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- PDB-1rcb: CRYSTAL STRUCTURE OF HUMAN RECOMBINANT INTERLEUKIN-4 AT 2.25 ANGS... -

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Basic information

Entry
Database: PDB / ID: 1rcb
TitleCRYSTAL STRUCTURE OF HUMAN RECOMBINANT INTERLEUKIN-4 AT 2.25 ANGSTROMS RESOLUTION
ComponentsINTERLEUKIN-4
KeywordsCYTOKINE
Function / homology
Function and homology information


interleukin-4 receptor binding / positive regulation of isotype switching to IgE isotypes / negative regulation of complement-dependent cytotoxicity / positive regulation of cellular respiration / Interleukin-18 signaling / regulation of isotype switching / negative regulation of neuroinflammatory response / negative regulation of epithelial cell migration / positive regulation of T-helper 2 cell cytokine production / dendritic cell differentiation ...interleukin-4 receptor binding / positive regulation of isotype switching to IgE isotypes / negative regulation of complement-dependent cytotoxicity / positive regulation of cellular respiration / Interleukin-18 signaling / regulation of isotype switching / negative regulation of neuroinflammatory response / negative regulation of epithelial cell migration / positive regulation of T-helper 2 cell cytokine production / dendritic cell differentiation / interleukin-4-mediated signaling pathway / neuroinflammatory response / positive regulation of isotype switching to IgG isotypes / positive regulation of interleukin-13 production / macrophage activation / positive regulation of amyloid-beta clearance / myeloid dendritic cell differentiation / positive regulation of MHC class II biosynthetic process / type 2 immune response / negative regulation of cellular response to transforming growth factor beta stimulus / positive regulation of T cell differentiation / negative regulation of osteoclast differentiation / positive regulation of ATP biosynthetic process / positive regulation of interleukin-10 production / positive regulation of macroautophagy / negative regulation of tumor necrosis factor production / cell surface receptor signaling pathway via JAK-STAT / regulation of immune response / negative regulation of endothelial cell apoptotic process / cholesterol metabolic process / positive regulation of B cell proliferation / positive regulation of T cell proliferation / T cell activation / B cell differentiation / cytokine activity / growth factor activity / positive regulation of receptor-mediated endocytosis / negative regulation of inflammatory response / positive regulation of cold-induced thermogenesis / Interleukin-4 and Interleukin-13 signaling / immune response / positive regulation of cell migration / 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: 2.25 Å
AuthorsWlodawer, A. / Pavlovsky, A. / Gustchina, A.
CitationJournal: FEBS Lett. / Year: 1992
Title: Crystal structure of human recombinant interleukin-4 at 2.25 A resolution.
Authors: Wlodawer, A. / Pavlovsky, A. / Gustchina, A.
History
DepositionAug 26, 1992Processing site: BNL
Revision 1.0Oct 31, 1993Provider: repository / Type: Initial release
Revision 1.1Mar 21, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: 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
Revision 1.4Oct 23, 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-4


Theoretical massNumber of molelcules
Total (without water)14,9891
Polymers14,9891
Non-polymers00
Water59433
1
A: INTERLEUKIN-4

A: INTERLEUKIN-4


Theoretical massNumber of molelcules
Total (without water)29,9782
Polymers29,9782
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Unit cell
Length a, b, c (Å)91.800, 91.800, 46.400
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Atom site foot note1: THE ELECTRON DENSITY FOR RESIDUES 38 - 40 IS POOR, AND THE TRACING IN THAT REGION IS UNCERTAIN.

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Components

#1: Protein 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
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 33 / 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: 3.26 Å3/Da / Density % sol: 62.28 %
Crystal grow
*PLUS
pH: 6 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
14 mg/mlprotein1drop
250 mMK-phosphate1drop
360-63 %ammonium sulfate1reservoir
450 mMK-phosphate1reservoir

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 2.23 Å / Num. obs: 8951 / % possible obs: 90.7 % / Observed criterion σ(F): 2 / Rmerge(I) obs: 0.06

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Processing

SoftwareName: PROLSQ / Classification: refinement
RefinementResolution: 2.25→10 Å
Details: THE ELECTRON DENSITY FOR RESIDUES 38 - 40 IS POOR, AND THE TRACING IN THAT REGION IS UNCERTAIN.
RfactorNum. reflection
obs0.218 8085
Refinement stepCycle: LAST / Resolution: 2.25→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1048 0 0 33 1081
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.020.02
X-RAY DIFFRACTIONp_angle_d0.0560.03
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0820.05
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it1.4681.5
X-RAY DIFFRACTIONp_mcangle_it3.3292
X-RAY DIFFRACTIONp_scbond_it3.3782
X-RAY DIFFRACTIONp_scangle_it5.5393
X-RAY DIFFRACTIONp_plane_restr0.0160.02
X-RAY DIFFRACTIONp_chiral_restr0.230.15
X-RAY DIFFRACTIONp_singtor_nbd0.2270.3
X-RAY DIFFRACTIONp_multtor_nbd0.3050.3
X-RAY DIFFRACTIONp_xhyhbond_nbd0.2310.3
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor5.17.5
X-RAY DIFFRACTIONp_staggered_tor2510
X-RAY DIFFRACTIONp_orthonormal_tor3710
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor
Refinement
*PLUS
Highest resolution: 2.25 Å / Lowest resolution: 10 Å / Num. reflection obs: 8085 / Rfactor obs: 0.218
Solvent computation
*PLUS
Displacement parameters
*PLUS

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