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- PDB-32oa: The ultra-high-resolution hyaluronan-binding domain of mouse CD44 -

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Basic information

Entry
Database: PDB / ID: 32oa
TitleThe ultra-high-resolution hyaluronan-binding domain of mouse CD44
ComponentsCD44 antigen
KeywordsPROTEIN BINDING / scFv / hyaluronan / antibody / CD44
Function / homology
Function and homology information


Hyaluronan metabolism / Hyaluronan degradation / positive regulation of monocyte aggregation / macrophage fusion / hyaluronic acid binding / macrophage migration inhibitory factor receptor complex / Degradation of the extracellular matrix / Cell surface interactions at the vascular wall / Integrin cell surface interactions / regulation of lamellipodium morphogenesis ...Hyaluronan metabolism / Hyaluronan degradation / positive regulation of monocyte aggregation / macrophage fusion / hyaluronic acid binding / macrophage migration inhibitory factor receptor complex / Degradation of the extracellular matrix / Cell surface interactions at the vascular wall / Integrin cell surface interactions / regulation of lamellipodium morphogenesis / postsynapse organization / monocyte aggregation / branching involved in prostate gland morphogenesis / wound healing involved in inflammatory response / hyaluronan catabolic process / NK T cell activation / negative regulation of CD4-positive, alpha-beta T cell proliferation / positive regulation of adaptive immune response / type II transforming growth factor beta receptor binding / negative regulation of mature B cell apoptotic process / positive regulation of neutrophil apoptotic process / regulation of modification of postsynaptic structure / branching involved in ureteric bud morphogenesis / channel regulator activity / positive regulation of heterotypic cell-cell adhesion / wound healing, spreading of cells / epidermal growth factor receptor binding / cargo receptor activity / negative regulation of regulatory T cell differentiation / 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 / cell projection / cellular response to fibroblast growth factor stimulus / Neutrophil degranulation / receptor-mediated endocytosis / T cell activation / regulation of cell growth / Wnt signaling pathway / phosphoprotein binding / negative regulation of inflammatory response / neuron projection development / cytokine-mediated signaling pathway / transmembrane signaling receptor activity / cell migration / presynapse / signaling receptor activity / basolateral plasma membrane / positive regulation of ERK1 and ERK2 cascade / cell adhesion / postsynapse / apical plasma membrane / inflammatory response / membrane raft / external side of plasma membrane / positive regulation of gene expression / negative regulation of apoptotic process / protein kinase binding / glutamatergic synapse / Golgi apparatus / cell surface / protein-containing complex / extracellular region / 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
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 0.775 Å
AuthorsBradshaw, W.J. / Katis, V.L. / Newman, J.A. / Gileadi, O.
Funding support United States, United Kingdom, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute on Aging (NIH/NIA)1U54AG065187-01 United States
Alzheimers Research UK (ARUK)520909 United Kingdom
CitationJournal: To Be Published
Title: The ultra-high-resolution hyaluronan-binding domain of mouse CD44
Authors: Bradshaw, W.J. / Katis, V.L. / Newman, J.A. / Gileadi, O.
History
DepositionJul 17, 2026Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 12, 2026Provider: repository / Type: Initial release

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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)17,2054
Polymers16,9711
Non-polymers2343
Water6,053336
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area530 Å2
ΔGint4 kcal/mol
Surface area7670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)30.960, 82.136, 32.225
Angle α, β, γ (deg.)90.000, 117.884, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein CD44 antigen / Extracellular matrix receptor III / ECMR-III / GP90 lymphocyte homing/adhesion receptor / HUTCH-I / ...Extracellular matrix receptor III / ECMR-III / GP90 lymphocyte homing/adhesion receptor / HUTCH-I / Hermes antigen / Hyaluronate receptor / Lymphocyte antigen 24 / Ly-24 / Phagocytic glycoprotein 1 / PGP-1 / Phagocytic glycoprotein I / PGP-I


Mass: 16970.891 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Cd44, Ly-24 / Production host: Escherichia coli (E. coli) / References: UniProt: P15379
#2: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 336 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationY

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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: 2.13 Å3/Da / Density % sol: 42.36 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 200 mM ammonium sulphate, 100 mM MES, 24% PEG5KMME

