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Yorodumi- PDB-5xyv: Crystal structure of drosophila melanogaster Rhino chromoshadow d... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5xyv | ||||||
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Title | Crystal structure of drosophila melanogaster Rhino chromoshadow domain in complex with Deadlock N-terminal domain | ||||||
Components |
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Keywords | PROTEIN BINDING / piRNA pathway / Chromoshadow / Complex | ||||||
Function / homology | Function and homology information piRNA transcription / positive regulation of piRNA transcription / Rhino-Deadlock-Cutoff Complex / oocyte localization involved in germarium-derived egg chamber formation / heterochromatin => GO:0000792 / germarium-derived egg chamber formation / fusome organization / positive regulation of snRNA transcription by RNA polymerase II / chorion-containing eggshell pattern formation / oocyte karyosome formation ...piRNA transcription / positive regulation of piRNA transcription / Rhino-Deadlock-Cutoff Complex / oocyte localization involved in germarium-derived egg chamber formation / heterochromatin => GO:0000792 / germarium-derived egg chamber formation / fusome organization / positive regulation of snRNA transcription by RNA polymerase II / chorion-containing eggshell pattern formation / oocyte karyosome formation / piRNA processing / multicellular organism development / oocyte development / oogenesis / chromosome organization / heterochromatin / pericentric heterochromatin / heterochromatin formation / methylated histone binding / mitotic spindle organization / transcription antitermination / centrosome / chromatin binding / chromatin / positive regulation of transcription by RNA polymerase II / nucleus / cytoplasm Similarity search - Function | ||||||
Biological species | Drosophila melanogaster (fruit fly) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | ||||||
Authors | Yu, B.W. / Huang, Y. | ||||||
Citation | Journal: EMBO Rep. / Year: 2018 Title: Structural insights into Rhino-Deadlock complex for germline piRNA cluster specification Authors: Yu, B. / Lin, Y.A. / Parhad, S.S. / Jin, Z. / Ma, J. / Theurkauf, W.E. / Zhang, Z.Z. / Huang, Y. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5xyv.cif.gz | 62.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5xyv.ent.gz | 44.2 KB | Display | PDB format |
PDBx/mmJSON format | 5xyv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5xyv_validation.pdf.gz | 461.3 KB | Display | wwPDB validaton report |
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Full document | 5xyv_full_validation.pdf.gz | 464.9 KB | Display | |
Data in XML | 5xyv_validation.xml.gz | 11.6 KB | Display | |
Data in CIF | 5xyv_validation.cif.gz | 15.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xy/5xyv ftp://data.pdbj.org/pub/pdb/validation_reports/xy/5xyv | HTTPS FTP |
-Related structure data
Related structure data | 5xywC 2fmmS 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
#1: Protein | Mass: 8577.806 Da / Num. of mol.: 2 / Fragment: UNP residues 353-418 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: rhi / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: L0CPQ5, UniProt: Q7JXA8*PLUS #2: Protein | Mass: 7107.214 Da / Num. of mol.: 2 / Fragment: UNP residues 1-60 Source method: isolated from a genetically manipulated source Details: In the electron density maps we only observed the main chain of 45R, so we used Alanine instead. Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: del, CG9252 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q9VIF5 #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: 2.19 Å3/Da / Density % sol: 43.95 % |
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Crystal grow | Temperature: 290 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 25%(W/V) PEG3350, 0.1 M HEPES (pH 7.5), 0.2 M NaCl |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.9793 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 12, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9793 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→30 Å / Num. obs: 16741 / % possible obs: 99.4 % / Redundancy: 8.1 % / Net I/σ(I): 22.8 |
Reflection shell | Resolution: 2.1→2.18 Å / Redundancy: 4.8 % / Mean I/σ(I) obs: 2.8 / Num. unique obs: 16741 / % possible all: 98.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2FMM Resolution: 2.1→29.651 Å / SU ML: 0.3 / Cross valid method: FREE R-VALUE / σ(F): 1.44 / Phase error: 24.67
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.1→29.651 Å
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Refine LS restraints |
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LS refinement shell |
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