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Yorodumi- PDB-4wnd: Crystal structure of the TPR domain of LGN in complex with Frmpd4... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4wnd | ||||||
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Title | Crystal structure of the TPR domain of LGN in complex with Frmpd4/Preso1 at 1.5 Angstrom resolution | ||||||
Components |
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Keywords | SIGNALING PROTEIN/PROTEIN BINDING / TETRATRICOPEPTIDE REPEAT / TPR / CELL POLARITY / CYTOPLASM AND CELL CORTEX / SIGNALING PROTEIN-PROTEIN BINDING COMPLEX | ||||||
Function / homology | Function and homology information lateral cell cortex / cell cortex region / maintenance of centrosome location / positive regulation of synapse structural plasticity / positive regulation of spindle assembly / GDP-dissociation inhibitor activity / dynein complex binding / mitotic spindle pole / establishment of mitotic spindle orientation / positive regulation of protein localization to cell cortex ...lateral cell cortex / cell cortex region / maintenance of centrosome location / positive regulation of synapse structural plasticity / positive regulation of spindle assembly / GDP-dissociation inhibitor activity / dynein complex binding / mitotic spindle pole / establishment of mitotic spindle orientation / positive regulation of protein localization to cell cortex / G-protein alpha-subunit binding / lateral plasma membrane / regulation of mitotic spindle organization / phosphatidylinositol-4,5-bisphosphate binding / mitotic spindle organization / : / cell cortex / G alpha (i) signalling events / dendritic spine / cytoskeleton / G protein-coupled receptor signaling pathway / cell division / protein domain specific binding / nucleotide binding / centrosome / protein-containing complex / identical protein binding / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å | ||||||
Authors | Takayanagi, H. / Yuzawa, S. / Sumimoto, H. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.F / Year: 2015 Title: Structural basis for the recognition of the scaffold protein Frmpd4/Preso1 by the TPR domain of the adaptor protein LGN Authors: Takayanagi, H. / Yuzawa, S. / Sumimoto, H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4wnd.cif.gz | 101 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4wnd.ent.gz | 73.1 KB | Display | PDB format |
PDBx/mmJSON format | 4wnd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wn/4wnd ftp://data.pdbj.org/pub/pdb/validation_reports/wn/4wnd | HTTPS FTP |
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-Related structure data
Related structure data | 4wneSC 4wnfC 4wngC S: Starting model for refinement 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
-Protein , 2 types, 2 molecules AB
#1: Protein | Mass: 44948.281 Da / Num. of mol.: 1 / Fragment: N-terminal TPR domain, UNP residues 20-421 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: GPSM2, LGN / Plasmid: pRSFDUET-1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P81274 |
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#2: Protein | Mass: 5831.625 Da / Num. of mol.: 1 / Fragment: FRMPD4-L, UNP residues 978-1025 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: FRMPD4, KIAA0316, PDZD10, PDZK10 / Plasmid: pGEX-6P-2 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q14CM0 |
-Non-polymers , 5 types, 317 molecules
#3: Chemical | ChemComp-SCN / #4: Chemical | ChemComp-PEG / #5: Chemical | ChemComp-PGE / | #6: Chemical | ChemComp-EDO / #7: 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: 1.96 Å3/Da / Density % sol: 37.22 % / Mosaicity: 0.483 ° |
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Crystal grow | Temperature: 293 K / Method: microbatch / pH: 7.5 Details: 0.1 M BisTrispropane (pH 7.5), 0.2 M potassium thiocyanate, 20% PEG 3350 |
-Data collection
Diffraction | Mean temperature: 90 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: RAYONIX MX300HE / Detector: CCD / Date: Apr 13, 2014 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.5→50 Å / Num. obs: 61319 / % possible obs: 98.8 % / Redundancy: 6.2 % / Rmerge(I) obs: 0.037 / Rpim(I) all: 0.014 / Rrim(I) all: 0.04 / Rsym value: 0.037 / Χ2: 0.986 / Net I/av σ(I): 36.531 / Net I/σ(I): 21.9 / Num. measured all: 379458 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Rejects: 0
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4WNE Resolution: 1.5→46.79 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.966 / WRfactor Rfree: 0.208 / WRfactor Rwork: 0.1869 / FOM work R set: 0.8847 / SU B: 1.189 / SU ML: 0.044 / SU R Cruickshank DPI: 0.0684 / SU Rfree: 0.0673 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.068 / ESU R Free: 0.067 / Stereochemistry target values: MAXIMUM LIKELIHOOD 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: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 81.59 Å2 / Biso mean: 24.126 Å2 / Biso min: 11.97 Å2
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Refinement step | Cycle: final / Resolution: 1.5→46.79 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.504→1.543 Å / Total num. of bins used: 20
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