+Open data
-Basic information
Entry | Database: PDB / ID: 5cff | ||||||
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Title | Crystal structure of Miranda/Staufen dsRBD5 complex | ||||||
Components |
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Keywords | TRANSCRIPTION/RNA BINDING PROTEIN / Coiled-coil and dsRNA-binding domain complex / TRANSCRIPTION-RNA BINDING PROTEIN complex | ||||||
Function / homology | Function and homology information germ plasm / regulation of intracellular mRNA localization / subsynaptic reticulum / pole plasm RNA localization / ganglion mother cell fate determination / bicoid mRNA localization / regulation of oskar mRNA translation / protein localization to cell cortex / pole plasm protein localization / posterior cell cortex ...germ plasm / regulation of intracellular mRNA localization / subsynaptic reticulum / pole plasm RNA localization / ganglion mother cell fate determination / bicoid mRNA localization / regulation of oskar mRNA translation / protein localization to cell cortex / pole plasm protein localization / posterior cell cortex / regulation of pole plasm oskar mRNA localization / asymmetric protein localization involved in cell fate determination / anterograde dendritic transport of messenger ribonucleoprotein complex / positive regulation of cytoplasmic mRNA processing body assembly / pole plasm assembly / neuroblast fate determination / positive regulation of synaptic assembly at neuromuscular junction / RNA localization / basal cortex / ventral cord development / neuronal ribonucleoprotein granule / anterior/posterior axis specification, embryo / messenger ribonucleoprotein complex / asymmetric neuroblast division / intracellular mRNA localization / apical cortex / protein localization to synapse / basal part of cell / regulation of proteolysis / oogenesis / myosin binding / germ cell development / neuroblast proliferation / long-term memory / dendrite cytoplasm / basal plasma membrane / mRNA 3'-UTR binding / P-body / cytoplasmic ribonucleoprotein granule / cytoplasmic stress granule / double-stranded RNA binding / apical part of cell / cell cortex / neuron projection / apical plasma membrane / mRNA binding / centrosome / neuronal cell body / RNA binding / membrane / plasma membrane / cytoplasm Similarity search - Function | ||||||
Biological species | Drosophila melanogaster (fruit fly) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.5 Å | ||||||
Authors | Shan, Z. / Wen, W. | ||||||
Citation | Journal: Nat Commun / Year: 2015 Title: The structural basis of Miranda-mediated Staufen localization during Drosophila neuroblast asymmetric division Authors: Jia, M. / Shan, Z. / Yang, Y. / Liu, C. / Li, J. / Luo, Z.G. / Zhang, M. / Cai, Y. / Wen, W. / Wang, W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5cff.cif.gz | 125.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5cff.ent.gz | 100.4 KB | Display | PDB format |
PDBx/mmJSON format | 5cff.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cf/5cff ftp://data.pdbj.org/pub/pdb/validation_reports/cf/5cff | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
NCS ensembles :
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-Components
#1: Protein | Mass: 10729.630 Da / Num. of mol.: 4 / Fragment: UNP residues 514-589 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: mira, CG12249, Dmel_CG12249 / Plasmid: pET.32M.3C / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q9VDR7 #2: Protein | Mass: 7944.774 Da / Num. of mol.: 4 Fragment: The fifth dsRNA-binding domain, UNP residues 953-1019 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: stau, CG5753 / Plasmid: pET.32M.3C / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: P25159 #3: Water | ChemComp-HOH / | |
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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: 3.61 Å3/Da / Density % sol: 65.91 % Description: THE ENTRY CONTAINS FRIEDEL PAIRS IN F_PLUS/MINUS COLUMNS. |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, hanging drop / pH: 4.8 / Details: sodium acetate,1,6-hexanediol,calcium chloride etc |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9792 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 28, 2013 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9792 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Redundancy: 5.5 % / Number: 189671 / Rmerge(I) obs: 0.078 / Χ2: 2.49 / D res high: 2.5 Å / D res low: 50 Å / Num. obs: 34191 / % possible obs: 94.9 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Diffraction reflection shell |
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Reflection | Resolution: 2.5→50 Å / Num. obs: 34191 / % possible obs: 94.9 % / Redundancy: 5.5 % / Biso Wilson estimate: 53.81 Å2 / Rmerge(I) obs: 0.078 / Χ2: 2.488 / Net I/av σ(I): 35.389 / Net I/σ(I): 13.9 / Num. measured all: 189671 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Rejects: 0
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-Phasing
Phasing | Method: SAD |
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-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.5→27.664 Å / FOM work R set: 0.7235 / SU ML: 0.37 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 33.26 / Stereochemistry target values: ML Details: SF FILE CONTAINS FRIEDEL PAIRS UNDER I/F_MINUS AND I/F_PLUS COLUMNS.
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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: 91.78 Å2 / Biso mean: 42.57 Å2 / Biso min: 14.05 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.5→27.664 Å
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Refine LS restraints |
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Refine LS restraints NCS |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 12
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