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- PDB-1ilk: INTERLEUKIN-10 CRYSTAL STRUCTURE REVEALS THE FUNCTIONAL DIMER WIT... -

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Basic information

Entry
Database: PDB / ID: 1ilk
TitleINTERLEUKIN-10 CRYSTAL STRUCTURE REVEALS THE FUNCTIONAL DIMER WITH AN UNEXPECTED TOPOLOGICAL SIMILARITY TO INTERFERON GAMMA
ComponentsINTERLEUKIN-10
KeywordsCYTOKINE
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 / response to carbon monoxide / positive regulation of plasma cell differentiation ...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 / response to carbon monoxide / positive regulation of plasma cell differentiation / positive regulation of B cell apoptotic process / chronic inflammatory response to antigenic stimulus / response to inactivity / cytoplasmic sequestering of NF-kappaB / negative regulation of membrane protein ectodomain proteolysis / 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 / 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 / type 2 immune response / negative regulation of oxidative stress-induced neuron intrinsic apoptotic signaling pathway / endothelial cell apoptotic process / positive regulation of MHC class II biosynthetic process / positive regulation of macrophage activation / leukocyte chemotaxis / positive regulation of heterotypic cell-cell adhesion / positive regulation of signaling receptor activity / 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 / positive regulation of sprouting angiogenesis / B cell proliferation / negative regulation of B cell proliferation / defense response to protozoan / negative regulation of vascular associated smooth muscle cell proliferation / Interleukin-10 signaling / negative regulation of interleukin-6 production / hemopoiesis / negative regulation of type II interferon production / negative regulation of tumor necrosis factor production / negative regulation of mitotic cell cycle / positive regulation of cell cycle / negative regulation of T cell proliferation / response to glucocorticoid / positive regulation of vascular associated smooth muscle cell proliferation / 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 activity / positive regulation of cytokine production / cytokine activity / cellular response to estradiol stimulus / liver regeneration / positive regulation of receptor signaling pathway via JAK-STAT / growth factor activity / response to insulin / response to molecule of bacterial origin / positive regulation of DNA-binding transcription factor activity / 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 / 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-10/19/20/22/24/26 family / Interleukin 10 / 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 / Resolution: 1.8 Å
AuthorsZdanov, A. / Schalk-Hihi, C. / Gustchina, A. / Wlodawer, A.
CitationJournal: Structure / Year: 1995
Title: Crystal structure of interleukin-10 reveals the functional dimer with an unexpected topological similarity to interferon gamma.
Authors: Zdanov, A. / Schalk-Hihi, C. / Gustchina, A. / Tsang, M. / Weatherbee, J. / Wlodawer, A.
History
DepositionApr 21, 1995Processing site: BNL
Revision 1.0Jul 10, 1995Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Jun 5, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site
Remark 650HELIX HELIX 1 IS DISTORTED AT SER 31 AND ARG 32; HELIX 3 IS DISTORTED AT GLU 74 AND GLU 75, IN THE ...HELIX HELIX 1 IS DISTORTED AT SER 31 AND ARG 32; HELIX 3 IS DISTORTED AT GLU 74 AND GLU 75, IN THE VICINITY OF PRO 78.

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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)17,8011
Polymers17,8011
Non-polymers00
Water2,306128
1
A: INTERLEUKIN-10

A: INTERLEUKIN-10


Theoretical massNumber of molelcules
Total (without water)35,6012
Polymers35,6012
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_556y,x,-z+11
Buried area8790 Å2
ΔGint-87 kcal/mol
Surface area15720 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)70.274, 70.274, 70.308
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Atom site foot note1: CIS PROLINE - PRO 16

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Components

#1: Protein INTERLEUKIN-10


Mass: 17800.598 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.: 128 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.81 Å3/Da / Density % sol: 56.3 %
Crystal grow
*PLUS
pH: 6.5 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
14 mg/mlprotein1drop
210 %ammonium sulfate1drop
350 mMsodium cacodylate1droppH6.5
460 %satammonium sulfate1reservoir
50.1 Msodium cacodylate1reservoirpH6.5

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Data collection

Diffraction sourceWavelength: 1.5418 Å
DetectorType: RIGAKU / Detector: IMAGE PLATE / Date: Sep 1, 1994
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionNum. obs: 15324 / % possible obs: 80.8 % / Observed criterion σ(I): 1 / Redundancy: 4.1 % / Rmerge(I) obs: 0.061
Reflection
*PLUS
Highest resolution: 1.8 Å

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Processing

Software
NameVersionClassification
MSCPROGRAM PACKAGEdata collection
X-PLORmodel building
X-PLORrefinement
PROFFTrefinement
MSCdata reduction
X-PLORphasing
RefinementResolution: 1.8→10 Å / σ(F): 3 /
RfactorNum. reflection
Rwork0.156 -
obs0.156 13105
Displacement parametersBiso mean: 22.4 Å2
Refinement stepCycle: LAST / Resolution: 1.8→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1234 0 0 128 1362
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.012
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it2.3252.5
X-RAY DIFFRACTIONx_mcangle_it3.3213.5
X-RAY DIFFRACTIONx_scbond_it5.9944
X-RAY DIFFRACTIONx_scangle_it9.0647
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal targetDev ideal
X-RAY DIFFRACTIONx_bond_d0.017
X-RAY DIFFRACTIONx_angle_d0.0440.047
X-RAY DIFFRACTIONx_planar_d0.0590.054
X-RAY DIFFRACTIONx_plane_restr0.0220.014
X-RAY DIFFRACTIONx_chiral_restr0.180.173

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