.0731528
X-RAY DIFFRACTIONr_chiral_restr0.1170.2701
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0214950
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02950
LS refinement shellResolution: 2.154→2.21 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.316 167 -
Rwork0.298 2738 -
all-2905 -
obs--98.88 %
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)
18.50341.252.93512.09970.3931.90040.43450.33-0.2751-0.6579-0.4019-0.1270.45710.222-0.03270.41230.19650.07350.1529-0.01980.07323.28155.239454.6311
22.5118-0.44962.26573.6917-1.22976.73430.24190.3228-0.022-0.47950.01080.2320.35210.2674-0.25270.09880.0436-0.05720.0621-0.02230.05211.231223.380452.0204
36.619-0.36991.35522.68180.53342.78580.1205-0.6762-0.09260.23610.3312-0.47750.05230.5364-0.45180.0995-0.0122-0.0140.2821-0.15280.161711.999726.968579.3283
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1L24 - 303
2X-RAY DIFFRACTION2C52 - 206
3X-RAY DIFFRACTION3H35 - 224

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