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- PDB-2int: CRYSTAL STRUCTURE OF RECOMBINANT HUMAN INTERLEUKIN-4 -

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Basic information

Entry
Database: PDB / ID: 2int
TitleCRYSTAL STRUCTURE OF RECOMBINANT HUMAN INTERLEUKIN-4
ComponentsINTERLEUKIN-4Interleukin 4
KeywordsCYTOKINE
Function / homology
Function and homology information


interleukin-4 receptor binding / positive regulation of isotype switching to IgE isotypes / positive regulation of eosinophil chemotaxis / B cell costimulation / negative regulation of complement-dependent cytotoxicity / negative regulation of macrophage activation / negative regulation of chronic inflammatory response / Interleukin-18 signaling / regulation of isotype switching / negative regulation of neuroinflammatory response ...interleukin-4 receptor binding / positive regulation of isotype switching to IgE isotypes / positive regulation of eosinophil chemotaxis / B cell costimulation / negative regulation of complement-dependent cytotoxicity / negative regulation of macrophage activation / negative regulation of chronic inflammatory response / Interleukin-18 signaling / regulation of isotype switching / negative regulation of neuroinflammatory response / positive regulation of cellular respiration / negative regulation of epithelial cell migration / negative regulation of T-helper 17 cell differentiation / dendritic cell differentiation / positive regulation of T-helper 2 cell cytokine production / positive regulation of isotype switching to IgG isotypes / positive regulation of amyloid-beta clearance / neuroinflammatory response / interleukin-4-mediated signaling pathway / macrophage activation / myeloid dendritic cell differentiation / positive regulation of mast cell degranulation / positive regulation of mononuclear cell migration / regulation of phosphorylation / type 2 immune response / activation of Janus kinase activity / positive regulation of MHC class II biosynthetic process / T-helper 2 cell differentiation / negative regulation of cellular response to transforming growth factor beta stimulus / positive regulation of T cell differentiation / positive regulation of interleukin-13 production / positive regulation of myoblast fusion / positive regulation of ATP biosynthetic process / negative regulation of osteoclast differentiation / positive regulation of macroautophagy / positive regulation of interleukin-10 production / negative regulation of acute inflammatory response / negative regulation of tumor necrosis factor production / regulation of immune response / negative regulation of endothelial cell apoptotic process / positive regulation of B cell proliferation / positive regulation of tyrosine phosphorylation of STAT protein / positive regulation of defense response to virus by host / extrinsic apoptotic signaling pathway in absence of ligand / cholesterol metabolic process / positive regulation of T cell proliferation / T cell activation / B cell differentiation / innate immune response in mucosa / cytokine activity / negative regulation of extrinsic apoptotic signaling pathway / microglial cell activation / growth factor activity / negative regulation of inflammatory response / positive regulation of receptor-mediated endocytosis / positive regulation of cold-induced thermogenesis / Interleukin-4 and Interleukin-13 signaling / positive regulation of cell migration / immune response / negative regulation of DNA-templated transcription / positive regulation of cell population proliferation / positive regulation of gene expression / negative regulation of apoptotic process / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / extracellular space / extracellular region
Similarity search - Function
Interleukin-4 / Interleukin 4 / Interleukin-4/interleukin-13 / Interleukin-4/interleukin-13, conserved site / Interleukins -4 and -13 signature. / Interleukins 4 and 13 / 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: 2.35 Å
AuthorsWalter, M.R. / Cook, W.J. / Zhao, B.G. / Cameron Junior, R. / Ealick, S.E. / Walter Junior, R.L. / Reichert, P. / Nagabhushan, T.L. / Trotta, P.P. / Bugg, C.E.
CitationJournal: J.Biol.Chem. / Year: 1992
Title: Crystal structure of recombinant human interleukin-4.
Authors: Walter, M.R. / Cook, W.J. / Zhao, B.G. / Cameron Jr., R.P. / Ealick, S.E. / Walter Jr., R.L. / Reichert, P. / Nagabhushan, T.L. / Trotta, P.P. / Bugg, C.E.
History
DepositionJul 22, 1993Processing site: BNL
Revision 1.0Jan 31, 1994Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 17, 2019Group: Data collection / Other / Refinement description / Category: pdbx_database_status / software
Item: _pdbx_database_status.process_site / _software.classification
Revision 1.4Aug 14, 2019Group: Data collection / Refinement description / Category: software / Item: _software.classification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: INTERLEUKIN-4


Theoretical massNumber of molelcules
Total (without water)14,9891
Polymers14,9891
Non-polymers00
Water0
1
A: INTERLEUKIN-4

A: INTERLEUKIN-4


Theoretical massNumber of molelcules
Total (without water)29,9782
Polymers29,9782
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Unit cell
Length a, b, c (Å)91.800, 91.800, 46.200
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein INTERLEUKIN-4 / Interleukin 4


Mass: 14989.248 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / References: UniProt: P05112

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.25 Å3/Da / Density % sol: 62.11 %
Crystal grow
*PLUS
Temperature: 22 ℃ / Method: vapor diffusion
Details: taken from Cook, W.J. et al (1991). J. Mol. Biol., 218, 675-678.
PH range low: 5.8 / PH range high: 5
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
140 mg/mlprotein1drop
250 %ammonium sulfate1drop
30.05 Msodium cacodylate1drop
450 %ammonium sulfate1reservoir
50.05 Msodium cacodylate1reservoir

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Data collection

Reflection
*PLUS
Highest resolution: 2.33 Å / Num. obs: 8531 / % possible obs: 94.9 % / Num. measured all: 86410 / Rmerge(I) obs: 0.0975

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Processing

Software
NameClassification
X-PLORmodel building
PROLSQrefinement
X-PLORrefinement
X-PLORphasing
RefinementResolution: 2.35→6 Å / σ(F): 0 /
RfactorNum. reflection
Rwork0.232 -
obs0.232 7470
Refinement stepCycle: LAST / Resolution: 2.35→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1047 0 0 0 1047
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.022
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_deg2.4
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_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Refinement
*PLUS
Rfactor obs: 0.232
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal targetDev ideal
X-RAY DIFFRACTIONx_bond_d0.02
X-RAY DIFFRACTIONx_angle_d2.4
X-RAY DIFFRACTIONx_planar_d0.050.061
X-RAY DIFFRACTIONx_plane_restr0.020.016
X-RAY DIFFRACTIONx_chiral_restr0.150.222

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