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.7338 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Dec 11, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.7338 Å / Relative weight: 1
ReflectionResolution: 0.775→41.068 Å / Num. obs: 132017 / % possible obs: 80.5 % / Redundancy: 86.9 % / CC1/2: 1 / Rmerge(I) obs: 0.276 / Rpim(I) all: 0.029 / Rrim(I) all: 0.277 / Net I/σ(I): 14.1
Reflection shellResolution: 0.775→0.826 Å / Redundancy: 39.4 % / Rmerge(I) obs: 5.997 / Mean I/σ(I) obs: 1.6 / Num. unique obs: 2643 / CC1/2: 0.672 / Rpim(I) all: 0.932 / Rrim(I) all: 6.072 / % possible all: 9.3

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Processing

Software
NameVersionClassification
REFMAC5.8.0431refinement
DIALSdata reduction
STARANISOdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 0.775→41.068 Å / Cor.coef. Fo:Fc: 0.985 / Cor.coef. Fo:Fc free: 0.986 / SU B: 0.294 / SU ML: 0.009 / Cross valid method: THROUGHOUT / ESU R: 0.012 / ESU R Free: 0.011
Details: Hydrogens have been used if present in the input file
RfactorNum. reflection% reflectionSelection details
Rfree0.1156 2015 1.526 %RANDOM
Rwork0.1104 130001 --
all0.111 ---
obs-132016 80.463 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 8.765 Å2
Baniso -1Baniso -2Baniso -3
1-0.001 Å20 Å20.006 Å2
2---0.062 Å20 Å2
3---0.035 Å2
Refinement stepCycle: LAST / Resolution: 0.775→41.068 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1171 0 12 336 1519
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0121478
X-RAY DIFFRACTIONr_bond_other_d0.0010.0161416
X-RAY DIFFRACTIONr_angle_refined_deg1.7561.8362057
X-RAY DIFFRACTIONr_angle_other_deg0.6831.7993246
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.5965213
X-RAY DIFFRACTIONr_dihedral_angle_2_deg12.894514
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.84310257
X-RAY DIFFRACTIONr_dihedral_angle_6_deg16.6971084
X-RAY DIFFRACTIONr_chiral_restr0.1130.2233
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.021865
X-RAY DIFFRACTIONr_gen_planes_other00.02393
X-RAY DIFFRACTIONr_nbd_refined0.290.2273
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1930.21357
X-RAY DIFFRACTIONr_nbtor_refined0.20.2686
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0960.2779
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.3110.2276
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.1490.26
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1270.217
X-RAY DIFFRACTIONr_nbd_other0.1940.236
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.260.257
X-RAY DIFFRACTIONr_mcbond_it2.2870.455687
X-RAY DIFFRACTIONr_mcbond_other2.2855559.887687
X-RAY DIFFRACTIONr_mcangle_it3.3270.826878
X-RAY DIFFRACTIONr_mcangle_other3.3362.214879
X-RAY DIFFRACTIONr_scbond_it3.8020.627791
X-RAY DIFFRACTIONr_scbond_other4.027792
X-RAY DIFFRACTIONr_scangle_it5.3791.0821149
X-RAY DIFFRACTIONr_scangle_other5.3771.0821150
X-RAY DIFFRACTIONr_lrange_it10.7211925
X-RAY DIFFRACTIONr_lrange_other8.0121725
X-RAY DIFFRACTIONr_rigid_bond_restr5.85731478
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 12

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
0.775-0.8090.355100.366770.36199610.9590.9533.44170.35
0.809-0.8490.2651270.25575360.255191680.9680.96339.97810.257
0.849-0.8950.2172340.193167880.193181960.9720.97693.5480.191
0.895-0.9490.1522550.142169650.142172590.9860.98799.7740.134
0.949-1.0150.1252200.112159540.112162000.990.99299.83950.103
1.015-1.0960.0952630.094147800.094150630.9940.99599.86720.085
1.096-1.20.0932300.081136510.081138880.9950.99699.94960.074
1.2-1.3420.1091820.086123800.087125680.9930.99599.95230.08
1.342-1.5490.0981250.086109720.087110990.9940.99599.9820.082
1.549-1.8970.1021540.09892150.09893690.9940.9941000.096
1.897-2.6790.1111510.10771030.10772560.9930.99399.97240.111
2.679-41.0680.103640.12339790.12340430.9930.991000.136

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