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Yorodumi- PDB-4nnm: Tax-Interacting Protein-1 (TIP-1) PDZ domain bound to Y-iCAL36 (Y... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4nnm | ||||||
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Title | Tax-Interacting Protein-1 (TIP-1) PDZ domain bound to Y-iCAL36 (YPTSII) peptide | ||||||
Components |
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Keywords | PROTEIN BINDING / Tax-Interacting Protein-1 / TIP-1 / PDZ / PDZ-peptide | ||||||
Function / homology | Function and homology information embryo development / negative regulation of protein localization to cell surface / receptor localization to synapse / RHO GTPases Activate Rhotekin and Rhophilins / establishment or maintenance of epithelial cell apical/basal polarity / activation of GTPase activity / negative regulation of Wnt signaling pathway / receptor clustering / Rho protein signal transduction / postsynaptic density membrane ...embryo development / negative regulation of protein localization to cell surface / receptor localization to synapse / RHO GTPases Activate Rhotekin and Rhophilins / establishment or maintenance of epithelial cell apical/basal polarity / activation of GTPase activity / negative regulation of Wnt signaling pathway / receptor clustering / Rho protein signal transduction / postsynaptic density membrane / neuromuscular junction / fibrillar center / beta-catenin binding / Wnt signaling pathway / cell-cell adhesion / actin cytoskeleton / chemical synaptic transmission / basolateral plasma membrane / neuron projection / negative regulation of cell population proliferation / intracellular membrane-bounded organelle / extracellular exosome / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å | ||||||
Authors | Amacher, J.F. / Madden, D.R. | ||||||
Citation | Journal: To be Published Title: A CAL Inhibitor with Single-PDZ Specificity Rescues deltaF508-CFTR Authors: Cushing, P.R. / Amacher, J.F. / Vouilleme, L. / Culatti, S. / Deng, B. / Gerber, S.A. / Boisguerin, P. / Madden, D.R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4nnm.cif.gz | 101.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4nnm.ent.gz | 78.3 KB | Display | PDB format |
PDBx/mmJSON format | 4nnm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4nnm_validation.pdf.gz | 461.4 KB | Display | wwPDB validaton report |
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Full document | 4nnm_full_validation.pdf.gz | 466.8 KB | Display | |
Data in XML | 4nnm_validation.xml.gz | 13.6 KB | Display | |
Data in CIF | 4nnm_validation.cif.gz | 18.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nn/4nnm ftp://data.pdbj.org/pub/pdb/validation_reports/nn/4nnm | HTTPS FTP |
-Related structure data
Related structure data | 3sfjSC 4nnlC 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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2 |
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Unit cell |
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Details | TIP-1 PDZ domain bound to peptide |
-Components
#1: Protein | Mass: 12459.160 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: TAX1BP3, TIP1 / Plasmid: pET16b / Production host: Escherichia coli (E. coli) / References: UniProt: O14907 #2: Protein/peptide | Mass: 692.801 Da / Num. of mol.: 2 / Source method: obtained synthetically #3: Chemical | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.32 Å3/Da / Density % sol: 47 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6 Details: 40% (w/v) polyethylene glycol (PEG) 3350, 0.15 M potassium thiocyanate (KSCN), 0.1 M 2-ethanesulfonic acid (MES), pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X6A / Wavelength: 0.8856 Å | ||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 270 / Detector: CCD / Date: Oct 18, 2011 | ||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: S1 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.8856 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.6→19.308 Å / Num. all: 31186 / Num. obs: 30055 / % possible obs: 96.4 % / Observed criterion σ(F): 4.9 / Observed criterion σ(I): 17.48 | ||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB: 3SFJ Resolution: 1.6→19.308 Å / SU ML: 0.24 / Cross valid method: omit peptide density / σ(F): 1.99 / Phase error: 26.2 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 55.524 Å2 / ksol: 0.455 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 1.6→19.308 Å
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Refine LS restraints |
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LS refinement shell |
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