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- PDB-4doh: IL20/IL201/IL20R2 Ternary Complex -

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Basic information

Entry
Database: PDB / ID: 4doh
TitleIL20/IL201/IL20R2 Ternary Complex
Components
  • Interleukin-20
  • Interleukin-20 receptor subunit alpha
  • Interleukin-20 receptor subunit beta
KeywordsSIGNALING PROTEIN / IL10 Family cytokine receptor complex / Alpha helical cytokine fold Beta sandwhich receptor fold / Signaling Complex / extracellular
Function / homology
Function and homology information


interleukin-20 receptor binding / CD8-positive, alpha-beta T cell homeostasis / negative regulation of type IV hypersensitivity / interleukin-20 binding / interleukin-22 receptor binding / immune response-inhibiting signal transduction / positive regulation of keratinocyte differentiation / inflammatory response to antigenic stimulus / positive regulation of osteoclast differentiation / cytokine receptor activity ...interleukin-20 receptor binding / CD8-positive, alpha-beta T cell homeostasis / negative regulation of type IV hypersensitivity / interleukin-20 binding / interleukin-22 receptor binding / immune response-inhibiting signal transduction / positive regulation of keratinocyte differentiation / inflammatory response to antigenic stimulus / positive regulation of osteoclast differentiation / cytokine receptor activity / regulation of bone resorption / positive regulation of tyrosine phosphorylation of STAT protein / Interleukin-20 family signaling / negative regulation of interleukin-2 production / positive regulation of epidermal cell differentiation / positive regulation of interleukin-4 production / negative regulation of type II interferon production / positive regulation of interleukin-10 production / T cell proliferation / positive regulation of intrinsic apoptotic signaling pathway / negative regulation of T cell proliferation / homeostasis of number of cells within a tissue / osteoclast differentiation / cytokine activity / cytokine-mediated signaling pathway / regulation of inflammatory response / immune response / extracellular space / extracellular region / plasma membrane
Similarity search - Function
Interleukin-20 / Interleukin-10 family / Interleukin 10 / Interleukin-10/19/20/22/24/26 family / Interleukin-10, conserved site / Interleukin-10 family signature. / Interferon/interleukin receptor domain / Interferon-alpha/beta receptor, fibronectin type III / : / Tissue factor ...Interleukin-20 / Interleukin-10 family / Interleukin 10 / Interleukin-10/19/20/22/24/26 family / Interleukin-10, conserved site / Interleukin-10 family signature. / Interferon/interleukin receptor domain / Interferon-alpha/beta receptor, fibronectin type III / : / Tissue factor / Growth Hormone; Chain: A; - #10 / Four-helical cytokine-like, core / Growth Hormone; Chain: A; / Fibronectin type-III domain profile. / Fibronectin type III / Fibronectin type III superfamily / Immunoglobulin-like fold / Immunoglobulins / Up-down Bundle / Immunoglobulin-like / Sandwich / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
Interleukin-20 receptor subunit beta / Interleukin-20 / Interleukin-20 receptor subunit alpha
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.8 Å
AuthorsLogsdon, N.J. / Walter, M.R.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2012
Title: Structural basis for receptor sharing and activation by interleukin-20 receptor-2 (IL-20R2) binding cytokines.
Authors: Logsdon, N.J. / Deshpande, A. / Harris, B.D. / Rajashankar, K.R. / Walter, M.R.
History
DepositionFeb 9, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 18, 2012Provider: repository / Type: Initial release
Revision 1.1Aug 8, 2012Group: Database references
Revision 1.2Jan 2, 2013Group: Database references
Revision 1.3Oct 16, 2013Group: Other
Revision 1.4Jul 29, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.5Nov 20, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
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
A: Interleukin-20
B: Interleukin-20 receptor subunit beta
R: Interleukin-20 receptor subunit alpha
C: Interleukin-20
D: Interleukin-20 receptor subunit beta
E: Interleukin-20 receptor subunit alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)132,99511
Polymers131,8896
Non-polymers1,1065
Water1,02757
1
A: Interleukin-20
B: Interleukin-20 receptor subunit beta
R: Interleukin-20 receptor subunit alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,6086
Polymers65,9443
Non-polymers6643
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Interleukin-20
D: Interleukin-20 receptor subunit beta
E: Interleukin-20 receptor subunit alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,3875
Polymers65,9443
Non-polymers4422
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)103.115, 111.764, 136.334
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Interleukin-20 / IL-20 / Cytokine Zcyto10


Mass: 17626.479 Da / Num. of mol.: 2 / Mutation: Q40N, Q134N, R111K, R113K
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IL20, ZCYTO10, UNQ852/PRO1801 / Production host: Drosophila (fruit flies) / References: UniProt: Q9NYY1
#2: Protein Interleukin-20 receptor subunit beta / IL-20 receptor subunit beta / IL-20R-beta / IL-20RB / IL-20R2


Mass: 23047.047 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IL20RB, DIRS1, UNQ557/PRO1114 / Production host: Drosophila (fruit flies) / References: UniProt: Q6UXL0
#3: Protein Interleukin-20 receptor subunit alpha / IL-20 receptor subunit alpha / IL-20R-alpha / IL-20RA / Cytokine receptor class-II member 8 / ...IL-20 receptor subunit alpha / IL-20R-alpha / IL-20RA / Cytokine receptor class-II member 8 / Cytokine receptor family 2 member 8 / CRF2-8 / IL-20R1 / ZcytoR7


Mass: 25270.729 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IL20RA, UNQ681/PRO1315 / Production host: Drosophila (fruit flies) / References: UniProt: Q9UHF4
#4: 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
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 57 / Source method: isolated from a natural source / Formula: H2O
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: 2.98 Å3/Da / Density % sol: 58.7 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 19% PEG 6000, 0.1M ADA, 0.1M MgCl2, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 6, 2006
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.8→50 Å / Num. all: 42596 / Num. obs: 38635 / % possible obs: 90.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3
Reflection shellResolution: 2.8→2.9 Å / % possible all: 90.7

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
PHENIXmodel building
CNS1refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.8→50 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.278 1952 Random
Rwork0.23 --
all0.23 38635 -
obs0.23 35822 -
Refinement stepCycle: LAST / Resolution: 2.8→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8822 0 70 57 8949

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