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- PDB-2jcp: The hyaluronan binding domain of murine CD44 -

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Basic information

Entry
Database: PDB / ID: 2jcp
TitleThe hyaluronan binding domain of murine CD44
ComponentsCD44 ANTIGEN
KeywordsSUGAR BINDING PROTEIN / SUGAR-BINDING PROTEIN / HYAURONAN / LINK-DOMAIN / PROTEOGLYCAN / POLYMORPHISM / BLOOD GROUP ANTIGEN / ALTERNATIVE SPLICING / LECTIN / ANTIGEN / MEMBRANE / RECEPTOR / SULFATION / GLYCOPROTEIN / C-TYPE LECTIN / CELL ADHESION / EXTRACELLULAR MATRIX / PYRROLIDONE CARBOXYLIC ACID / TRANSMEMBRANE / PHOSPHORYLATION
Function / homology
Function and homology information


Hyaluronan uptake and degradation / positive regulation of monocyte aggregation / hyaluronic acid binding / macrophage fusion / macrophage migration inhibitory factor receptor complex / Degradation of the extracellular matrix / negative regulation of regulatory T cell differentiation / regulation of lamellipodium morphogenesis / Integrin cell surface interactions / Cell surface interactions at the vascular wall ...Hyaluronan uptake and degradation / positive regulation of monocyte aggregation / hyaluronic acid binding / macrophage fusion / macrophage migration inhibitory factor receptor complex / Degradation of the extracellular matrix / negative regulation of regulatory T cell differentiation / regulation of lamellipodium morphogenesis / Integrin cell surface interactions / Cell surface interactions at the vascular wall / hyaluronan catabolic process / positive regulation of adaptive immune response / monocyte aggregation / wound healing involved in inflammatory response / branching involved in prostate gland morphogenesis / type II transforming growth factor beta receptor binding / negative regulation of mature B cell apoptotic process / negative regulation of CD4-positive, alpha-beta T cell proliferation / positive regulation of neutrophil apoptotic process / channel regulator activity / cellular response to fibroblast growth factor stimulus / cargo receptor activity / positive regulation of heterotypic cell-cell adhesion / wound healing, spreading of cells / branching involved in ureteric bud morphogenesis / epidermal growth factor receptor binding / 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 / receptor-mediated endocytosis / Neutrophil degranulation / T cell activation / cell projection / regulation of cell growth / phosphoprotein binding / negative regulation of inflammatory response / Wnt signaling pathway / cytokine-mediated signaling pathway / neuron projection development / positive regulation of peptidyl-tyrosine phosphorylation / cell migration / transmembrane signaling receptor activity / positive regulation of peptidyl-serine phosphorylation / basolateral plasma membrane / positive regulation of ERK1 and ERK2 cascade / cell adhesion / inflammatory response / membrane raft / apical plasma membrane / external side of plasma membrane / positive regulation of gene expression / negative regulation of apoptotic process / protein kinase binding / Golgi apparatus / cell surface / protein-containing complex / extracellular region / 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 speciesMUS MUSCULUS (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 Å
AuthorsBanerji, S. / Wright, A.J. / Noble, M.E.M. / Mahoney, D.J. / Campbell, I.D. / Day, A.J. / Jackson, D.G.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2008
Title: Structures of the Cd44-Hyaluronan Complex Provide Insight Into a Fundamental Carbohydrate-Protein Interaction.
Authors: Banerji, S. / Wright, A.J. / Noble, M.E.M. / Mahoney, D.J. / Campbell, I.D. / Day, A.J. / Jackson, D.G.
History
DepositionJan 3, 2007Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 30, 2007Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 8, 2019Group: Data collection / Experimental preparation / Other
Category: exptl_crystal_grow / pdbx_database_proc / pdbx_database_status
Item: _exptl_crystal_grow.method / _pdbx_database_status.recvd_author_approval
Revision 1.4Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf
Revision 1.5Feb 7, 2024Group: Structure summary / Category: struct_keywords / Item: _struct_keywords.text

