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Yorodumi- PDB-1poz: SOLUTION STRUCTURE OF THE HYALURONAN BINDING DOMAIN OF HUMAN CD44 -
+Open data
-Basic information
Entry | Database: PDB / ID: 1poz | |||||||||
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Title | SOLUTION STRUCTURE OF THE HYALURONAN BINDING DOMAIN OF HUMAN CD44 | |||||||||
Components | CD44 antigen | |||||||||
Keywords | CELL ADHESION / HYALURONAN-BINDING DOMAIN / CARBOHYDRATE-BINDING DOMAIN / LINK MODULE / GLYCOPROTEIN | |||||||||
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 / neutrophil degranulation / regulation of lamellipodium morphogenesis / hyaluronan catabolic process / cellular response to fibroblast growth factor stimulus / positive regulation of heterotypic cell-cell adhesion ...positive regulation of monocyte aggregation / Hyaluronan uptake and degradation / hyaluronic acid binding / monocyte aggregation / macrophage migration inhibitory factor receptor complex / neutrophil degranulation / 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 / leukocyte migration / negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / plasma membrane => GO:0005886 / negative regulation of DNA damage response, signal transduction by p53 class mediator / lamellipodium membrane / microvillus / extracellular matrix disassembly / Integrin cell surface interactions / type II interferon-mediated signaling pathway / collagen binding / T cell activation / Degradation of the extracellular matrix / extracellular matrix organization / 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 | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | SOLUTION NMR / torsion angle dynamics simulated annealing refinement by molecular dynamics | |||||||||
Authors | Teriete, P. / Banerji, S. / Blundell, C.D. / Kahmann, J.D. / Pickford, A.R. / Wright, A.J. / Campbell, I.D. / Jackson, D.G. / Day, A.J. | |||||||||
Citation | Journal: Mol.Cell / Year: 2004 Title: Structure of the Regulatory Hyaluronan Binding Domain in the Inflammatory Leukocyte Homing Receptor CD44. Authors: Teriete, P. / Banerji, S. / Noble, M. / Blundell, C.D. / Wright, A.J. / Pickford, A.R. / Lowe, E. / Mahoney, D.J. / Tammi, M.I. / Kahmann, J.D. / Campbell, I.D. / Day, A.J. / Jackson, D.G. #1: Journal: Cell(Cambridge,Mass.) / Year: 1989 Title: A lymphocyte molecule implicated in lymph node homing is a member of the cartilage link protein family. Authors: Stamenkovic, I. / Amiot, M. / Pesando, J.M. / Seed, B. #2: Journal: Cell(Cambridge,Mass.) / Year: 1989 Title: A human lymphocyte homing receptor, the hermes antigen, is related to cartilage proteoglycan core and link proteins. Authors: A Goldstien, L. / Zhou, D.F.H. / Picker, L.J. / Minty, C.N. / Bargatze, R.F. / Din, J.F. / Butcher, E.C. #3: Journal: Cell(Cambridge,Mass.) / Year: 1990 Title: CD44 is the principal cell surface receptor for hyaluronate. Authors: Aruffo, A. / Stamenkovic, I. / Melnick, M. / Underhill, C.B. / Seed, B. #4: Journal: J.Cell Biol. / Year: 1993 Title: Identification of hyaluronic acid binding sites in the extracellular domain of CD44. Authors: Peach, R.J. / Hollenbaugh, D. / Stamenkovic, I. / Aruffo, A. #5: Journal: Cell(Cambridge,Mass.) / Year: 1996 Title: Solution Structure of the Link Module: A Hyaluronan-Binding Domain Involved in Extracellular Matrix Stability and Cell Migration Authors: Kohda, D. / Morton, C.J. / Parkar, A.A. / Hatanaka, H. / Inagaki, F.M. / Campbell, I.D. / Day, A.J. #6: Journal: J.Biol.Chem. / Year: 1998 Title: Identification of CD44 residues important for hyaluronan binding and delineation of the binding site Authors: Bajorath, J. / Greenfield, B. / Munro, S.B. / Day, A.J. / Aruffo, A. #7: Journal: Cancer Res. / Year: 1998 Title: Site-specific de-N-glycosylation of CD44 can activate hyaluronan binding, and CD44 activation states show distinct threshold densities for hyaluronan binding Authors: English, N.M. / Lesley, J.F. / Hyman, R. #8: Journal: Protein Expr.Purif. / Year: 1998 Title: Characterization of a functional hyaluronan-binding domain from the human CD44 molecule expressed in Escherichia coli Authors: Banerji, S. / Day, A.J. / Kahmann, J.D. / Jackson, D.G. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1poz.cif.gz | 935.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1poz.ent.gz | 804.3 KB | Display | PDB format |
PDBx/mmJSON format | 1poz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1poz_validation.pdf.gz | 346.9 KB | Display | wwPDB validaton report |
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Full document | 1poz_full_validation.pdf.gz | 641.9 KB | Display | |
Data in XML | 1poz_validation.xml.gz | 107 KB | Display | |
Data in CIF | 1poz_validation.cif.gz | 140.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/po/1poz ftp://data.pdbj.org/pub/pdb/validation_reports/po/1poz | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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NMR ensembles |
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-Components
#1: Protein | Mass: 17601.486 Da / Num. of mol.: 1 / Fragment: HYALURONAN BINDING DOMAIN Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CD44 / Plasmid: pET19b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: Q16208, UniProt: P16070*PLUS |
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-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||||||||||||||||||
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NMR experiment |
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-Sample preparation
Details |
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Sample |
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Sample conditions | Ionic strength: <5mM / pH: 6.5 / Pressure: ambient / Temperature: 298 K | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: other / Details: NMR |
-NMR measurement
NMR spectrometer |
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-Processing
NMR software |
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Refinement | Method: torsion angle dynamics simulated annealing refinement by molecular dynamics Software ordinal: 1 Details: The structures are calculated from 2271 restraints, 2168 are NOE based, 47 dihedral constraints and 56 distance restraints from hydrogen bonds | ||||||||||||||||||||||||||||
NMR representative | Selection criteria: lowest energy | ||||||||||||||||||||||||||||
NMR ensemble | Conformer selection criteria: structures with the least restraint violations,structures with the lowest energy,target function Conformers calculated total number: 500 / Conformers submitted total number: 20 |