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- PDB-2h24: Crystal structure of human IL-10 -

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Basic information

Entry
Database: PDB / ID: 2h24
TitleCrystal structure of human IL-10
ComponentsInterleukin-10
KeywordsCYTOKINE / alpha-helix bundle
Function / homology
Function and homology information


negative regulation of chronic inflammatory response to antigenic stimulus / interleukin-10 receptor binding / regulation of response to wounding / negative regulation of cytokine 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 chronic inflammatory response to antigenic stimulus / interleukin-10 receptor binding / regulation of response to wounding / negative regulation of cytokine 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 / 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 interleukin-1 production / negative regulation of MHC class II biosynthetic process / interleukin-10-mediated signaling pathway / branching involved in labyrinthine layer morphogenesis / negative regulation of interleukin-8 production / negative regulation of nitric oxide biosynthetic process / negative regulation of interleukin-12 production / response to carbon monoxide / 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 / negative regulation of mitotic cell cycle / 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 / regulation of synapse organization / negative regulation of B cell proliferation / 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 tumor necrosis factor production / positive regulation of DNA-binding transcription factor activity / positive regulation of vascular associated smooth muscle cell proliferation / negative regulation of T cell proliferation / positive regulation of cell cycle / positive regulation of endothelial cell proliferation / liver regeneration / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / negative regulation of autophagy / FCGR3A-mediated IL10 synthesis / response to glucocorticoid / positive regulation of cytokine production / B cell differentiation / response to activity / cytokine 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 / Signaling by ALK fusions and activated point mutants / regulation of gene expression / cellular response to lipopolysaccharide / Interleukin-4 and Interleukin-13 signaling / protein dimerization activity / defense response to bacterium / immune response / 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
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. / Growth Hormone; Chain: A; - #10 / Four-helical cytokine-like, core / Growth Hormone; Chain: A; / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 2 Å
AuthorsYoon, S.I. / Walter, M.R.
CitationJournal: J.Biol.Chem. / Year: 2006
Title: Conformational changes mediate interleukin-10 receptor 2 (IL-10R2) binding to IL-10 and assembly of the signaling complex.
Authors: Yoon, S.I. / Logsdon, N.J. / Sheikh, F. / Donnelly, R.P. / Walter, M.R.
History
DepositionMay 18, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 17, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Aug 30, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site
Revision 1.4Nov 20, 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
A: Interleukin-10


Theoretical massNumber of molelcules
Total (without water)18,6721
Polymers18,6721
Non-polymers00
Water1,53185
1
A: Interleukin-10

A: Interleukin-10


Theoretical massNumber of molelcules
Total (without water)37,3452
Polymers37,3452
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area8610 Å2
ΔGint-85 kcal/mol
Surface area15570 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)36.370, 36.370, 220.970
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
DetailsThe second chain of the biological assembly is generated by the two fold axis: Y,X,-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
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: P22301
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 85 / 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

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Sample preparation

CrystalDensity Matthews: 1.96 Å3/Da / Density % sol: 37.12 %
Crystal growpH: 7.2 / Details: 35% ammonium sulfate, 0.1 M Hepes, pH 7.2

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Data collection

DiffractionMean temperature: 295 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7B / Wavelength: 0.87 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Sep 1, 1994
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.87 Å / Relative weight: 1
ReflectionResolution: 2→20 Å / Num. all: 10087 / Num. obs: 10087 / % possible obs: 93 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 4.2 % / Rmerge(I) obs: 0.08

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Processing

Software
NameVersionClassification
DENZOdata reduction
CNS1.1refinement
SCALEPACKdata scaling
RefinementMethod to determine structure: MIR
Starting model: PDB entry 1INR

1inr


Resolution: 2→10 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.254 1030 random
Rwork0.204 --
all-9988 -
obs-9988 -
Displacement parametersBiso mean: 36.5 Å2
Refinement stepCycle: LAST / Resolution: 2→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1148 0 0 85 1233
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.3139
X-RAY DIFFRACTIONc_bond_d0.009573
X-RAY DIFFRACTIONc_dihedral_angle_d18.46168
X-RAY DIFFRACTIONc_improper_angle_d0.77552

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