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Yorodumi- PDB-3o6e: Crystal Structure of human Hiwi1 PAZ domain (residues 277-399) in... -
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-Basic information
Entry | Database: PDB / ID: 3o6e | ||||||
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Title | Crystal Structure of human Hiwi1 PAZ domain (residues 277-399) in complex with 14-mer RNA (12-bp + 2-nt overhang) containing 2'-OCH3 at its 3'-end | ||||||
Components |
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Keywords | RNA BINDING PROTEIN/RNA / Piwi / PAZ / RNA silencing / pi-RNA / Hiwi1 / Hili / PAZ domain / RNA BINDING PROTEIN-RNA complex | ||||||
Function / homology | Function and homology information primary piRNA processing / mRNA cap binding complex binding / piRNA-mediated retrotransposon silencing by heterochromatin formation / piRNA binding / : / sperm DNA condensation / chromatoid body / dense body / P granule / regulatory ncRNA-mediated gene silencing ...primary piRNA processing / mRNA cap binding complex binding / piRNA-mediated retrotransposon silencing by heterochromatin formation / piRNA binding / : / sperm DNA condensation / chromatoid body / dense body / P granule / regulatory ncRNA-mediated gene silencing / Hydrolases; Acting on ester bonds; Endoribonucleases producing 5'-phosphomonoesters / PIWI-interacting RNA (piRNA) biogenesis / spermatid development / RNA endonuclease activity / meiotic cell cycle / regulation of translation / spermatogenesis / single-stranded RNA binding / mRNA binding / protein kinase binding / metal ion binding / nucleus / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.904 Å | ||||||
Authors | Tian, Y. / Simanshu, D.K. / Ma, J.-B. / Patel, D.J. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2011 Title: Inaugural Article: Structural basis for piRNA 2'-O-methylated 3'-end recognition by Piwi PAZ (Piwi/Argonaute/Zwille) domains. Authors: Tian, Y. / Simanshu, D.K. / Ma, J.B. / Patel, D.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3o6e.cif.gz | 77.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3o6e.ent.gz | 54.2 KB | Display | PDB format |
PDBx/mmJSON format | 3o6e.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/o6/3o6e ftp://data.pdbj.org/pub/pdb/validation_reports/o6/3o6e | HTTPS FTP |
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-Related structure data
Related structure data | 3o3iC 3o7vSC 3o7xC C: citing same article (ref.) S: Starting model for refinement |
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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
#1: Protein | Mass: 14625.195 Da / Num. of mol.: 1 / Fragment: PAZ domain (UNP Residues 277-399) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: HIWI, Piwi-like protein 1, PIWIL1 / Plasmid: pET-28b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q96J94 |
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#2: RNA chain | Mass: 4438.678 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Chemically synthesized |
#3: 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: 1.87 Å3/Da / Density % sol: 34.13 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 4.6 Details: 1-5% PEG3350, 50 mM NaCl, 50 mM Na-acetate buffer, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.9792 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Sep 15, 2009 / Details: vertical focusing mirror | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Rosenbaum-Rock double crystal sagittal focusing monochromator Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9792 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.9→30 Å / Num. obs: 3451 / % possible obs: 95.3 % / Redundancy: 10.4 % / Rmerge(I) obs: 0.083 / Χ2: 1.29 / Net I/σ(I): 32.5 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3O7V Resolution: 2.904→15 Å / Cor.coef. Fo:Fc: 0.911 / Cor.coef. Fo:Fc free: 0.866 / WRfactor Rfree: 0.2717 / WRfactor Rwork: 0.2279 / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.7753 / SU B: 51.553 / SU ML: 0.418 / SU R Cruickshank DPI: 0.4752 / SU Rfree: 0.5689 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.569 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 101.65 Å2 / Biso mean: 61.5548 Å2 / Biso min: 33.31 Å2
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Refinement step | Cycle: LAST / Resolution: 2.904→15 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.904→2.977 Å / Total num. of bins used: 20
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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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