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- PDB-5nt7: Structure of the LOTUS domain of Oskar in complex with the C-term... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5nt7 | ||||||
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Title | Structure of the LOTUS domain of Oskar in complex with the C-terminal RecA-like domain of Vasa | ||||||
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![]() | hydrolase/hydrolase regulator / DEAD-box RNA helicase / ATPase / RNA binding / regulator / stimulator / germ plasm / nuage / LOTUS / hydrolase- hydrolase regulator complex / hydrolase-hydrolase regulator complex | ||||||
Function / homology | ![]() posterior abdomen determination / pole plasm mRNA localization / regulation of oskar mRNA translation / P granule assembly / pole plasm protein localization / oocyte microtubule cytoskeleton polarization / pole plasm / secondary piRNA processing / posterior cell cortex / thermosensory behavior ...posterior abdomen determination / pole plasm mRNA localization / regulation of oskar mRNA translation / P granule assembly / pole plasm protein localization / oocyte microtubule cytoskeleton polarization / pole plasm / secondary piRNA processing / posterior cell cortex / thermosensory behavior / pole plasm assembly / segmentation / P granule organization / pole cell formation / visual behavior / gamete generation / P granule / germ cell nucleus / cortical actin cytoskeleton organization / oogenesis / germ cell development / protein localization to nucleus / long-term memory / regulation of mRNA stability / visual learning / protein localization / cell cortex / RNA helicase activity / cell differentiation / endosome / RNA helicase / mRNA binding / ATP hydrolysis activity / ATP binding / nucleus / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Jeske, M. / Ephrussi, A. / Mueller, C.W. | ||||||
![]() | ![]() Title: The LOTUS domain is a conserved DEAD-box RNA helicase regulator essential for the recruitment of Vasa to the germ plasm and nuage. Authors: Jeske, M. / Muller, C.W. / Ephrussi, A. | ||||||
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 217 KB | Display | ![]() |
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PDB format | ![]() | 174.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
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-Validation report
Summary document | ![]() | 434 KB | Display | ![]() |
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Full document | ![]() | 438.5 KB | Display | |
Data in XML | ![]() | 26.3 KB | Display | |
Data in CIF | ![]() | 39.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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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: 18247.666 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: The N-terminal residues GH (Glycine, Histidine) stem from the TEV cleavage site Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Protein | Mass: 11917.491 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: The N-terminal residues GPLGS stem from the 3C cleavage site Source: (gene. exp.) ![]() ![]() ![]() ![]() #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.42 Å3/Da / Density % sol: 49.25 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop Details: 100 mM Tris pH 7.5, 200 mM potassium thiocyanate, 16% PEG 3350 |
-Data collection
Diffraction | Mean temperature: 80 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 1, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97908 Å / Relative weight: 1 |
Reflection | Resolution: 1.4→50 Å / Num. obs: 102457 / % possible obs: 91.4 % / Redundancy: 2.16 % / Rmerge(I) obs: 0.048 / Net I/σ(I): 10.44 |
Reflection shell | Resolution: 1.4→1.48 Å / Redundancy: 2.18 % / Rmerge(I) obs: 1.382 / Mean I/σ(I) obs: 0.74 / CC1/2: 0.394 / % possible all: 87.5 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5A49, 2DB3 Resolution: 1.4→48.713 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.93 / Phase error: 24.95
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.4→48.713 Å
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