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- PDB-1inr: CYTOKINE SYNTHESIS -

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Basic information

Entry
Database: PDB / ID: 1inr
TitleCYTOKINE SYNTHESIS
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 / chronic inflammatory response to antigenic stimulus / negative regulation of membrane protein ectodomain proteolysis ...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 / negative regulation of membrane protein ectodomain proteolysis / response to inactivity / 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 / branching involved in labyrinthine layer morphogenesis / negative regulation of interleukin-8 production / negative regulation of interleukin-12 production / negative regulation of nitric oxide biosynthetic process / response to carbon monoxide / 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 / regulation of synapse organization / positive regulation of sprouting angiogenesis / Interleukin-10 signaling / negative regulation of type II interferon production / negative regulation of interleukin-6 production / B cell proliferation / hemopoiesis / 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 / 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 / FCGR3A-mediated IL10 synthesis / negative regulation of autophagy / 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 / Signaling by ALK fusions and activated point mutants / cellular response to lipopolysaccharide / regulation of gene expression / 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 / Resolution: 2 Å
AuthorsWalter, M.R.
Citation
Journal: Biochemistry / Year: 1995
Title: Crystal structure of interleukin 10 reveals an interferon gamma-like fold.
Authors: Walter, M.R. / Nagabhushan, T.L.
#1: Journal: Proteins / Year: 1995
Title: Crystallization and Preliminary X-Ray Investigation of Human Interleukin-10
Authors: Cook, W.J. / Windsor, W.T. / Murgola, N.J. / Tindall, S.H. / Nagabhushan, T.L. / Walter, M.R.
History
DepositionJul 31, 1995Processing site: BNL
Revision 1.0Oct 14, 1996Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 30, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: INTERLEUKIN-10


Theoretical massNumber of molelcules
Total (without water)18,6721
Polymers18,6721
Non-polymers00
Water75742
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 area8170 Å2
ΔGint-82 kcal/mol
Surface area13530 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

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Components

#1: Protein INTERLEUKIN-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.: 42 / 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: 38 %
Crystal grow
*PLUS
pH: 7.2 / Method: unknown
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
135 %satammonium sulfate11
2100 mMHEPES11

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Data collection

DiffractionMean temperature: 295 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7B / Wavelength: 0.87
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Sep 1, 1994
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.87 Å / Relative weight: 1
ReflectionResolution: 2→20 Å / Num. obs: 10087 / Observed criterion σ(I): 0 / Redundancy: 4.2 % / Rmerge(I) obs: 0.08
Reflection
*PLUS
% possible obs: 92 % / Num. measured all: 42251

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
X-PLOR3.1model building
X-PLOR3.1refinement
X-PLOR3.1phasing
RefinementResolution: 2→10 Å / σ(F): 0
RfactorNum. reflection% reflection
Rfree0.337 -10 %
Rwork0.221 --
obs0.221 9888 83 %
Displacement parametersBiso mean: 31.7 Å2
Refinement stepCycle: LAST / Resolution: 2→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1072 0 0 42 1114
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.02
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_deg3.79
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d21.84
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.57
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg21.84
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.57

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