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- PDB-1j7v: HUMAN IL-10 / IL-10R1 COMPLEX -

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Basic information

Entry
Database: PDB / ID: 1j7v
TitleHUMAN IL-10 / IL-10R1 COMPLEX
Components
  • INTERLEUKIN-10
  • INTERLEUKIN-10 RECEPTOR ALPHA CHAIN
KeywordsCYTOKINE/RECEPTOR / cytokine receptor complex / 4 helix bundle / class 2 receptor / interleukin-10 / CYTOKINE-RECEPTOR COMPLEX
Function / homology
Function and homology information


interleukin-10 binding / negative regulation of chronic inflammatory response to antigenic stimulus / interleukin-10 receptor binding / regulation of response to wounding / negative regulation of cytokine activity / interleukin-10 receptor activity / negative regulation of interleukin-18 production / negative regulation of myeloid dendritic cell activation / negative regulation of interferon-alpha production / negative regulation of chemokine (C-C motif) ligand 5 production ...interleukin-10 binding / negative regulation of chronic inflammatory response to antigenic stimulus / interleukin-10 receptor binding / regulation of response to wounding / negative regulation of cytokine activity / interleukin-10 receptor activity / negative regulation of interleukin-18 production / negative regulation of myeloid dendritic cell activation / negative regulation of interferon-alpha production / negative regulation of chemokine (C-C motif) ligand 5 production / chronic inflammatory response to antigenic stimulus / response to inactivity / negative regulation of membrane protein ectodomain proteolysis / positive regulation of plasma cell differentiation / ubiquitin-dependent endocytosis / positive regulation of B cell apoptotic process / response to carbon monoxide / regulation of isotype switching / negative regulation of heterotypic cell-cell adhesion / negative regulation of cytokine production involved in immune response / negative regulation of interleukin-1 production / intestinal epithelial structure maintenance / interleukin-10-mediated signaling pathway / branching involved in labyrinthine layer morphogenesis / negative regulation of interleukin-8 production / negative regulation of MHC class II biosynthetic process / negative regulation of nitric oxide biosynthetic process / negative regulation of interleukin-12 production / endothelial cell apoptotic process / positive regulation of MHC class II biosynthetic process / positive regulation of macrophage activation / negative regulation of oxidative stress-induced neuron intrinsic apoptotic signaling pathway / positive regulation of heterotypic cell-cell adhesion / leukocyte chemotaxis / type 2 immune response / CD163 mediating an anti-inflammatory response / negative regulation of cytokine production / positive regulation of immunoglobulin production / cellular response to hepatocyte growth factor stimulus / negative regulation of B cell proliferation / regulation of synapse organization / defense response to protozoan / positive regulation of sprouting angiogenesis / Interleukin-10 signaling / negative regulation of interleukin-6 production / negative regulation of vascular associated smooth muscle cell proliferation / negative regulation of type II interferon production / B cell proliferation / hemopoiesis / negative regulation of mitotic cell cycle / negative regulation of tumor necrosis factor production / Nuclear events stimulated by ALK signaling in cancer / positive regulation of vascular associated smooth muscle cell proliferation / positive regulation of DNA-binding transcription factor activity / negative regulation of T cell proliferation / positive regulation of cell cycle / positive regulation of endothelial cell proliferation / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / negative regulation of autophagy / B cell differentiation / FCGR3A-mediated IL10 synthesis / response to glucocorticoid / positive regulation of cytokine production / response to activity / cytokine activity / positive regulation of receptor signaling pathway via JAK-STAT / liver regeneration / cellular response to estradiol stimulus / growth factor activity / response to molecule of bacterial origin / response to insulin / positive regulation of miRNA transcription / negative regulation of inflammatory response / Signaling by ALK fusions and activated point mutants / cytokine-mediated signaling pathway / signaling receptor activity / regulation of gene expression / cellular response to lipopolysaccharide / Interleukin-4 and Interleukin-13 signaling / response to lipopolysaccharide / protein dimerization activity / defense response to bacterium / immune response / cilium / apical plasma membrane / response to xenobiotic stimulus / negative regulation of cell population proliferation / negative regulation of apoptotic process / positive regulation of DNA-templated transcription / positive regulation of transcription by RNA polymerase II / extracellular space / extracellular region / nucleoplasm / plasma membrane / cytosol
Similarity search - Function
Interleukin-10 / Interleukin-10 family / Interleukin 10 / Interleukin-10/19/20/22/24/26 family / Interleukin-10, conserved site / Interleukin-10 family signature. / : / Tissue factor / Growth Hormone; Chain: A; - #10 / Four-helical cytokine-like, core ...Interleukin-10 / Interleukin-10 family / Interleukin 10 / Interleukin-10/19/20/22/24/26 family / Interleukin-10, conserved site / Interleukin-10 family signature. / : / Tissue factor / Growth Hormone; Chain: A; - #10 / Four-helical cytokine-like, core / Growth Hormone; Chain: A; / 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-10 / Interleukin-10 receptor subunit alpha
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.9 Å
AuthorsJosephson, K. / Logsdon, N. / Walter, M.R.
CitationJournal: Immunity / Year: 2001
Title: Crystal structure of the IL-10/IL-10R1 complex reveals a shared receptor binding site.
Authors: Josephson, K. / Logsdon, N.J. / Walter, M.R.
History
DepositionMay 18, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 19, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 27, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4Oct 30, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / 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
L: INTERLEUKIN-10
R: INTERLEUKIN-10 RECEPTOR ALPHA CHAIN


