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- PDB-4pz3: High-resolution crystal structure of the human CD44 hyaluronan bi... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4pz3 | ||||||
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Title | High-resolution crystal structure of the human CD44 hyaluronan binding domain complex with undefined peptides | ||||||
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![]() | CELL ADHESION / Link module / Binding protein / Hyaluronan / Ectodomain | ||||||
Function / homology | ![]() positive regulation of monocyte aggregation / Hyaluronan uptake and degradation / hyaluronic acid binding / monocyte aggregation / macrophage migration inhibitory factor receptor complex / regulation of lamellipodium morphogenesis / hyaluronan catabolic process / cellular response to fibroblast growth factor stimulus / positive regulation of heterotypic cell-cell adhesion / cartilage development ...positive regulation of monocyte aggregation / Hyaluronan uptake and degradation / hyaluronic acid binding / monocyte aggregation / macrophage migration inhibitory factor receptor complex / regulation of lamellipodium morphogenesis / hyaluronan catabolic process / cellular response to fibroblast growth factor stimulus / positive regulation of heterotypic cell-cell adhesion / cartilage development / wound healing, spreading of cells / cytokine receptor activity / 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 / Integrin cell surface interactions / collagen binding / T cell activation / Degradation of the extracellular matrix / cell-matrix adhesion / secretory granule membrane / cell projection / Cell surface interactions at the vascular wall / negative regulation of cysteine-type endopeptidase activity involved in apoptotic process / cell-cell adhesion / transmembrane signaling receptor activity / positive regulation of peptidyl-tyrosine phosphorylation / Interferon gamma signaling / cell migration / positive regulation of peptidyl-serine phosphorylation / basolateral plasma membrane / positive regulation of ERK1 and ERK2 cascade / cell adhesion / inflammatory response / apical plasma membrane / focal adhesion / Neutrophil degranulation / negative regulation of apoptotic process / Golgi apparatus / cell surface / extracellular exosome / plasma membrane / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() ![]() | ||||||
![]() | Liu, L.K. / Finzel, B. | ||||||
![]() | ![]() Title: High-resolution crystal structures of alternate forms of the human CD44 hyaluronan-binding domain reveal a site for protein interaction. Authors: Liu, L.K. / Finzel, B. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 80.3 KB | Display | ![]() |
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PDB format | ![]() | 64.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 470.3 KB | Display | ![]() |
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Full document | ![]() | 474.8 KB | Display | |
Data in XML | ![]() | 18.3 KB | Display | |
Data in CIF | ![]() | 27.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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1 |
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Unit cell |
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Components
-Protein / Protein/peptide , 2 types, 3 molecules ABC
#1: Protein | Mass: 16959.965 Da / Num. of mol.: 2 / Fragment: HYALURONAN BINDING DOMAIN, RESIDUES 18-170 / Mutation: S18A, L19M Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Protein/peptide | | Mass: 330.379 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: Undefined peptides from the expression system co-purified with the target protein Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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-Non-polymers , 4 types, 376 molecules ![](data/chem/img/PEG.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/MES.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/MES.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | ChemComp-PEG / | ||||
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#4: Chemical | #5: Chemical | ChemComp-MES / | #6: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.2 Å3/Da / Density % sol: 44.09 % |
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Crystal grow | Temperature: 277 K / Method: hanging drop / pH: 6.5 Details: 30% PEG MME 5000, 100 mM MES, 200 mM (NH4)2SO4, 5%DMSO, pH 6.5, hanging drop, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: PSI PILATUS 6M / Detector: PIXEL / Date: Nov 17, 2012 / Details: mirrors |
Radiation | Monochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.083→44.676 Å / Num. all: 123233 / Num. obs: 122395 / % possible obs: 97.1 % / Redundancy: 3.1 % / Rmerge(I) obs: 0.031 / Net I/σ(I): 21.2 |
Reflection shell | Resolution: 1.083→1.086 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.154 / Mean I/σ(I) obs: 5.4 / Num. unique all: 834 / Rsym value: 0.284 / % possible all: 69.3 |
-Phasing
Phasing | Method: ![]() | |||||||||
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Phasing MR | Rfactor: 24.86 / Model details: Phaser MODE: MR_AUTO
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Processing
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Refinement | Method to determine structure: ![]() Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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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 max: 36.94 Å2 / Biso mean: 11.604 Å2 / Biso min: 4.68 Å2
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Refinement step | Cycle: LAST / Resolution: 1.083→44.67 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.083→1.111 Å / Total num. of bins used: 20
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