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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)17,1431
Polymers17,1431
Non-polymers00
Water3,207178
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)30.726, 82.097, 32.336
Angle α, β, γ (deg.)90.00, 117.92, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein CD44 ANTIGEN / PHAGOCYTIC GLYCOPROTEIN 1 / PGP-1 / HUTCH-I / EXTRACELLULAR MATRIX RECEPTOR III / GP90 LYMPHOCYTE ...PHAGOCYTIC GLYCOPROTEIN 1 / PGP-1 / HUTCH-I / EXTRACELLULAR MATRIX RECEPTOR III / GP90 LYMPHOCYTE HOMING/ADHESION RECEPTOR / HERMES ANTIGEN / HYALURONATE RECEPTOR / LYMPHOCYTE ANTIGEN LY-24 / CD44


Mass: 17143.072 Da / Num. of mol.: 1 / Fragment: HYALURONAN BINDING DOMAIN, RESIDUES 23-174
Source method: isolated from a genetically manipulated source
Details: ENCODED RESIDUES 25-174, EQUIVALENT TO RESIDUES 1-151 OF THE MATURE PROTEIN, WITH ADDITIONAL RESIDUES M, N ADDED AT THE N-TERMINUS
Source: (gene. exp.) MUS MUSCULUS (house mouse) / Plasmid: PET19B / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / Variant (production host): DE3 PLYSS / References: UniProt: P15379
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 178 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.12 Å3/Da / Density % sol: 42 %
Crystal growMethod: vapor diffusion, sitting drop / pH: 6.5
Details: DROPLETS COMPRISING 200NL CD4425-174 (AT A CONCENTRATION OF 0.5MM) MIXED WITH 200NL WELL SOLUTION WERE DISPENSED AS SITTING DROPS AND UNDERWENT VAPOR DIFFUSION WITH A WELL SOLUTION OF 30% ...Details: DROPLETS COMPRISING 200NL CD4425-174 (AT A CONCENTRATION OF 0.5MM) MIXED WITH 200NL WELL SOLUTION WERE DISPENSED AS SITTING DROPS AND UNDERWENT VAPOR DIFFUSION WITH A WELL SOLUTION OF 30% PEG MONOMETHYLETHER 5000, AND 200 MM (NH4)2SO4 IN 100 MM MES BUFFER PH 6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933
DetectorType: ADSC CCD / Detector: CCD / Date: May 9, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 1.3→41.05 Å / Num. obs: 34562 / % possible obs: 99.5 % / Observed criterion σ(I): 0 / Redundancy: 2.6 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 6.4
Reflection shellResolution: 1.3→1.37 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.2 / Mean I/σ(I) obs: 3.2 / % possible all: 99.2

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1UUH

1uuh


Resolution: 1.3→41.17 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.946 / SU B: 1.397 / SU ML: 0.028 / Cross valid method: THROUGHOUT / ESU R: 0.055 / ESU R Free: 0.053 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. RESIDUE H23, A MET IN THIS CONSTRUCT, IS MISSING. RESIDUE Q24, AN ASN IN THIS CONSTRUCT, IS POORLY VISIBLE AND IS BUILT AS A Q
RfactorNum. reflection% reflectionSelection details
Rfree0.191 1736 5 %RANDOM
Rwork0.157 ---
obs0.158 32795 99.4 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 11.82 Å2
Baniso -1Baniso -2Baniso -3
1--0.1 Å20 Å2-0.1 Å2
2--0.03 Å20 Å2
3----0.038 Å2
Refinement stepCycle: LAST / Resolution: 1.3→41.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1172 0 0 178 1350
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0211284
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2621.9321762
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8185167
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.0224.28663
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.80215204
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.975158
X-RAY DIFFRACTIONr_chiral_restr0.0810.2194
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021020
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1960.2615
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3130.2919
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2740.2144
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1970.247
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0860.214
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.041.5814
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.60321317
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.4053517
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.3054.5445
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.3→1.33 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.166 137
Rwork0.145 2371

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