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Yorodumi- PDB-7wek: Crystal structure of the mouse Wdr47 NTD in complex with the WBR ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7wek | ||||||
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Title | Crystal structure of the mouse Wdr47 NTD in complex with the WBR motif form Camsap3. | ||||||
Components |
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Keywords | PROTEIN BINDING / LisH motif containing protein | ||||||
Function / homology | Function and homology information regulation of organelle organization / zonula adherens maintenance / microtubule minus-end / microtubule minus-end binding / protein transport along microtubule / regulation of Golgi organization / microtubule anchoring / establishment or maintenance of microtubule cytoskeleton polarity / cilium movement / epithelial cell-cell adhesion ...regulation of organelle organization / zonula adherens maintenance / microtubule minus-end / microtubule minus-end binding / protein transport along microtubule / regulation of Golgi organization / microtubule anchoring / establishment or maintenance of microtubule cytoskeleton polarity / cilium movement / epithelial cell-cell adhesion / zonula adherens / negative regulation of microtubule depolymerization / establishment of epithelial cell apical/basal polarity / motile cilium / embryo development ending in birth or egg hatching / regulation of focal adhesion assembly / spectrin binding / regulation of microtubule polymerization / axoneme / regulation of microtubule cytoskeleton organization / cytoplasmic microtubule organization / regulation of cell migration / ciliary basal body / microtubule cytoskeleton organization / neuron projection development / microtubule cytoskeleton / actin filament binding / in utero embryonic development / microtubule / calmodulin binding / centrosome / cytoplasm Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.21 Å | ||||||
Authors | Ren, J.Q. / Li, D. / Feng, W. | ||||||
Funding support | China, 1items
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Citation | Journal: Cell Rep / Year: 2022 Title: Intertwined Wdr47-NTD dimer recognizes a basic-helical motif in Camsap proteins for proper central-pair microtubule formation. Authors: Ren, J. / Li, D. / Liu, J. / Liu, H. / Yan, X. / Zhu, X. / Feng, W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7wek.cif.gz | 118.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7wek.ent.gz | 90.8 KB | Display | PDB format |
PDBx/mmJSON format | 7wek.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/we/7wek ftp://data.pdbj.org/pub/pdb/validation_reports/we/7wek | HTTPS FTP |
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-Related structure data
Related structure data | 7wejSC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 33550.934 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Wdr47, Kiaa0893 / Production host: Escherichia (bacteria) / References: UniProt: Q8CGF6 #2: Protein/peptide | Mass: 3215.610 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Mus musculus (house mouse) / References: UniProt: Q80VC9 |
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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: 3.24 Å3/Da / Density % sol: 62.05 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: 0.1M Tris-HCl, 20% (w/v) PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.979 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 19, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 3.2→30 Å / Num. obs: 16169 / % possible obs: 99.8 % / Redundancy: 6.7 % / CC1/2: 0.994 / CC star: 0.999 / Net I/σ(I): 18.3 |
Reflection shell | Resolution: 3.2→3.31 Å / Mean I/σ(I) obs: 1.148 / Num. unique obs: 1569 / CC1/2: 0.664 / CC star: 0.893 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 7WEJ Resolution: 3.21→24.18 Å / SU ML: 0.48 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 34.42 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 240.53 Å2 / Biso min: 28.94 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 3.21→24.18 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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