[English] 日本語
Yorodumi- PDB-4ytd: Crystal structure of the C-terminal Coiled Coil of mouse Bicaudal D1 -
+Open data
-Basic information
Entry | Database: PDB / ID: 4ytd | |||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Title | Crystal structure of the C-terminal Coiled Coil of mouse Bicaudal D1 | |||||||||||||||
Components | Protein bicaudal D homolog 1 | |||||||||||||||
Keywords | TRANSPORT PROTEIN / Retrograde transport / Cytoplasmic dynein / Bicaudal D1 / Coiled Coil / CARGO BINDING | |||||||||||||||
Function / homology | Function and homology information regulation of proteinase activated receptor activity / negative regulation of phospholipase C-activating G protein-coupled receptor signaling pathway / microtubule anchoring at microtubule organizing center / minus-end-directed organelle transport along microtubule / proteinase activated receptor binding / host cell viral assembly compartment / small GTPase binding => GO:0031267 / COPI-independent Golgi-to-ER retrograde traffic / protein localization to organelle / : ...regulation of proteinase activated receptor activity / negative regulation of phospholipase C-activating G protein-coupled receptor signaling pathway / microtubule anchoring at microtubule organizing center / minus-end-directed organelle transport along microtubule / proteinase activated receptor binding / host cell viral assembly compartment / small GTPase binding => GO:0031267 / COPI-independent Golgi-to-ER retrograde traffic / protein localization to organelle / : / positive regulation of protein localization to centrosome / cytoskeletal anchor activity / dynein intermediate chain binding / dynein complex binding / cytoplasmic microtubule / dynactin binding / regulation of microtubule cytoskeleton organization / stress granule assembly / viral process / trans-Golgi network / positive regulation of receptor-mediated endocytosis / cytoplasmic vesicle / centrosome / protein kinase binding / perinuclear region of cytoplasm / Golgi apparatus / membrane / cytosol Similarity search - Function | |||||||||||||||
Biological species | Mus musculus (house mouse) | |||||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.5 Å | |||||||||||||||
Authors | Terawaki, S. / Yoshikane, A. / Higuchi, Y. / Wakamatsu, K. | |||||||||||||||
Funding support | Japan, 4items
| |||||||||||||||
Citation | Journal: Biochem.Biophys.Res.Commun. / Year: 2015 Title: Structural basis for cargo binding and autoinhibition of Bicaudal-D1 by a parallel coiled-coil with homotypic registry Authors: Terawaki, S.I. / Yoshikane, A. / Higuchi, Y. / Wakamatsu, K. | |||||||||||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 4ytd.cif.gz | 102.2 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb4ytd.ent.gz | 83.9 KB | Display | PDB format |
PDBx/mmJSON format | 4ytd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yt/4ytd ftp://data.pdbj.org/pub/pdb/validation_reports/yt/4ytd | HTTPS FTP |
---|
-Related structure data
Similar structure data |
---|
-Links
-Assembly
Deposited unit |
| |||||||||
---|---|---|---|---|---|---|---|---|---|---|
1 |
| |||||||||
Unit cell |
| |||||||||
Components on special symmetry positions |
|
-Components
#1: Protein | Mass: 11964.788 Da / Num. of mol.: 2 / Fragment: UNP residues 711-808 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Bicd1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8BR07 #2: Chemical | ChemComp-PO4 / #3: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
---|
-Sample preparation
Crystal | Density Matthews: 2.33 Å3/Da / Density % sol: 47.3 % |
---|---|
Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8.2 Details: 48% MPD, 0.1 M Tris-HCL, 0.2 M ammonium phosphate, 10 mM TCEP |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 0.97924 Å |
Detector | Type: ADSC QUANTUM 270 / Detector: CCD / Date: Dec 16, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97924 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→50 Å / Num. obs: 35669 / % possible obs: 99.6 % / Redundancy: 7.2 % / Net I/σ(I): 44.6 |
Reflection shell | Resolution: 1.5→1.53 Å |
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: SAD / Resolution: 1.5→31.113 Å / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 21.1 / Stereochemistry target values: ML Details: the entry contains Friedel pairs in F_Plus/Minus columns
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.5→31.113 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|