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Yorodumi- PDB-6y9q: Crystal structure of Whirlin PDZ3_C-ter in complex with Taperin i... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6y9q | ||||||
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Title | Crystal structure of Whirlin PDZ3_C-ter in complex with Taperin internal PDZ binding motif peptide | ||||||
Components |
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Keywords | STRUCTURAL PROTEIN / Whirlin / PDZ / Myosin 15a / complex | ||||||
Function / homology | Function and homology information stereocilium maintenance / stereocilium base / stereocilium / auditory receptor cell stereocilium organization / phosphatase binding / sensory perception of sound Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.315 Å | ||||||
Authors | Zhu, Y. / Delhommel, F. / Haouz, A. / Caillet-Saguy, C. / Vaney, M. / Mechaly, A.E. / Wolff, N. | ||||||
Funding support | France, 1items
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Citation | Journal: J.Mol.Biol. / Year: 2020 Title: Deciphering the Unexpected Binding Capacity of the Third PDZ Domain of Whirlin to Various Cochlear Hair Cell Partners. Authors: Zhu, Y. / Delhommel, F. / Cordier, F. / Luchow, S. / Mechaly, A. / Colcombet-Cazenave, B. / Girault, V. / Pepermans, E. / Bahloul, A. / Gautier, C. / Brule, S. / Raynal, B. / Hoos, S. / ...Authors: Zhu, Y. / Delhommel, F. / Cordier, F. / Luchow, S. / Mechaly, A. / Colcombet-Cazenave, B. / Girault, V. / Pepermans, E. / Bahloul, A. / Gautier, C. / Brule, S. / Raynal, B. / Hoos, S. / Haouz, A. / Caillet-Saguy, C. / Ivarsson, Y. / Wolff, N. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6y9q.cif.gz | 39.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6y9q.ent.gz | 25.5 KB | Display | PDB format |
PDBx/mmJSON format | 6y9q.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6y9q_validation.pdf.gz | 431 KB | Display | wwPDB validaton report |
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Full document | 6y9q_full_validation.pdf.gz | 432.1 KB | Display | |
Data in XML | 6y9q_validation.xml.gz | 8.4 KB | Display | |
Data in CIF | 6y9q_validation.cif.gz | 11.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/y9/6y9q ftp://data.pdbj.org/pub/pdb/validation_reports/y9/6y9q | HTTPS FTP |
-Related structure data
Related structure data | 6y38C 6y9nC 6y9oC 6y9pC 1ufxS 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 on special symmetry positions |
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-Components
#1: Protein | Mass: 11359.070 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Whrn, Dfnb31, Kiaa1526 Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) References: UniProt: Q80VW5 |
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#2: Protein/peptide | Mass: 1845.953 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q4KMQ1 |
#3: 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: 2.48 Å3/Da / Density % sol: 50.4 % |
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Crystal grow | Temperature: 277.15 K / Method: vapor diffusion, sitting drop / Details: 0.2 M LiCl, 25 %w/v PEG 8000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.9786 Å |
Detector | Type: DECTRIS PILATUS 300K / Detector: PIXEL / Date: Jan 31, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9786 Å / Relative weight: 1 |
Reflection | Resolution: 1.315→29.71 Å / Num. obs: 31851 / % possible obs: 99.61 % / Redundancy: 19.5 % / CC1/2: 1 / CC star: 1 / Net I/σ(I): 33.87 |
Reflection shell | Resolution: 1.315→1.362 Å / Num. unique obs: 3089 / CC1/2: 0.975 / CC star: 0.994 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1UFX Resolution: 1.315→29.71 Å / Cross valid method: FREE R-VALUE
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Displacement parameters | Biso mean: 21.88 Å2 | ||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.315→29.71 Å
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Refine LS restraints |
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