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- PDB-1bbn: THREE-DIMENSIONAL SOLUTION STRUCTURE OF HUMAN INTERLEUKIN-4 BY MU... -

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Entry
Database: PDB / ID: 1bbn
TitleTHREE-DIMENSIONAL SOLUTION STRUCTURE OF HUMAN INTERLEUKIN-4 BY MULTI-DIMENSIONAL HETERONUCLEAR MAGNETIC RESONANCE SPECTROSCOPY
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 / myeloid dendritic cell differentiation / positive regulation of amyloid-beta clearance / regulation of phosphorylation / positive regulation of MHC class II biosynthetic process / negative regulation of cellular response to transforming growth factor beta stimulus / type 2 immune response / positive regulation of T cell differentiation / positive regulation of ATP biosynthetic process / negative regulation of osteoclast differentiation / 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 / positive regulation of T cell proliferation / positive regulation of B cell proliferation / B cell differentiation / cholesterol metabolic process / T cell activation / 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)
MethodSOLUTION NMR
AuthorsClore, G.M. / Powers, B. / Garrett, D.S. / Gronenborn, A.M.
Citation
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.
#1: 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.
#2: 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. / March, C.J. / Frieden, E.A. / Clore, G.M. / Gronenborn, A.M.
History
DepositionMay 1, 1992Processing site: BNL
Revision 1.0Oct 31, 1993Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Sep 5, 2012Group: Database references
Revision 1.4Jun 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 / 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
Revision 1.5Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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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)1 / -
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
Has protein modificationY
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. IN ADDITION, THE TWO POTENTIAL N-LINKED GLYCOSYLATION SITES AT ASN 42 AND ASN 109 HAVE BEEN CHANGED TO ASP BY SITE DIRECTED MUTAGENESIS 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: THE STRUCTURES ARE BASED ON 823 INTERPROTON DISTANCE RESTRAINTS FROM NOE MEASUREMENTS; 98 HYDROGEN-BONDING DISTANCE RESTRAINTS FOR 49 HYDROGEN-BONDS IDENTIFIED ON THE BASIS OF THE NOE AND ...Details: THE STRUCTURES ARE BASED ON 823 INTERPROTON DISTANCE RESTRAINTS FROM NOE MEASUREMENTS; 98 HYDROGEN-BONDING DISTANCE RESTRAINTS FOR 49 HYDROGEN-BONDS IDENTIFIED ON THE BASIS OF THE NOE AND AMIDE PROTON EXCHANGE DATA, AS WELL AS THE INITIAL STRUCTURE CALCULATIONS; AND 101 PHI AND 82 PSI BACKBONE 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 (M. NILGES, G. M. CLORE, AND A. M. GRONENBORN FEBS LETT. 229, 317-324 (1988)). DETAILS OF THE STRUCTURE DETERMINATION AND ALL STRUCTURAL STATISTICS ARE GIVEN IN REFERENCE 1 (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. RESIDUES 1 - 6 AND 132 - 133 AT THE N- AND C-TERMINI ARE DISORDERED. THE RESTRAINED MINIMIZED AVERAGE STRUCTURE IS PRESENTED IN THIS ENTRY. THIS WAS OBTAINED BY AVERAGING THE COORDINATES OF THE INDIVIDUAL STRUCTURES AND SUBJECTING THE RESULTING COORDINATES TO RESTRAINED MINIMIZATION. MODELS 1 - 22, PRESENTED IN PROTEIN DATA BANK ENTRY 1BCN, REPRESENT THE INDIVIDUAL MODELS. THE (SA)R RESTRAINED MINIMIZED MEAN STRUCTURE WAS DERIVED BY AVERAGING THE COORDINATES OF THE INDIVIDUAL SA STRUCTURES (BEST FITTED TO RESIDUES 7 - 131), AND SUBJECTING THE RESULTING COORDINATES TO RESTRAINED MINIMIZATION. THE QUANTITY PRESENTED IN COLUMNS 61 - 66 IN THIS ENTRY REPRESENTS THE ATOMIC RMS DEVIATIONS OF THE 22 INDIVIDUAL SA STRUCTURES ABOUT THE MEAN STRUCTURE.
NMR ensembleConformers submitted total number: 1

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