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Open data
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Basic information
Entry | Database: PDB / ID: 5kl1 | ||||||
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Title | Crystal structure of the Pumilio-Nos-hunchback RNA complex | ||||||
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![]() | RNA binding protein/RNA / RNA-binding proteins / RNA binding protein-RNA complex | ||||||
Function / homology | ![]() type Is terminal bouton / positive regulation of deadenylation-independent decapping of nuclear-transcribed mRNA / : / type Ib terminal bouton / postsynapse of neuromuscular junction / head involution / negative regulation of synaptic assembly at neuromuscular junction / oocyte anterior/posterior axis specification / pole plasm / muscle cell postsynaptic specialization ...type Is terminal bouton / positive regulation of deadenylation-independent decapping of nuclear-transcribed mRNA / : / type Ib terminal bouton / postsynapse of neuromuscular junction / head involution / negative regulation of synaptic assembly at neuromuscular junction / oocyte anterior/posterior axis specification / pole plasm / muscle cell postsynaptic specialization / : / regulation of synaptic assembly at neuromuscular junction / CCR4-NOT complex binding / segmentation / : / post-transcriptional gene silencing / neuronal ribonucleoprotein granule / anterior/posterior axis specification, embryo / germ-line stem cell population maintenance / behavioral response to ethanol / germ cell migration / sequence-specific mRNA binding / dendrite morphogenesis / nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / positive regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / post-transcriptional regulation of gene expression / oogenesis / negative regulation of epidermal growth factor receptor signaling pathway / germ cell development / positive regulation of nuclear-transcribed mRNA poly(A) tail shortening / negative regulation of cell cycle / long-term memory / mRNA regulatory element binding translation repressor activity / mRNA 3'-UTR binding / positive regulation of translation / modulation of chemical synaptic transmission / neuromuscular junction / cell migration / nuclear envelope / mitotic cell cycle / spermatogenesis / chemical synaptic transmission / negative regulation of translation / negative regulation of DNA-templated transcription / mRNA binding / negative regulation of apoptotic process / perinuclear region of cytoplasm / RNA binding / zinc ion binding / nucleus / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Qiu, C. / Hall, T.M.T. | ||||||
![]() | ![]() Title: Drosophila Nanos acts as a molecular clamp that modulates the RNA-binding and repression activities of Pumilio. Authors: Weidmann, C.A. / Qiu, C. / Arvola, R.M. / Lou, T.F. / Killingsworth, J. / Campbell, Z.T. / Tanaka Hall, T.M. / Goldstrohm, A.C. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 93.7 KB | Display | ![]() |
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PDB format | ![]() | 67.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 5kl8C ![]() 5klaC ![]() 3alrS ![]() 3h3dS C: citing same article ( S: Starting model for refinement |
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Similar 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: 38728.398 Da / Num. of mol.: 1 / Fragment: UNP residues 1091-1426 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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#2: Protein | Mass: 12958.698 Da / Num. of mol.: 1 / Fragment: UNP residues 289-401 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
#3: RNA chain | Mass: 5090.103 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) ![]() ![]() |
#4: Chemical |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 5.28 Å3/Da / Density % sol: 76.72 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / Details: 1.1 M ammonium sulfate, 0.1 M MES, pH 5.6 |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Apr 24, 2015 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 3.7→50 Å / Num. obs: 13652 / % possible obs: 99.9 % / Redundancy: 11.3 % / Biso Wilson estimate: 140.14 Å2 / Rmerge(I) obs: 0.128 / Rpim(I) all: 0.042 / Rrim(I) all: 0.135 / Χ2: 0.983 / Net I/av σ(I): 19.114 / Net I/σ(I): 5.2 / Num. measured all: 154091 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3H3D, 3ALR Resolution: 3.701→38.325 Å / SU ML: 0.54 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 35.55
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 292.59 Å2 / Biso mean: 173.681 Å2 / Biso min: 56.83 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 3.701→38.325 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 17
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