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- PDB-2i83: hyaluronan-binding domain of CD44 in its ligand-bound form -

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Basic information

Entry
Database: PDB / ID: 2i83
Titlehyaluronan-binding domain of CD44 in its ligand-bound form
ComponentsCD44 antigen
KeywordsCELL ADHESION / Link module
Function / homology
Function and homology information


positive regulation of monocyte aggregation / Hyaluronan uptake and degradation / hyaluronic acid binding / monocyte aggregation / macrophage migration inhibitory factor receptor complex / regulation of lamellipodium morphogenesis / hyaluronan catabolic process / cellular response to fibroblast growth factor stimulus / positive regulation of heterotypic cell-cell adhesion / cartilage development ...positive regulation of monocyte aggregation / Hyaluronan uptake and degradation / hyaluronic acid binding / monocyte aggregation / macrophage migration inhibitory factor receptor complex / regulation of lamellipodium morphogenesis / hyaluronan catabolic process / cellular response to fibroblast growth factor stimulus / positive regulation of heterotypic cell-cell adhesion / cartilage development / wound healing, spreading of cells / cytokine receptor activity / negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / negative regulation of DNA damage response, signal transduction by p53 class mediator / microvillus / lamellipodium membrane / Integrin cell surface interactions / collagen binding / T cell activation / Degradation of the extracellular matrix / cell-matrix adhesion / secretory granule membrane / cell projection / Cell surface interactions at the vascular wall / negative regulation of cysteine-type endopeptidase activity involved in apoptotic process / cell-cell adhesion / transmembrane signaling receptor activity / positive regulation of peptidyl-tyrosine phosphorylation / Interferon gamma signaling / cell migration / positive regulation of peptidyl-serine phosphorylation / basolateral plasma membrane / positive regulation of ERK1 and ERK2 cascade / cell adhesion / inflammatory response / apical plasma membrane / focal adhesion / Neutrophil degranulation / negative regulation of apoptotic process / Golgi apparatus / cell surface / extracellular exosome / plasma membrane / cytosol
Similarity search - Function
CD44 antigen / CD44 antigen-like / Link domain / Extracellular link domain / Link domain signature. / Link domain profile. / Link (Hyaluronan-binding) / C-type lectin-like/link domain superfamily / C-type lectin fold
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsTakeda, M. / Ogino, S. / Umemoto, R. / Sakakura, M. / Kajiwara, M. / Sugahara, K.N. / Hayasaka, H. / Miyasaka, M. / Terasawa, H. / Shimada, I.
CitationJournal: J.Biol.Chem. / Year: 2006
Title: Ligand-induced Structural Changes of the CD44 Hyaluronan-binding Domain Revealed by NMR
Authors: Takeda, M. / Ogino, S. / Umemoto, R. / Sakakura, M. / Kajiwara, M. / Sugahara, K.N. / Hayasaka, H. / Miyasaka, M. / Terasawa, H. / Shimada, I.
History
DepositionSep 1, 2006Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Nov 21, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 9, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_spectrometer ...database_2 / pdbx_nmr_spectrometer / 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_nmr_spectrometer.model / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CD44 antigen


Theoretical massNumber of molelcules
Total (without water)17,7331
Polymers17,7331
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 / 200structures with the least restraint violations
RepresentativeModel #1lowest energy

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Components

#1: Protein CD44 antigen / Phagocytic glycoprotein I / PGP-1 / HUTCH-I / Extracellular matrix receptor-III / ECMR-III / GP90 ...Phagocytic glycoprotein I / PGP-1 / HUTCH-I / Extracellular matrix receptor-III / ECMR-III / GP90 lymphocyte homing/adhesion receptor / Hermes antigen / Hyaluronate receptor / Heparan sulfate proteoglycan / Epican / CDw44


Mass: 17732.686 Da / Num. of mol.: 1 / Fragment: Hyaluronan binding domain residue 21-178
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pET11 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P16070

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111NOESY
1223D 13C-separated NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
12.0mM CD44HABD U-15N,13C; 6.0mM hyaluronan; 50mM phosphate buffer; 150mM NaCl; 90% H2O, 10% D2O90% H2O/10% D2O
22.0mM CD44HABD U-15N,13C; 6.0mM hyaluronan; 50mM phosphate buffer; 150mM NaCl; 100% D2O100% D2O
Sample conditionsIonic strength: 150mM NaCl / pH: 6.7 / Pressure: AMBIENT / Temperature: 310 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCEBrukerAVANCE6001
Bruker AVANCEBrukerAVANCE8002

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Processing

NMR software
NameVersionDeveloperClassification
CYANA2.1P.GUNTERT ET AL.refinement
CYANA2structure solution
RefinementMethod: torsion angle dynamics / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 200 / Conformers submitted total number: 20

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