+Open data
-Basic information
Entry | Database: PDB / ID: 6hu6 | |||||||||
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Title | Structure of ARF1 RNA | |||||||||
Components |
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Keywords | RNA / dsRBD / RNA localization / SMD / Staufen | |||||||||
Function / homology | AMMONIUM ION / RNA / RNA (> 10) Function and homology information | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.904 Å | |||||||||
Authors | Emmerich, C. / Lazzaretti, D. / Bandholz-Cajamarca, L. / Bono, F. | |||||||||
Funding support | Germany, 2items
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Citation | Journal: Life Sci Alliance / Year: 2018 Title: The crystal structure of Staufen1 in complex with a physiological RNA sheds light on substrate selectivity. Authors: Lazzaretti, D. / Bandholz-Cajamarca, L. / Emmerich, C. / Schaaf, K. / Basquin, C. / Irion, U. / Bono, F. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6hu6.cif.gz | 87.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6hu6.ent.gz | 69.2 KB | Display | PDB format |
PDBx/mmJSON format | 6hu6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hu/6hu6 ftp://data.pdbj.org/pub/pdb/validation_reports/hu/6hu6 | HTTPS FTP |
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-Related 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
-RNA chain , 4 types, 4 molecules AEBF
#1: RNA chain | Mass: 6092.688 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) |
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#2: RNA chain | Mass: 6071.617 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) |
#3: RNA chain | Mass: 3240.012 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) |
#4: RNA chain | Mass: 2808.703 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) |
-Non-polymers , 2 types, 43 molecules
#5: Chemical | #6: 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: 2.29 Å3/Da / Density % sol: 46.32 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / Details: 1.7 M (NH4)2SO4, 100 mM Tri-sodium citrate pH 6.2 |
-Data collection
Diffraction | Mean temperature: 80 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 24, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→38 Å / Num. obs: 25323 / % possible obs: 99.9 % / Redundancy: 10.3 % / Net I/σ(I): 13.52 |
Reflection shell | Resolution: 1.9→2.02 Å |
-Processing
Software |
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Refinement | Resolution: 1.904→37.802 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 32.17
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.904→37.802 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: -9.0468 Å / Origin y: 12.2677 Å / Origin z: -37.7518 Å
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Refinement TLS group | Selection details: all |