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- PDB-4mre: Crystal structure of the murine CD44 hyaluronan binding domain co... -

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Basic information

Entry
Database: PDB / ID: 4mre
TitleCrystal structure of the murine CD44 hyaluronan binding domain complex with a small molecule
ComponentsCD44 antigen
KeywordsCell adhesion/inhibitor / Link module / Cell receptor / Hyaluronan binding / Cell surface / Cell adhesion-inhibitor complex
Function / homology
Function and homology information


Hyaluronan uptake and degradation / macrophage fusion / hyaluronic acid binding / macrophage migration inhibitory factor receptor complex / negative regulation of regulatory T cell differentiation / Degradation of the extracellular matrix / regulation of lamellipodium morphogenesis / Integrin cell surface interactions / Cell surface interactions at the vascular wall / hyaluronan catabolic process ...Hyaluronan uptake and degradation / macrophage fusion / hyaluronic acid binding / macrophage migration inhibitory factor receptor complex / negative regulation of regulatory T cell differentiation / Degradation of the extracellular matrix / regulation of lamellipodium morphogenesis / Integrin cell surface interactions / Cell surface interactions at the vascular wall / hyaluronan catabolic process / wound healing involved in inflammatory response / positive regulation of adaptive immune response / positive regulation of neutrophil apoptotic process / 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 / wound healing, spreading of cells / cargo receptor activity / 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 / channel regulator activity / negative regulation of DNA damage response, signal transduction by p53 class mediator / microvillus / lamellipodium membrane / Neutrophil degranulation / receptor-mediated endocytosis / cell projection / regulation of cell growth / phosphoprotein binding / Wnt signaling pathway / cytokine-mediated signaling pathway / negative regulation of inflammatory response / positive regulation of peptidyl-tyrosine phosphorylation / neuron projection development / transmembrane signaling receptor activity / cell migration / 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 / protein kinase binding / cell surface / protein-containing complex / extracellular region / plasma membrane
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
3-methylbenzene-1,2-diamine / CD44 antigen
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.58 Å
AuthorsLiu, L.K. / Finzel, B.
Citation
Journal: J.Med.Chem. / Year: 2014
Title: Fragment-Based Identification of an Inducible Binding Site on Cell Surface Receptor CD44 for the Design of Protein-Carbohydrate Interaction Inhibitors.
Authors: Liu, L.K. / Finzel, B.C.
#1: Journal: Nat.Struct.Mol.Biol. / Year: 2007
Title: Structures of the Cd44-hyaluronan complex provide insight into a fundamental carbohydrate-protein interaction.
Authors: Banerji, S. / Wright, A.J. / Noble, M. / Mahoney, D.J. / Campbell, I.D. / Day, A.J. / Jackson, D.G.
History
DepositionSep 17, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 16, 2014Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.2Nov 6, 2024Group: Structure summary / Category: 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,9253
Polymers16,7251
Non-polymers2002
Water1,00956
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)30.863, 82.242, 32.074
Angle α, β, γ (deg.)90.000, 117.660, 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: 16724.604 Da / Num. of mol.: 1 / Fragment: HYALURONAN BINDING DOMAIN, RESIDUES 23-171
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Cd44, Cd44 Ly-24, Ly-24 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P15379
#2: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#3: Chemical ChemComp-2C9 / 3-methylbenzene-1,2-diamine


Mass: 122.168 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H10N2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 56 / Source method: isolated from a natural source / Formula: H2O
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: 2.16 Å3/Da / Density % sol: 42.94 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 30% PEG MME 5000, 100 mM MES, 200 mM (NH4)2SO4, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 21, 2012
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.58→41.12 Å / Num. all: 19012 / Num. obs: 18681 / % possible obs: 96.3 % / Redundancy: 3.3 % / Biso Wilson estimate: 16.3 Å2 / Rmerge(I) obs: 0.061 / Rsym value: 0.083 / Net I/σ(I): 18.9
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.58-1.673.10.2012.8814926350.20193.6
1.67-1.773.50.1523.7905126030.15297.5
1.77-1.893.30.1095.3813724390.10997.4
1.89-2.043.40.0777.9788923000.07797.7
2.04-2.233.30.06310687221010.06398.2
2.23-2.53.30.05511.3635619150.05597.6
2.5-2.883.30.04912.7545416710.04997.7
2.88-3.533.30.04413.5454013870.04494.5
3.53-53.10.04512321910480.04592.9
5-41.1213.10.0431318135820.04390.7

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 32.3 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å41.12 Å
Translation2.5 Å41.12 Å

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Processing

Software
NameVersionClassificationNB
SCALA3.3.16data scaling
PHASER2.1.4phasing
REFMACrefinement
PDB_EXTRACT3.11data extraction
JDirectordata collection
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 2JCP

2jcp


Resolution: 1.58→41.12 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.907 / WRfactor Rfree: 0.2433 / WRfactor Rwork: 0.1999 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.8802 / SU B: 1.41 / SU ML: 0.053 / SU R Cruickshank DPI: 0.0946 / SU Rfree: 0.0973 / Cross valid method: THROUGHOUT / ESU R: 0.095 / ESU R Free: 0.097 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2234 945 5.1 %RANDOM
Rwork0.1834 ---
obs0.1855 17623 96.14 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 34.08 Å2 / Biso mean: 9.7479 Å2 / Biso min: 2 Å2
Baniso -1Baniso -2Baniso -3
1--0.25 Å2-0 Å2-0.06 Å2
2--0.1 Å20 Å2
3---0.1 Å2
Refinement stepCycle: LAST / Resolution: 1.58→41.12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1171 0 13 56 1240
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0211235
X-RAY DIFFRACTIONr_angle_refined_deg1.531.9431686
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8655155
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.73124.16760
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.00215191
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.875158
X-RAY DIFFRACTIONr_chiral_restr0.1010.2188
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.021965
X-RAY DIFFRACTIONr_mcbond_it0.9661.5766
X-RAY DIFFRACTIONr_mcangle_it1.80521252
X-RAY DIFFRACTIONr_scbond_it3.0193469
X-RAY DIFFRACTIONr_scangle_it4.824.5434
LS refinement shellResolution: 1.58→1.621 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.195 54 -
Rwork0.163 1136 -
all-1190 -
obs-1136 90.29 %

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