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- PDB-2jcq: The hyaluronan binding domain of murine CD44 in a Type A complex ... -

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Basic information

Entry
Database: PDB / ID: 2jcq
TitleThe hyaluronan binding domain of murine CD44 in a Type A complex with an HA 8-mer
ComponentsCD44 ANTIGEN
KeywordsSUGAR BINDING PROTEIN / SUGAR-BINDING PROTEIN / HYAURONAN / LINK-DOMAIN / PROTEOGLYCAN / BLOOD GROUP ANTIGEN / LECTIN / ANTIGEN / MEMBRANE / RECEPTOR / SULFATION / GLYCOPROTEIN / C-TYPE LECTIN / CELL ADHESION / EXTRACELLULAR MATRIX / PYRROLIDONE CARBOXYLIC ACID / TRANSMEMBRANE / SUGAR- BINDING / PHOSPHORYLATION
Function / homologyExtracellular link domain / CD44 antigen / Link domain profile. / Link domain signature. / Link domain / C-type lectin fold / C-type lectin-like/link domain superfamily / macrophage fusion / positive regulation of monocyte aggregation / hyaluronic acid binding ...Extracellular link domain / CD44 antigen / Link domain profile. / Link domain signature. / Link domain / C-type lectin fold / C-type lectin-like/link domain superfamily / macrophage fusion / positive regulation of monocyte aggregation / hyaluronic acid binding / negative regulation of regulatory T cell differentiation / macrophage migration inhibitory factor receptor complex / positive regulation of adaptive immune response / monocyte aggregation / regulation of lamellipodium morphogenesis / branching involved in prostate gland morphogenesis / wound healing involved in inflammatory response / hyaluronan catabolic process / positive regulation of neutrophil apoptotic process / type II transforming growth factor beta receptor binding / negative regulation of CD4-positive, alpha-beta T cell proliferation / negative regulation of mature B cell apoptotic process / positive regulation of kinase activity / wound healing, spreading of cells / positive regulation of heterotypic cell-cell adhesion / cellular response to fibroblast growth factor stimulus / negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / branching involved in ureteric bud morphogenesis / epidermal growth factor receptor binding / negative regulation of DNA damage response, signal transduction by p53 class mediator / lamellipodium membrane / regulation of cell growth / cell projection / negative regulation of inflammatory response / phosphoprotein binding / neuron projection development / microvillus / negative regulation of cysteine-type endopeptidase activity involved in apoptotic process / transmembrane signaling receptor activity / positive regulation of peptidyl-tyrosine phosphorylation / apical plasma membrane / cell migration / positive regulation of peptidyl-serine phosphorylation / Wnt signaling pathway / basolateral plasma membrane / positive regulation of ERK1 and ERK2 cascade / cell adhesion / inflammatory response / external side of plasma membrane / cytokine-mediated signaling pathway / positive regulation of gene expression / protein kinase binding / negative regulation of apoptotic process / Golgi apparatus / cell surface / protein-containing complex / integral component of membrane / plasma membrane / nucleus / cytosol / CD44 antigen
Function and homology information
Specimen sourceMUS MUSCULUS (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / 1.25 Å resolution
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.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Jan 3, 2007 / Release: Jan 30, 2007
RevisionDateData content typeGroupProviderType
1.0Jan 30, 2007Structure modelrepositoryInitial release
1.1Aug 24, 2016Structure modelAtomic model / Database references / Derived calculations / Non-polymer description / Other / Refinement description / Source and taxonomy / Structure summary / Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CD44 ANTIGEN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,6889
Polyers17,1291
Non-polymers1,5598
Water3,153175
1


TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
γ
α
β
Length a, b, c (Å)30.794, 82.051, 32.278
Angle α, β, γ (deg.)90.00, 117.89, 90.00
Int Tables number4
Space group name H-MP 1 21 1

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Components

#1: Protein/peptide CD44 ANTIGEN / 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: 17129.047 Da / Num. of mol.: 1
Details: ENCODED RESIDUES 25-174, EQUIVALENT TO RESIDUES 1-151 OF THE MATURE PROTEIN, WITH ADDITIONAL ...ENCODED RESIDUES 25-174, EQUIVALENT TO RESIDUES 1-151 OF THE MATURE PROTEIN, WITH ADDITIONAL RESIDUES M, N ADDED AT THE N-TERMINUS
Fragment: HYALURONAN BINDING DOMAIN, RESIDUES 23-174 / Source: (gene. exp.) MUS MUSCULUS (house mouse) / Plasmid name: PET19B / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): PLYSS / References: UniProt: P15379
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Formula: C3H8O3 / Glycerol
#3: Chemical
ChemComp-NAG / N-ACETYL-D-GLUCOSAMINE


Mass: 221.208 Da / Num. of mol.: 4 / Formula: C8H15NO6 / N-Acetylglucosamine
#4: Chemical ChemComp-BDP / BETA-D-GLUCOPYRANURONIC ACID / D-GLUCURONIC ACID


Mass: 194.139 Da / Num. of mol.: 3 / Formula: C6H10O7 / Glucuronic acid
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 175 / Formula: H2O / Water

