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- PDB-4mrg: Crystal structure of the murine cd44 hyaluronan binding domain co... -

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Basic information

Entry
Database: PDB / ID: 4mrg
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 / 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 / positive regulation of adaptive immune response / wound healing involved in inflammatory response ...Hyaluronan uptake and 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 / positive regulation of adaptive immune response / wound healing involved in inflammatory response / hyaluronan catabolic process / branching involved in prostate gland morphogenesis / type II transforming growth factor beta receptor binding / channel regulator activity / 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 / 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 / Neutrophil degranulation / receptor-mediated endocytosis / cell projection / cytokine-mediated signaling pathway / negative regulation of inflammatory response / Wnt 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
1,2,3,4-tetrahydroisoquinolin-5-amine / CD44 antigen
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.69 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 20, 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)17,2316
Polymers16,7251
Non-polymers5075
Water1,53185
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)30.850, 81.580, 32.130
Angle α, β, γ (deg.)90.000, 117.930, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 1 molecules A

#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 23-174 / Mutation: H23M, Q24N
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

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Non-polymers , 5 types, 90 molecules

#2: Chemical ChemComp-24W / 1,2,3,4-tetrahydroisoquinolin-5-amine


Mass: 148.205 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H12N2
#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: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 85 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.14 Å3/Da / Density % sol: 42.41 %
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: ALS / Beamline: 4.2.2 / Wavelength: 1 Å
DetectorType: NOIR-1 / Detector: CCD / Date: Dec 16, 2012
RadiationMonochromator: Rosenbaum-Rock monochromator Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.69→40.8 Å / Num. all: 56490 / Num. obs: 56490 / % possible obs: 95.7 % / Redundancy: 3.7 % / Biso Wilson estimate: 18.4 Å2 / Rmerge(I) obs: 0.039 / Rsym value: 0.046 / Net I/σ(I): 27.2
Reflection shellResolution: 1.69→1.73 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.197 / Mean I/σ(I) obs: 5.3 / Num. unique all: 871 / Rsym value: 0.243 / % possible all: 74.8

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 32.85 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å19.64 Å
Translation2.5 Å19.64 Å

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHASER2.1.4phasing
REFMACrefinement
PDB_EXTRACT3.11data extraction
Blu-Icedata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 2JCP

2jcp


Resolution: 1.69→40.8 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.919 / WRfactor Rfree: 0.1951 / WRfactor Rwork: 0.1536 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.8898 / SU B: 1.811 / SU ML: 0.062 / SU R Cruickshank DPI: 0.1081 / SU Rfree: 0.1098 / Cross valid method: THROUGHOUT / ESU R: 0.108 / ESU R Free: 0.11 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.206 778 5.1 %RANDOM
Rwork0.1604 ---
obs0.1627 15170 96.66 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 43.54 Å2 / Biso mean: 10.718 Å2 / Biso min: 2.87 Å2
Baniso -1Baniso -2Baniso -3
1--0.39 Å2-0 Å2-0.18 Å2
2--0.27 Å2-0 Å2
3----0.05 Å2
Refinement stepCycle: LAST / Resolution: 1.69→40.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1171 0 32 85 1288
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0211294
X-RAY DIFFRACTIONr_angle_refined_deg1.5631.9591767
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0465162
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.88923.8163
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.54815201
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.2591510
X-RAY DIFFRACTIONr_chiral_restr0.1070.2193
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0211011
X-RAY DIFFRACTIONr_mcbond_it0.8741.5789
X-RAY DIFFRACTIONr_mcangle_it1.43421294
X-RAY DIFFRACTIONr_scbond_it2.5443505
X-RAY DIFFRACTIONr_scangle_it4.0154.5473
LS refinement shellResolution: 1.691→1.735 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.169 43 -
Rwork0.184 876 -
all-919 -
obs-876 80.76 %

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