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

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Basic information

Entry
Database: PDB / ID: 4mrh
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 degradation / 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 / wound healing involved in inflammatory response / hyaluronan catabolic process ...Hyaluronan degradation / 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 / wound healing involved in inflammatory response / hyaluronan catabolic process / positive regulation of adaptive immune response / branching involved in prostate gland morphogenesis / type II transforming growth factor beta receptor binding / negative regulation of mature B cell apoptotic process / channel regulator activity / negative regulation of CD4-positive, alpha-beta T cell proliferation / wound healing, spreading of cells / cargo receptor activity / branching involved in ureteric bud morphogenesis / negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / microvillus / negative regulation of DNA damage response, signal transduction by p53 class mediator / lamellipodium membrane / Neutrophil degranulation / receptor-mediated endocytosis / cell projection / negative regulation of inflammatory response / Wnt signaling pathway / cytokine-mediated signaling pathway / basolateral plasma membrane / positive regulation of ERK1 and ERK2 cascade / cell adhesion / apical plasma membrane / membrane raft / external side of plasma membrane / positive regulation of gene expression / cell surface / 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
4-chloro-5-methylbenzene-1,2-diamine / CD44 antigen
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.12 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 30, 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 1.2Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CD44 antigen
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,9593
Polymers16,7251
Non-polymers2352
Water2,216123
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)30.987, 81.744, 32.236
Angle α, β, γ (deg.)90.000, 118.210, 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-2CQ / 4-chloro-5-methylbenzene-1,2-diamine


Mass: 156.613 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H9ClN2
#3: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 123 / 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: 2.15 Å3/Da / Density % sol: 42.82 %
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: Nov 17, 2012
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.12→81.74 Å / Num. all: 53169 / Num. obs: 52863 / % possible obs: 97.7 % / Redundancy: 3.2 % / Biso Wilson estimate: 12.2 Å2 / Rmerge(I) obs: 0.036 / Rsym value: 0.049 / Net I/σ(I): 16.7
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.12-1.1830.1594.52208674540.15994.7
1.18-1.253.30.1295.42377972450.12997
1.25-1.343.30.10172292868510.10197.7
1.34-1.453.30.0828.62096663970.08298
1.45-1.583.30.05712.11959859000.05798.5
1.58-1.773.20.04614.81743053850.04698.8
1.77-2.043.20.03617.51546247830.03699.2
2.04-2.53.10.03119.91262440270.03198.9
2.5-3.543.20.02820.7986631020.02898.5
3.54-81.7443.20.02623.1547017190.02697.6

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 29.91 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å40.87 Å
Translation2.5 Å40.87 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: 1.12→40.87 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.96 / WRfactor Rfree: 0.1911 / WRfactor Rwork: 0.1742 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.903 / SU B: 0.441 / SU ML: 0.022 / SU R Cruickshank DPI: 0.034 / SU Rfree: 0.0348 / Cross valid method: THROUGHOUT / ESU R: 0.034 / ESU R Free: 0.035 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1838 2706 5.1 %RANDOM
Rwork0.1691 ---
obs0.1699 52824 97.5 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 37.99 Å2 / Biso mean: 11.8071 Å2 / Biso min: 4.44 Å2
Baniso -1Baniso -2Baniso -3
1--0.14 Å2-0 Å2-0.34 Å2
2---0.02 Å20 Å2
3----0.16 Å2
Refinement stepCycle: LAST / Resolution: 1.12→40.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1171 0 14 123 1308
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0221274
X-RAY DIFFRACTIONr_angle_refined_deg1.5411.9531745
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3145163
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.34323.60761
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.02915202
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.4841510
X-RAY DIFFRACTIONr_chiral_restr0.1040.2194
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0211004
X-RAY DIFFRACTIONr_mcbond_it0.9351.5787
X-RAY DIFFRACTIONr_mcangle_it1.62821292
X-RAY DIFFRACTIONr_scbond_it2.4233487
X-RAY DIFFRACTIONr_scangle_it3.8124.5452
LS refinement shellResolution: 1.12→1.149 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.22 186 -
Rwork0.198 3501 -
all-3687 -
obs-3501 92.24 %

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