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Yorodumi- PDB-2jcq: The hyaluronan binding domain of murine CD44 in a Type A complex ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2jcq | |||||||||
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Title | The hyaluronan binding domain of murine CD44 in a Type A complex with an HA 8-mer | |||||||||
Components | CD44 ANTIGEN | |||||||||
Keywords | SUGAR BINDING PROTEIN / SUGAR-BINDING PROTEIN / HYAURONAN / LINK-DOMAIN / PROTEOGLYCAN / BLOOD GROUP ANTIGEN / LECTIN / ANTIGEN / MEMBRANE / RECEPTOR / SULFATION / GLYCOPROTEIN / C-TYPE LECTIN / CELL ADHESION / EXTRACELLULAR MATRIX / PYRROLIDONE CARBOXYLIC ACID / TRANSMEMBRANE / SUGAR- BINDING / PHOSPHORYLATION | |||||||||
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 / cargo receptor activity / 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 / 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 / negative regulation of inflammatory response / transmembrane signaling receptor activity / Wnt signaling pathway / cytokine-mediated signaling pathway / positive regulation of peptidyl-tyrosine phosphorylation / positive regulation of peptidyl-serine phosphorylation / neuron projection development / cell migration / basolateral plasma membrane / positive regulation of ERK1 and ERK2 cascade / cell adhesion / apical plasma membrane / inflammatory response / membrane raft / 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 | |||||||||
Biological species | MUS MUSCULUS (house mouse) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.25 Å | |||||||||
Authors | Banerji, S. / Wright, A.J. / Noble, M.E.M. / Mahoney, D.J. / Campbell, I.D. / Day, A.J. / Jackson, D.G. | |||||||||
Citation | Journal: Nat.Struct.Mol.Biol. / Year: 2008 Title: Structures of the Cd44-Hyaluronan Complex Provide Insight Into a Fundamental Carbohydrate-Protein Interaction. Authors: Banerji, S. / Wright, A.J. / Noble, M.E.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 | 2jcq.cif.gz | 145.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2jcq.ent.gz | 116 KB | Display | PDB format |
PDBx/mmJSON format | 2jcq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2jcq_validation.pdf.gz | 703.6 KB | Display | wwPDB validaton report |
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Full document | 2jcq_full_validation.pdf.gz | 706.2 KB | Display | |
Data in XML | 2jcq_validation.xml.gz | 11 KB | Display | |
Data in CIF | 2jcq_validation.cif.gz | 15.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jc/2jcq ftp://data.pdbj.org/pub/pdb/validation_reports/jc/2jcq | HTTPS FTP |
-Related structure data
Related structure data | 2jcpC 2jcrC 1uuhS C: citing same article (ref.) S: Starting model for refinement |
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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: 17129.047 Da / Num. of mol.: 1 / Fragment: HYALURONAN BINDING DOMAIN, RESIDUES 23-174 Source method: isolated from a genetically manipulated source Details: ENCODED RESIDUES 25-174, EQUIVALENT TO RESIDUES 1-151 OF THE MATURE PROTEIN, WITH ADDITIONAL RESIDUES M, N ADDED AT THE N-TERMINUS Source: (gene. exp.) MUS MUSCULUS (house mouse) / Plasmid: PET19B / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): PLYSS / References: UniProt: P15379 |
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#2: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-beta-D-glucopyranuronic acid-(1-3)-2-acetamido-2- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-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-(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-GOL / |
#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: 2.12 Å3/Da / Density % sol: 42 % |
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Crystal grow | pH: 7 Details: CO-CRYSTALS OF THE CD44/HA8 COMPLEX WERE PREPARED AFTER ADDITION OF HA8 (2MM FINAL CONCENTRATION) TO THE 0.5MM PROTEIN SOLUTION FOLLOWED BY MIXING 1:1 WITH WELL SOLUTIONS CONTAINING 25% (W/V) ...Details: CO-CRYSTALS OF THE CD44/HA8 COMPLEX WERE PREPARED AFTER ADDITION OF HA8 (2MM FINAL CONCENTRATION) TO THE 0.5MM PROTEIN SOLUTION FOLLOWED BY MIXING 1:1 WITH WELL SOLUTIONS CONTAINING 25% (W/V) PEG 3350 AND 100MM NACL IN 100MM HEPES BUFFERED AT EITHER PH 7.0 OR PH 8.0 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Apr 1, 2004 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.934 Å / Relative weight: 1 |
Reflection | Resolution: 1.25→23.42 Å / Num. obs: 36225 / % possible obs: 92.7 % / Observed criterion σ(I): 0 / Redundancy: 5.44 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 6.75 |
Reflection shell | Resolution: 1.25→1.32 Å / Redundancy: 2.65 % / Rmerge(I) obs: 0.42 / Mean I/σ(I) obs: 1.77 / % possible all: 56.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1UUH Resolution: 1.25→41.03 Å / Cor.coef. Fo:Fc: 0.976 / Cor.coef. Fo:Fc free: 0.97 / SU B: 1.234 / SU ML: 0.025 / Cross valid method: THROUGHOUT / ESU R: 0.043 / ESU R Free: 0.041 / 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: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 7.6 Å2
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Refinement step | Cycle: LAST / Resolution: 1.25→41.03 Å
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Refine LS restraints |
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