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Yorodumi- PDB-4mrd: Crystal structure of the murine cd44 hyaluronan binding domain co... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4mrd | |||||||||
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Title | Crystal structure of the murine cd44 hyaluronan binding domain complex with a small molecule | |||||||||
Components | CD44 antigen | |||||||||
Keywords | CELL ADHESION / Link module / Cell receptor / Hyaluronan binding / Cell surface | |||||||||
Function / homology | Function and homology information Hyaluronan uptake and degradation / positive regulation of monocyte aggregation / hyaluronic acid binding / macrophage fusion / macrophage migration inhibitory factor receptor complex / Degradation of the extracellular matrix / negative regulation of regulatory T cell differentiation / regulation of lamellipodium morphogenesis / Integrin cell surface interactions / Cell surface interactions at the vascular wall ...Hyaluronan uptake and degradation / positive regulation of monocyte aggregation / hyaluronic acid binding / macrophage fusion / macrophage migration inhibitory factor receptor complex / Degradation of the extracellular matrix / negative regulation of regulatory T cell differentiation / regulation of lamellipodium morphogenesis / Integrin cell surface interactions / Cell surface interactions at the vascular wall / hyaluronan catabolic process / positive regulation of adaptive immune response / monocyte aggregation / wound healing involved in inflammatory response / 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 / positive regulation of neutrophil apoptotic process / channel regulator activity / cellular response to fibroblast growth factor stimulus / cargo receptor activity / positive regulation of heterotypic cell-cell adhesion / wound healing, spreading of cells / 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 / negative regulation of DNA damage response, signal transduction by p53 class mediator / microvillus / lamellipodium membrane / receptor-mediated endocytosis / Neutrophil degranulation / T cell activation / cell projection / regulation of cell growth / phosphoprotein binding / negative regulation of inflammatory response / Wnt signaling pathway / cytokine-mediated signaling pathway / neuron projection development / 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 / membrane raft / apical plasma membrane / external side of plasma membrane / positive regulation of gene expression / negative regulation of apoptotic process / protein kinase binding / Golgi apparatus / cell surface / protein-containing complex / extracellular region / plasma membrane / cytosol Similarity search - Function | |||||||||
Biological species | Mus musculus (house mouse) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.55 Å | |||||||||
Authors | Liu, 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4mrd.cif.gz | 40.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4mrd.ent.gz | 29.9 KB | Display | PDB format |
PDBx/mmJSON format | 4mrd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mr/4mrd ftp://data.pdbj.org/pub/pdb/validation_reports/mr/4mrd | HTTPS FTP |
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-Related structure data
Related structure data | 4mreC 4mrfC 4mrgC 4mrhC 4np2C 4np3C C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 16610.502 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 |
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#2: Polysaccharide | beta-D-glucopyranuronic acid-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-beta-D- ...beta-D-glucopyranuronic acid-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-beta-D-glucopyranuronic acid-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source |
#3: Chemical | ChemComp-SO4 / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.18 Å3/Da / Density % sol: 43.56 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 30% PEG MME 5000, 100 mM MES, 200mM (NH4)2SO4, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 1 Å |
Detector | Type: NOIR-1 / Detector: CCD / Date: Jan 29, 2013 / Details: mirror |
Radiation | Monochromator: Rosenbaum-Rock monochromator Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.55→41.14 Å / Num. all: 17746 / Num. obs: 17738 / % possible obs: 98.7 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 3.8 % / Rmerge(I) obs: 0.123 / Rsym value: 0.143 / Net I/σ(I): 11.1 |
Reflection shell | Resolution: 2.55→2.61 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.391 / Mean I/σ(I) obs: 3.4 / Rsym value: 0.462 / % possible all: 94.6 |
-Phasing
Phasing | Method: molecular replacement | |||||||||
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Phasing MR | Rfactor: 35.59 / Model details: Phaser MODE: MR_AUTO
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.55→41.14 Å / Cor.coef. Fo:Fc: 0.926 / Cor.coef. Fo:Fc free: 0.839 / Occupancy max: 1 / Occupancy min: 1 / SU B: 11.63 / SU ML: 0.25 / Cross valid method: THROUGHOUT / ESU R Free: 0.338 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 14.022 Å2
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Refinement step | Cycle: LAST / Resolution: 2.55→41.14 Å
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