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- PDB-1uuh: Hyaluronan binding domain of human CD44 -

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Basic information

Entry
Database: PDB / ID: 1uuh
TitleHyaluronan binding domain of human CD44
ComponentsCD44 ANTIGEN
KeywordsLECTIN / HYALURONAN / EXTRACELLULAR MATRIX / RECEPTOR / LINK-DOMAIN / C- TYPE LECTIN / SUGAR-BINDING
Function / homology
Function and homology information


Hyaluronan uptake and degradation / positive regulation of monocyte aggregation / hyaluronic acid binding / macrophage migration inhibitory factor receptor complex / regulation of lamellipodium morphogenesis / hyaluronan catabolic process / monocyte aggregation / cellular response to fibroblast growth factor stimulus / cartilage development / positive regulation of heterotypic cell-cell adhesion ...Hyaluronan uptake and degradation / positive regulation of monocyte aggregation / hyaluronic acid binding / macrophage migration inhibitory factor receptor complex / regulation of lamellipodium morphogenesis / hyaluronan catabolic process / monocyte aggregation / cellular response to fibroblast growth factor stimulus / cartilage development / positive regulation of heterotypic cell-cell adhesion / wound healing, spreading of cells / 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 / Degradation of the extracellular matrix / T cell activation / 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 / cytokine-mediated signaling pathway / Interferon gamma signaling / 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 / 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)
MethodX-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 2.2 Å
AuthorsTeriete, P. / Banerji, S. / Noble, M. / Blundell, C. / Wright, A. / Pickford, A. / Lowe, E. / Mahoney, D. / Tammi, M. / Kahmann, J. ...Teriete, P. / Banerji, S. / Noble, M. / Blundell, C. / Wright, A. / Pickford, A. / Lowe, E. / Mahoney, D. / Tammi, M. / Kahmann, J. / Campbell, I. / Day, A. / Jackson, D.
CitationJournal: 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. / Wright, A. / Pickford, A. / Lowe, E. / Mahoney, D. / Tammi, M. / Kahmann, J. / Campbell, I. / Day, A. / Jackson, D.
History
DepositionDec 19, 2003Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 4, 2004Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 29, 2019Group: Data collection / Derived calculations ...Data collection / Derived calculations / Experimental preparation / Other
Category: exptl_crystal_grow / pdbx_database_proc ...exptl_crystal_grow / pdbx_database_proc / pdbx_database_status / struct_biol / struct_conn
Item: _exptl_crystal_grow.method / _pdbx_database_status.recvd_author_approval / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CD44 ANTIGEN
B: CD44 ANTIGEN


Theoretical massNumber of molelcules
Total (without water)35,3912
Polymers35,3912
Non-polymers00
Water4,720262
1
A: CD44 ANTIGEN


Theoretical massNumber of molelcules
Total (without water)17,6951
Polymers17,6951
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: CD44 ANTIGEN


Theoretical massNumber of molelcules
Total (without water)17,6951
Polymers17,6951
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)48.881, 77.266, 87.668
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.74746, -0.61772, -0.24439), (0.43944, -0.73566, 0.51545), (0.4982, -0.27789, -0.82133)
Vector: -13.39, -13.608, -23.469)

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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: 17695.275 Da / Num. of mol.: 2 / Fragment: HYALURONAN BINDING DOMAIN, RESIDUES 20-178
Source method: isolated from a genetically manipulated source
Details: FIRST RESIDUE IS IN FACT THE LAST RESIDUE OF THE SIGNAL PEPTIDE, AND WOULD NORMALLY BE CLEAVED
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PET19B / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / Variant (production host): DE3 PLYSS / References: UniProt: P16070
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 262 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsHYALURONAN BINDING DOMAIN ONLY

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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: 2.3 Å3/Da / Density % sol: 40 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 5.5
Details: HANGING-DROP PROTEIN 13 MG/ML; WELL BUFFER 12% PEG 3350, 50MM NACL, 10% GLYCEROL, pH 5.50
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
112 %PEG33501reservoir
250 mM1reservoirNaCl
310 %glycerol1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9795
DetectorType: ADSC CCD / Detector: CCD / Date: May 15, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.2→23.31 Å / Num. obs: 17476 / % possible obs: 99.8 % / Redundancy: 3.82 % / Rmerge(I) obs: 0.076 / Net I/σ(I): 7.2989
Reflection shellResolution: 2.2→2.32 Å / Redundancy: 3.53 % / Rmerge(I) obs: 0.18 / Mean I/σ(I) obs: 3.16 / % possible all: 99.6
Reflection
*PLUS
Highest resolution: 2.2 Å / Lowest resolution: 23.31 Å / % possible obs: 99.4 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.076
Reflection shell
*PLUS
% possible obs: 98.2 % / Redundancy: 3.5 % / Rmerge(I) obs: 0.181 / Mean I/σ(I) obs: 3.1

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Processing

Software
NameVersionClassification
REFMAC5.1.9999refinement
SOLVE/RESOLVEphasing
RefinementMethod to determine structure: OTHER / Resolution: 2.2→57.73 Å / Cor.coef. Fo:Fc: 0.933 / Cor.coef. Fo:Fc free: 0.878 / SU B: 5.483 / SU ML: 0.141 / Cross valid method: THROUGHOUT / ESU R: 0.261 / ESU R Free: 0.216 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.249 881 5.13 %RANDOM
Rwork0.186 ---
obs-16553 99.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL PLUS MASK
Displacement parametersBiso mean: 17.45 Å2
Baniso -1Baniso -2Baniso -3
1--0.28 Å20 Å20 Å2
2--0.47 Å20 Å2
3----0.19 Å2
Refinement stepCycle: LAST / Resolution: 2.2→57.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2334 0 0 262 2596
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0212390
X-RAY DIFFRACTIONr_bond_other_d0.0020.022068
X-RAY DIFFRACTIONr_angle_refined_deg1.9561.9373258
X-RAY DIFFRACTIONr_angle_other_deg1.00434818
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.4155298
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1380.2366
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022700
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02492
X-RAY DIFFRACTIONr_nbd_refined0.240.2462
X-RAY DIFFRACTIONr_nbd_other0.2630.22531
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.0980.21416
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2160.2120
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2330.214
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2730.263
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1760.215
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.9821.51496
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.76922436
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.8543894
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it4.4854.5822
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: 2.2→2.26 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.239 52
Rwork0.19 1200
Refinement
*PLUS
Lowest resolution: 23.31 Å / % reflection Rfree: 5 % / Rfactor Rfree: 0.24 / Rfactor Rwork: 0.18
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.011
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg1.309
LS refinement shell
*PLUS
Lowest resolution: 2.28 Å / Rfactor Rfree: 0.24 / Rfactor Rwork: 0.19

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