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- PDB-1iti: THE HIGH RESOLUTION THREE-DIMENSIONAL SOLUTION STRUCTURE OF HUMAN... -

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Entry
Database: PDB / ID: 1iti
TitleTHE HIGH RESOLUTION THREE-DIMENSIONAL SOLUTION STRUCTURE OF HUMAN INTERLEUKIN-4 DETERMINED BY MULTI-DIMENSIONAL HETERONUCLEAR MAGNETIC RESONANCE SPECTROSCOPY
ComponentsINTERLEUKIN-4
KeywordsCYTOKINE / INTERLEUKIN-4
Function / homology
Function and homology information


positive regulation of eosinophil chemotaxis / interleukin-4 receptor binding / positive regulation of isotype switching to IgE isotypes / B cell costimulation / negative regulation of complement-dependent cytotoxicity / negative regulation of macrophage activation / negative regulation of chronic inflammatory response / positive regulation of cellular respiration / regulation of isotype switching / Interleukin-18 signaling ...positive regulation of eosinophil chemotaxis / interleukin-4 receptor binding / positive regulation of isotype switching to IgE isotypes / B cell costimulation / negative regulation of complement-dependent cytotoxicity / negative regulation of macrophage activation / negative regulation of chronic inflammatory response / positive regulation of cellular respiration / regulation of isotype switching / Interleukin-18 signaling / negative regulation of neuroinflammatory response / 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 / neuroinflammatory response / interleukin-4-mediated signaling pathway / macrophage activation / positive regulation of interleukin-13 production / myeloid dendritic cell differentiation / positive regulation of mast cell degranulation / regulation of phosphorylation / positive regulation of mononuclear cell migration / positive regulation of amyloid-beta clearance / 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 myoblast fusion / positive regulation of ATP biosynthetic process / negative regulation of osteoclast differentiation / negative regulation of acute inflammatory response / positive regulation of interleukin-10 production / positive regulation of macroautophagy / negative regulation of tumor necrosis factor production / regulation of immune response / negative regulation of endothelial cell apoptotic process / positive regulation of T cell proliferation / positive regulation of B cell proliferation / positive regulation of tyrosine phosphorylation of STAT protein / extrinsic apoptotic signaling pathway in absence of ligand / positive regulation of defense response to virus by host / T cell activation / cholesterol metabolic process / 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)
MethodSOLUTION NMR
AuthorsClore, G.M. / Powers, B. / Garrett, D.S. / Gronenborn, A.M.
Citation
Journal: Biochemistry / Year: 1993
Title: The high-resolution, three-dimensional solution structure of human interleukin-4 determined by multidimensional heteronuclear magnetic resonance spectroscopy.
Authors: Powers, R. / Garrett, D.S. / March, C.J. / Frieden, E.A. / Gronenborn, A.M. / Clore, G.M.
#1: Journal: Science / Year: 1992
Title: Three-Dimensional Solution Structure of Human Interleukin-4 by Multidimensional Heteronuclear Magnetic Resonance Spectroscopy
Authors: Powers, R. / Garrett, D.S. / March, C.J. / Frieden, E.A. / Gronenborn, A.M. / Clore, G.M.
#2: Journal: Biochemistry / Year: 1992
Title: 1H, 15N, 13C and 13Co Assignments of Human Interleukin-4 Using Three Dimensional Double-and Triple-Resonance Heteronuclear Magnetic Resonance Spectroscopy
Authors: Powers, R. / Garrett, D.S. / March, C.J. / Frieden, E.A. / Gronenborn, A.M. / Clore, G.M.
#3: Journal: Biochemistry / Year: 1992
Title: Determination of the Secondary Structure and Folding Topology of Human Interleukin-4 Using Three-Dimensional Heteronuclear Magnetic Resonance Spectroscopy
Authors: Garrett, D.S. / Powers, R. / Frieden, D.J.March.E.A. / Clore, G.M. / Gronenborn, A.M.
History
DepositionApr 12, 1993Processing site: BNL
Revision 1.0Jul 15, 1993Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 23, 2022Group: Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _struct_ref_seq_dif.details

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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)15,3921
Polymers15,3921
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)31 / -
Representative

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Components

#1: Protein INTERLEUKIN-4


Mass: 15391.601 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: POTENTIAL / References: UniProt: P05112
Sequence detailsTHE NUMBERING SCHEME IN THIS STRUCTURE INCLUDES THE FOUR-RESIDUE SEQUENCE GLU-ALA-GLU-ALA AT THE N- ...THE NUMBERING SCHEME IN THIS STRUCTURE INCLUDES THE FOUR-RESIDUE SEQUENCE GLU-ALA-GLU-ALA AT THE N-TERMINUS OF THE RECOMBINANT PROTEIN WHICH IS NOT PART OF THE NATURAL HUMAN IL-4; THE NATURAL IL-4 SEQUENCE THEREFORE STARTS AT RESIDUE 5. THE TWO POTENTIAL N-LINKED GLYCOSYLATION SITES AT ASN 42 AND ASN 109 IN THE NATURAL SEQUENCE WERE CHANGED TO ASP TO PREVENT HYPERGLYCOSYLATION IN THE YEAST HOST.