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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 / Density percent sol: 42 %
Crystal growpH: 7
Details: CO-CRYSTALS OF THE CD44/HA8 COMPLEX WERE PREPARED AFTER ADDITION OF HA8 (2MM FINAL CONCENTRATION) TO THE 0.5MM PROTEIN SOLUTION FOLLOWED BY MIXING 1:1 WITH WELL SOLUTIONS CONTAINING 25% (W/V) PEG 3350 AND 100MM NACL IN 100MM HEPES BUFFERED AT EITHER PH 7.0 OR PH 8.0

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Data collection

DiffractionMean temperature: 1 kelvins
SourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934
DetectorType: ADSC CCD / Detector: CCD / Collection date: Apr 1, 2004
RadiationDiffraction protocol: SINGLE WAVELENGTH / Monochromatic or laue m l: M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionD resolution high: 1.25 Å / D resolution low: 23.42 Å / Number obs: 36225 / Observed criterion sigma I: 0 / Rmerge I obs: 0.07 / NetI over sigmaI: 6.75 / Redundancy: 5.44 % / Percent possible obs: 92.7
Reflection shellRmerge I obs: 0.42 / Highest resolution: 1.25 Å / Lowest resolution: 1.32 Å / MeanI over sigI obs: 1.77 / Redundancy: 2.65 % / Percent possible all: 56.2

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefineMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1UUH
Correlation coeff Fo to Fc: 0.976 / Correlation coeff Fo to Fc free: 0.97 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. / Overall SU B: 1.234 / Overall SU ML: 0.025 / R Free selection details: RANDOM / Cross valid method: THROUGHOUT / Overall ESU R: 0.043 / Overall ESU R Free: 0.041 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Solvent computationSolvent ion probe radii: 0.8 Å / Solvent shrinkage radii: 0.8 Å / Solvent vdw probe radii: 1.2 Å / Solvent model details: MASK
Displacement parametersB iso mean: 7.6 Å2 / Aniso B11: 0.04 Å2 / Aniso B12: 0 Å2 / Aniso B13: -0.26 Å2 / Aniso B22: -0.15 Å2 / Aniso B23: 0 Å2 / Aniso B33: -0.13 Å2
Least-squares processR factor R free: 0.156 / R factor R work: 0.13 / R factor obs: 0.132 / Highest resolution: 1.25 Å / Lowest resolution: 41.03 Å / Number reflection R free: 1945 / Number reflection obs: 36568 / Percent reflection R free: 5.1 / Percent reflection obs: 98.4
Refine hist #LASTHighest resolution: 1.25 Å / Lowest resolution: 41.03 Å
Number of atoms included #LASTProtein: 1164 / Nucleic acid: 0 / Ligand: 99 / Solvent: 175 / Total: 1438
Refine LS restraints
Refine IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0211382
X-RAY DIFFRACTIONr_bond_other_d0.0020.0201162
X-RAY DIFFRACTIONr_angle_refined_deg1.7742.0221907
X-RAY DIFFRACTIONr_angle_other_deg0.8603.0002710
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1695.000166
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.88724.19462
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.84115.000203
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.85615.0008
X-RAY DIFFRACTIONr_chiral_restr0.1010.200229
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0201521
X-RAY DIFFRACTIONr_gen_planes_other0.0020.020267
X-RAY DIFFRACTIONr_nbd_refined0.2370.200259
X-RAY DIFFRACTIONr_nbd_other0.1950.2001254
X-RAY DIFFRACTIONr_nbtor_refined0.1860.200714
X-RAY DIFFRACTIONr_nbtor_other0.0850.200855
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1800.200130
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2500.20011
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2500.20056
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1540.20022
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.7181.5001015
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.1292.0001311
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.2003.000653
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it4.0644.500596
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
Refine LS shellHighest resolution: 1.25 Å / R factor R free: 0.236 / R factor R work: 0.211 / Lowest resolution: 1.28 Å / Number reflection R free: 158 / Number reflection R work: 2622 / Total number of bins used: 20
Refine TLSMethod: refined / L11: 0.741 deg.2 / L12: -0.0363 deg.2 / L13: 0.1673 deg.2 / L22: 0.5171 deg.2 / L23: -0.0496 deg.2 / L33: 1.2897 deg.2 / S11: 0.0061 Å deg. / S12: -0.0019 Å deg. / S13: 0.0249 Å deg. / S21: 0.0152 Å deg. / S22: -0.015 Å deg. / S23: -0.049 Å deg. / S31: -0.0236 Å deg. / S32: 0.0404 Å deg. / S33: 0.0089 Å deg. / T11: -0.0352 Å2 / T12: -0.0049 Å2 / T13: 0.0002 Å2 / T22: -0.0256 Å2 / T23: -0.0011 Å2 / T33: -0.0201 Å2 / Origin x: 2.324 Å / Origin y: -1.311 Å / Origin z: 2.869 Å
Refine TLS group

Beg auth asym ID: A / End auth asym ID: A / Refine ID: X-RAY DIFFRACTION / Refine TLS ID: 1

IDBeg auth seq IDEnd auth seq ID
1211699
211751181

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