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- PDB-7wek: Crystal structure of the mouse Wdr47 NTD in complex with the WBR ... -
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Open data
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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. | ||||||
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![]() | PROTEIN BINDING / LisH motif containing protein | ||||||
Function / homology | ![]() regulation of organelle organization / zonula adherens maintenance / microtubule minus-end / 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 ...regulation of organelle organization / zonula adherens maintenance / microtubule minus-end / 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 / microtubule minus-end binding / 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 / microtubule / in utero embryonic development / calmodulin binding / centrosome / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Ren, J.Q. / Li, D. / Feng, W. | ||||||
Funding support | ![]()
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![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 118.4 KB | Display | ![]() |
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PDB format | ![]() | 90.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 446.1 KB | Display | ![]() |
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Full document | ![]() | 448.5 KB | Display | |
Data in XML | ![]() | 19.9 KB | Display | |
Data in CIF | ![]() | 26.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7wejSC S: Starting model for refinement C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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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.) ![]() ![]() ![]() ![]() #2: Protein/peptide | Mass: 3215.610 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) ![]() ![]() |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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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: ![]() ![]() ![]() |
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 |
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Processing
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Refinement | Method to determine structure: ![]() 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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