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- PDB-1poz: SOLUTION STRUCTURE OF THE HYALURONAN BINDING DOMAIN OF HUMAN CD44 -

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Basic information

Entry
Database: PDB / ID: 1poz
TitleSOLUTION STRUCTURE OF THE HYALURONAN BINDING DOMAIN OF HUMAN CD44
ComponentsCD44 antigen
KeywordsCELL ADHESION / HYALURONAN-BINDING DOMAIN / CARBOHYDRATE-BINDING DOMAIN / LINK MODULE / GLYCOPROTEIN
Function / homology
Function and homology information


positive regulation of monocyte aggregation / Hyaluronan degradation / monocyte aggregation / hyaluronic acid binding / macrophage migration inhibitory factor receptor complex / regulation of lamellipodium morphogenesis / hyaluronan catabolic process / positive regulation of heterotypic cell-cell adhesion / cartilage development / wound healing, spreading of cells ...positive regulation of monocyte aggregation / Hyaluronan degradation / monocyte aggregation / hyaluronic acid binding / macrophage migration inhibitory factor receptor complex / regulation of lamellipodium morphogenesis / hyaluronan catabolic process / positive regulation of heterotypic cell-cell adhesion / cartilage development / wound healing, spreading of cells / negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / microvillus / negative regulation of DNA damage response, signal transduction by p53 class mediator / lamellipodium membrane / Integrin cell surface interactions / collagen binding / cellular response to fibroblast growth factor stimulus / Degradation of the extracellular matrix / secretory granule membrane / T cell activation / cell-matrix adhesion / Cell surface interactions at the vascular wall / cell projection / cell-cell adhesion / cytokine-mediated signaling pathway / Interferon gamma signaling / transmembrane signaling receptor activity / cell migration / basolateral plasma membrane / positive regulation of ERK1 and ERK2 cascade / cell adhesion / apical plasma membrane / inflammatory response / focal adhesion / Neutrophil degranulation / negative regulation of apoptotic process / cell surface / Golgi apparatus / extracellular exosome / plasma membrane / cytosol
Similarity search - Function
CD44 antigen / CD44 antigen-like / Link domain signature. / Link domain / Extracellular link domain / Link domain profile. / Link (Hyaluronan-binding) / C-type lectin-like/link domain superfamily / C-type lectin fold
Similarity search - Domain/homology
CD44 antigen / CD44 antigen
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / torsion angle dynamics simulated annealing refinement by molecular dynamics
AuthorsTeriete, 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
DepositionJun 16, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 16, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 2.0Oct 27, 2021Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Experimental preparation
Category: atom_site / database_2 ...atom_site / database_2 / diffrn / diffrn_radiation / diffrn_radiation_wavelength / pdbx_nmr_exptl_sample / pdbx_nmr_sample_details / pdbx_nmr_software / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _atom_site.occupancy / _database_2.pdbx_DOI ..._atom_site.occupancy / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_sample_details.contents / _pdbx_nmr_sample_details.label / _pdbx_nmr_sample_details.solvent_system / _pdbx_nmr_sample_details.type / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.manufacturer / _pdbx_nmr_spectrometer.model
Revision 2.1Oct 30, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

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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)17,6011
Polymers17,6011
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 500structures with the least restraint violations,structures with the lowest energy,target function
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: 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
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 15N-separated NOESY
1242D NOESY
1352D NOESY
1442D TOCSY
152HMQC-J
161CBCA(CO)NH
173NH-Exchange HSQC

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
solution11 mM [U-13C; U-15N] protein, 95% H2O/5% D2Osample_195% H2O/5% D2O
solution21 mM [U-15N] protein, 95% H2O/5% D2Osample_295% H2O/5% D2O
solution31 mM [U-15N] protein, 100% D2Osample_3100% D2O
solution41 mM protein, 95% H2O/5% D2Osample_495% H2O/5% D2O
solution51 mM protein, 100% D2Osample_5100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mMprotein[U-13C; U-15N]1
1 mMprotein[U-15N]2
1 mMprotein[U-15N]3
1 mMproteinnatural abundance4
1 mMproteinnatural abundance5
Sample conditionsIonic strength: <5mM / pH: 6.5 / Pressure: ambient / Temperature: 298 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
GE OMEGAGEOMEGA7501
GE OMEGAGEOMEGA6002
GE OMEGAGEOMEGA5003

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Processing

NMR software
NameVersionDeveloperClassification
CNS1.1Brunger, A.T.structure solution
Felix2.3MSI, San Diegoprocessing
SOPHIE1Pickford, A.R.structure solution
Sparky2Goddard, T.D.data analysis
XEASY3.13Xia, Tdata analysis
SOPHIE1Pickford, A.R.refinement
RefinementMethod: 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 representativeSelection criteria: lowest energy
NMR ensembleConformer 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

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