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Yorodumi- PDB-6fql: Crystal structure of Danio rerio Lin41 filamin-NHL domains in com... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6fql | ||||||
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Title | Crystal structure of Danio rerio Lin41 filamin-NHL domains in complex with mab-10 3'UTR 13mer RNA | ||||||
Components |
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Keywords | RNA BINDING PROTEIN / post-transcriptional regulation | ||||||
Function / homology | Function and homology information Antigen processing: Ubiquitination & Proteasome degradation / regulation of neural precursor cell proliferation / miRNA-mediated gene silencing by inhibition of translation / neural tube development / miRNA binding / fibroblast growth factor receptor signaling pathway / protein autoubiquitination / stem cell proliferation / P-body / RING-type E3 ubiquitin transferase ...Antigen processing: Ubiquitination & Proteasome degradation / regulation of neural precursor cell proliferation / miRNA-mediated gene silencing by inhibition of translation / neural tube development / miRNA binding / fibroblast growth factor receptor signaling pathway / protein autoubiquitination / stem cell proliferation / P-body / RING-type E3 ubiquitin transferase / protein polyubiquitination / G1/S transition of mitotic cell cycle / ubiquitin-protein transferase activity / ubiquitin protein ligase activity / proteasome-mediated ubiquitin-dependent protein catabolic process / zinc ion binding Similarity search - Function | ||||||
Biological species | Danio rerio (zebrafish) Caenorhabditis elegans (invertebrata) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.349 Å | ||||||
Authors | Kumari, P. / Aeschimann, F. / Gaidatzis, D. / Keusch, J.J. / Ghosh, P. / Neagu, A. / Pachulska-Wieczorek, K. / Bujnicki, J.M. / Gut, H. / Grosshans, H. / Ciosk, R. | ||||||
Citation | Journal: Nat Commun / Year: 2018 Title: Evolutionary plasticity of the NHL domain underlies distinct solutions to RNA recognition. Authors: Kumari, P. / Aeschimann, F. / Gaidatzis, D. / Keusch, J.J. / Ghosh, P. / Neagu, A. / Pachulska-Wieczorek, K. / Bujnicki, J.M. / Gut, H. / Grosshans, H. / Ciosk, R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6fql.cif.gz | 186.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6fql.ent.gz | 145.2 KB | Display | PDB format |
PDBx/mmJSON format | 6fql.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6fql_validation.pdf.gz | 448.7 KB | Display | wwPDB validaton report |
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Full document | 6fql_full_validation.pdf.gz | 449.6 KB | Display | |
Data in XML | 6fql_validation.xml.gz | 16.7 KB | Display | |
Data in CIF | 6fql_validation.cif.gz | 23.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fq/6fql ftp://data.pdbj.org/pub/pdb/validation_reports/fq/6fql | HTTPS FTP |
-Related structure data
Related structure data | 6fptSC 6fq3C S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 44624.820 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: Fragment: Lin41 filamin-NHL domains (residues 435-824) Source: (gene. exp.) Danio rerio (zebrafish) / Gene: trim71, lin41 / Production host: Spodoptera frugiperda (fall armyworm) / Variant (production host): SF9 References: UniProt: E7FAM5, RING-type E3 ubiquitin transferase | ||
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#2: RNA chain | Mass: 4103.470 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Fragment of C. elegans mab-10 3'UTR / Source: (synth.) Caenorhabditis elegans (invertebrata) | ||
#3: Chemical | ChemComp-CL / #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.32 Å3/Da / Density % sol: 62.99 % |
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Crystal grow | Temperature: 273 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 10% PEG 8000 20% ethylene glycol 0.1 M carboxylic acids 0.1 M MES/imidazole pH 6.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 30, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.349→50 Å / Num. obs: 27367 / % possible obs: 99.4 % / Redundancy: 16.4 % / Biso Wilson estimate: 62.8 Å2 / CC1/2: 0.99 / Rsym value: 0.124 / Net I/σ(I): 16 |
Reflection shell | Resolution: 2.349→2.41 Å / Redundancy: 15.4 % / Num. unique obs: 1846 / CC1/2: 0.429 / Rsym value: 2.468 / % possible all: 92.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6FPT Resolution: 2.349→46.3 Å / SU ML: 0.32 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 22.78
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 67.1 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.349→46.3 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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