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- PDB-1t8c: Structure of the C-type lectin domain of CD23 -

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Basic information

Entry
Database: PDB / ID: 1t8c
TitleStructure of the C-type lectin domain of CD23
ComponentsLow affinity immunoglobulin epsilon Fc receptor
KeywordsIMMUNE SYSTEM / c-type lectin / fcerII / fc receptor / IgE
Function / homology
Function and homology information


low-affinity IgE receptor activity / B cell antigen processing and presentation / Fc receptor-mediated immune complex endocytosis / positive regulation of humoral immune response mediated by circulating immunoglobulin / NOTCH2 intracellular domain regulates transcription / macrophage activation / IgE binding / positive regulation of killing of cells of another organism / positive regulation of nitric-oxide synthase biosynthetic process / Interleukin-10 signaling ...low-affinity IgE receptor activity / B cell antigen processing and presentation / Fc receptor-mediated immune complex endocytosis / positive regulation of humoral immune response mediated by circulating immunoglobulin / NOTCH2 intracellular domain regulates transcription / macrophage activation / IgE binding / positive regulation of killing of cells of another organism / positive regulation of nitric-oxide synthase biosynthetic process / Interleukin-10 signaling / positive regulation of nitric-oxide synthase activity / integrin binding / carbohydrate binding / Interleukin-4 and Interleukin-13 signaling / immune response / external side of plasma membrane / extracellular exosome / metal ion binding / plasma membrane
Similarity search - Function
CD209-like, C-type lectin-like domain / C-type lectin, conserved site / C-type lectin domain signature. / Mannose-Binding Protein A; Chain A / Mannose-Binding Protein A, subunit A / Lectin C-type domain / C-type lectin domain profile. / C-type lectin-like / C-type lectin (CTL) or carbohydrate-recognition domain (CRD) / C-type lectin-like/link domain superfamily ...CD209-like, C-type lectin-like domain / C-type lectin, conserved site / C-type lectin domain signature. / Mannose-Binding Protein A; Chain A / Mannose-Binding Protein A, subunit A / Lectin C-type domain / C-type lectin domain profile. / C-type lectin-like / C-type lectin (CTL) or carbohydrate-recognition domain (CRD) / C-type lectin-like/link domain superfamily / C-type lectin fold / Roll / Alpha Beta
Similarity search - Domain/homology
Low affinity immunoglobulin epsilon Fc receptor
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / STANDARD RECOMMENDED PROTOCOL
AuthorsHibbert, R.G. / Teriete, P. / Grundy, G.J. / Sutton, B.J. / Gould, H.J. / McDonnell, J.M.
CitationJournal: J.Exp.Med. / Year: 2005
Title: The structure of human CD23 and its interactions with IgE and CD21
Authors: Hibbert, R.G. / Teriete, P. / Grundy, G.J. / Beavil, R.L. / Reljic, R. / Holers, V.M. / Hannan, J.P. / Sutton, B.J. / Gould, H.J. / McDonnell, J.M.
History
DepositionMay 12, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 26, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 2, 2022Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Low affinity immunoglobulin epsilon Fc receptor


Theoretical massNumber of molelcules
Total (without water)16,1651
Polymers16,1651
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)20 / 100structures with the lowest energy
RepresentativeModel #1

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Components

#1: Protein Low affinity immunoglobulin epsilon Fc receptor / Lymphocyte IgE receptor / Fc-epsilon-RII / CD23 / Immunoglobulin E-binding factor


Mass: 16164.986 Da / Num. of mol.: 1 / Fragment: derCD23
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FCER2, IGEBF / Plasmid: pET5a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P06734

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
11115N EDITED NOESY-HSQC
12113C EDITED NOESY-HSQC

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Sample preparation

DetailsContents: 25mM Tris, 125mM NaCl, 4mM CaCl2, 0.02% NaN3, 2mM soluble CD23
Sample conditionsIonic strength: 162 mM / pH: 6.8 / Pressure: 1 atm / Temperature: 308 K

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
GE/HOMEBUILT OMEGAGE/HOMEBUILTOMEGA5001
GE/HOMEBUILT OMEGAGE/HOMEBUILTOMEGA6002
GE/HOMEBUILT OMEGAGE/HOMEBUILTOMEGA7503

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Processing

NMR software
NameVersionDeveloperClassification
CNS1.1A.T.BRUNGER, P.D.ADAMS, G.M.CLORE, W.L.Delano, P.Gros, R.W.Grosse-Kunstleve, J.-S.Jiang, J.Kuszewski, M.Nilges, N.S.Pannu, R.J.Read, L.M.Rice, T.Simonson, G.L.Warrenrefinement
CNS1.1structure solution
RefinementMethod: STANDARD RECOMMENDED PROTOCOL / Software ordinal: 1
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20

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