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR

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Sample preparation

Crystal grow
*PLUS
Method: other / Details: NMR

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Processing

RefinementSoftware ordinal: 1
Details: DETAILS OF THE STRUCTURE DETERMINATION AND ALL STRUCTURAL STATISTICS ARE GIVEN IN THE REFERENCE LISTED ON THE JRNL RECORDS ABOVE (I.E. AGREEMENT WITH EXPERIMENTAL RESTRAINTS, DEVIATIONS FROM ...Details: DETAILS OF THE STRUCTURE DETERMINATION AND ALL STRUCTURAL STATISTICS ARE GIVEN IN THE REFERENCE LISTED ON THE JRNL RECORDS ABOVE (I.E. AGREEMENT WITH EXPERIMENTAL RESTRAINTS, DEVIATIONS FROM IDEALITY FOR BOND LENGTHS, ANGLES, PLANES AND CHIRALITY, NON-BONDED CONTACTS, ATOMIC RMS DIFFERENCES BETWEEN THE CALCULATED STRUCTURES). THE STRUCTURES ARE BASED ON A TOTAL OF 2973 EXPERIMENTAL NMR RESTRAINTS COMPRISING: 2515 INTERPROTON DISTANCE RESTRAINTS DERIVED FROM NOE MEASUREMENTS; 102 HYDROGEN-BONDING DISTANCE RESTRAINTS FOR 51 HYDROGEN-BONDS IDENTIFIED ON THE BASIS OF THE NOE AND AMIDE PROTON EXCHANGE DATA, AS WELL AS THE INITIAL STRUCTURE CALCULATIONS; AND 130 PHI, 119 PSI, 73 CHI1, 32 CHI2 AND 2 CHI3 TORSION ANGLE RESTRAINTS DERIVED FROM COUPLING CONSTANTS, NOE DATA, AND 13C SECONDARY CHEMICAL SHIFTS. THE METHOD USED TO DETERMINE THE STRUCTURES IS THE HYBRID METRIC MATRIX DISTANCE GEOMETRY-DYNAMICAL SIMULATED ANNEALING METHOD [NILGES, M., CLORE, G.M. & GRONENBORN, A.M., FEBS LETT. 229, 317-324 (1988)]. A TOTAL OF 30 STRUCTURES WERE CALCULATED. THE ATOMIC RMS DISTRIBUTION ABOUT THE MEAN COORDINATE POSITIONS FOR RESIDUES 8 - 129 IS 0.44 (+/-0.03) ANGSTROMS FOR THE BACKBONE ATOMS, 0.83 (+/-0.03) ANGSTROMS FOR ALL ATOMS, AND 0.51 (+/-0.04) ANGSTROMS FOR ALL ATOMS EXCLUDING DISORDERED SIDE CHAINS. THE N- (RESIDUES 1 - 7) AND C- (RESIDUES 130 - 133) TERMINAL RESIDUES ARE DISORDERED. THE COORDINATES OF THE RESTRAINED MINIMIZED STRUCTURE ARE LISTED FIRST AS MODEL 0. THIS (SA)R RESTRAINED MINIMIZED MEAN STRUCTURE WAS DERIVED BY AVERAGING THE COORDINATES OF THE INDIVIDUAL SA STRUCTURES (BEST FITTED TO RESIDUES 8 - 129) AND SUBJECTING THE RESULTING COORDINATES TO RESTRAINED MINIMIZATION. THE QUANTITY PRESENTED IN THE TEMPERATURE FACTOR FIELD (COLUMNS 61 - 66) REPRESENTS THE ATOMIC RMS DEVIATIONS OF THE 30 INDIVIDUAL SA STRUCTURES ABOUT THE MEAN STRUCTURE. RESIDUES 1 - 7 AND 130 - 133 AT THE N- AND C-TERMINI, RESPECTIVELY, ARE DISORDERED.
NMR ensembleConformers submitted total number: 31

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