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- PDB-1y6k: Crystal structure of human IL-10 complexed with the soluble IL-10... -

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Basic information

Entry
Database: PDB / ID: 1y6k
TitleCrystal structure of human IL-10 complexed with the soluble IL-10R1 chain
Components
  • Interleukin-10
  • Interleukin-10 receptor alpha chain
KeywordsIMMUNE SYSTEM / HELIX BUNDLE / 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 / negative regulation of membrane protein ectodomain proteolysis / response to inactivity / ubiquitin-dependent endocytosis / positive regulation of plasma cell differentiation / positive regulation of B cell apoptotic process / regulation of isotype switching / negative regulation of heterotypic cell-cell adhesion / negative regulation of cytokine production involved in immune response / negative regulation of MHC class II biosynthetic process / negative regulation of interleukin-1 production / interleukin-10-mediated signaling pathway / intestinal epithelial structure maintenance / branching involved in labyrinthine layer morphogenesis / response to carbon monoxide / negative regulation of interleukin-8 production / negative regulation of interleukin-12 production / negative regulation of nitric oxide biosynthetic process / endothelial cell apoptotic process / positive regulation of MHC class II biosynthetic process / positive regulation of macrophage activation / positive regulation of heterotypic cell-cell adhesion / negative regulation of oxidative stress-induced neuron intrinsic apoptotic signaling pathway / leukocyte chemotaxis / negative regulation of mitotic cell cycle / type 2 immune response / CD163 mediating an anti-inflammatory response / positive regulation of immunoglobulin production / negative regulation of cytokine production / cellular response to hepatocyte growth factor stimulus / negative regulation of B cell proliferation / defense response to protozoan / positive regulation of sprouting angiogenesis / regulation of synapse organization / Interleukin-10 signaling / negative regulation of type II interferon production / negative regulation of interleukin-6 production / hemopoiesis / B cell proliferation / negative regulation of vascular associated smooth muscle cell proliferation / negative regulation of tumor necrosis factor production / : / positive regulation of vascular associated smooth muscle cell proliferation / negative regulation of T cell proliferation / Nuclear events stimulated by ALK signaling in cancer / positive regulation of endothelial cell proliferation / positive regulation of cell cycle / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / liver regeneration / negative regulation of autophagy / FCGR3A-mediated IL10 synthesis / response to glucocorticoid / B cell differentiation / positive regulation of cytokine production / cytokine activity / response to activity / positive regulation of receptor signaling pathway via JAK-STAT / growth factor activity / cellular response to estradiol stimulus / response to molecule of bacterial origin / response to insulin / positive regulation of miRNA transcription / negative regulation of inflammatory response / cytokine-mediated signaling pathway / Signaling by ALK fusions and activated point mutants / signaling receptor activity / cellular response to lipopolysaccharide / regulation of gene expression / 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 / MOLECULAR REPLACEMENT / Resolution: 2.52 Å
AuthorsYoon, S.I. / Jones, B.C. / Josepson, K. / Logsdon, N.J. / Walter, M.R.
CitationJournal: Structure / Year: 2005
Title: Same structure, different function crystal structure of the Epstein-Barr virus IL-10 bound to the soluble IL-10R1 chain.
Authors: Yoon, S.I. / Jones, B.C. / Logsdon, N.J. / Walter, M.R.
History
DepositionDec 6, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 20, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 20, 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 1.4Aug 23, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.5Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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
Water84747
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)46.440, 46.440, 309.250
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number153
Space group name H-MP3212
Detailshe second part of the biological assembly is generated by the two fold axis: x, x-y, -z.

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Components

#1: Protein Interleukin-10 / IL-10 / Cytokine synthesis inhibitory factor / CSIF


Mass: 18672.447 Da / Num. of mol.: 1 / Fragment: residues 19-178
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IL10 / Plasmid: pET-32 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: P22301
#2: Protein Interleukin-10 receptor alpha chain / IL-10R-A / IL-10R1


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) / Gene: IL10RA, IL10R / Plasmid: pMTV5HIS / 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.: 47 / 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: 44.5 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.2
Details: PEG 6000, magnesium chloride, ADA, cymal-6, pH 6.2, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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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
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 2.52→50 Å / Num. all: 11441 / Num. obs: 11441 / % possible obs: 84.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.1 % / Biso Wilson estimate: 63 Å2 / Rmerge(I) obs: 0.037
Reflection shellResolution: 2.52→2.61 Å / Rmerge(I) obs: 0.308 / % possible all: 68.7

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1j7V

1j7v


Resolution: 2.52→50 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.279 661 Random
Rwork0.229 --
all0.233 11365 -
obs0.233 11365 -
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--4.97 Å2-9.52 Å20 Å2
2---4.97 Å20 Å2
3----9.94 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.42 Å0.37 Å
Luzzati sigma a0.28 Å0.29 Å
Refinement stepCycle: LAST / Resolution: 2.52→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2841 0 0 47 2888
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.36
LS refinement shellResolution: 2.52→2.59 Å
RfactorNum. reflection% reflection
Rfree0.4338 14 -
Rwork0.3588 --
obs-723 52 %

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