Theoretical massNumber of molelcules
Total (without water)43,1792
Polymers43,1792
Non-polymers00
Water37821
1
L: INTERLEUKIN-10
R: INTERLEUKIN-10 RECEPTOR ALPHA CHAIN

L: INTERLEUKIN-10
R: INTERLEUKIN-10 RECEPTOR ALPHA CHAIN


Theoretical massNumber of molelcules
Total (without water)86,3584
Polymers86,3584
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555x,x-y,-z1
Unit cell
Length a, b, c (Å)46.230, 46.230, 307.780
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number153
Space group name H-MP3212

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Components

#1: Protein INTERLEUKIN-10 / IL-10 / CYTOKINE SYNTHESIS INHIBITORY FACTOR / CSIF


Mass: 18672.447 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: P22301
#2: Protein INTERLEUKIN-10 RECEPTOR ALPHA CHAIN / IL-10R1 / IL-10R-A


Mass: 24506.551 Da / Num. of mol.: 1 / Fragment: EXTRACELLULAR DOMAIN, RESIDUES 22-235 / Mutation: N29Q,N53Q,N89Q,N133Q,N156Q,N168Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): Schneider cells / Production host: Drosophila melanogaster (fruit fly) / References: UniProt: Q13651
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 21 / 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: 2.2 Å3/Da / Density % sol: 44.04 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.2
Details: PEG 6000, MgCl2, pH 6.2, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
110 mg/mlprotein1drop
220 mMTris-HCl1drop
3150 mM1dropNaCl
42 mMCymal-61drop
50.1 MADA1reservoir
68 %PEG60001reservoir
70.1 M1reservoirMgCl2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.9184 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 30, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 2.9→50 Å / Num. all: 8189 / Num. obs: 8189 / % possible obs: 92.8 % / Observed criterion σ(F): 1.7 / Observed criterion σ(I): 0 / Redundancy: 2.8 % / Biso Wilson estimate: 62 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 9.1
Reflection shellResolution: 2.9→2.97 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.122 / Mean I/σ(I) obs: 5.2 / % possible all: 75
Reflection
*PLUS
Lowest resolution: 50 Å / Num. measured all: 24449 / Rmerge(I) obs: 0.05
Reflection shell
*PLUS
% possible obs: 75 %

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing
MLPHAREphasing
DMmodel building
CNS1refinement
CCP4(SCALA)data scaling
DMphasing
RefinementMethod to determine structure: MAD / Resolution: 2.9→50 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh and Huber
RfactorNum. reflectionSelection details
Rfree0.286 571 RANDOM
Rwork0.231 --
all-8135 -
obs-8135 -
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--4.483 Å2-11.158 Å2-
2---4.483 Å2-
3---8.966 Å2
Refinement stepCycle: LAST / Resolution: 2.9→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2897 0 0 21 2918
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.43
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.9 Å / Lowest resolution: 50 Å / σ(F): 0 / % reflection Rfree: 5 % / Rfactor obs: 0.231
Solvent computation
*PLUS
Displacement parameters
*PLUS

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