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Yorodumi- PDB-4b9w: Structure of extended Tudor domain TD3 from mouse TDRD1 in comple... -
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-Basic information
Entry | Database: PDB / ID: 4b9w | ||||||
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Title | Structure of extended Tudor domain TD3 from mouse TDRD1 in complex with MILI peptide containing dimethylarginine 45. | ||||||
Components |
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Keywords | REPLICATION | ||||||
Function / homology | Function and homology information siRNA-mediated retrotransposon silencing by heterochromatin formation / perinucleolar chromocenter / PET complex / pi-body / retrotransposon silencing by mRNA destabilization / secondary piRNA processing / piRNA-mediated retrotransposon silencing by heterochromatin formation / retrotransposon silencing by heterochromatin formation / P granule organization / positive regulation of meiosis I ...siRNA-mediated retrotransposon silencing by heterochromatin formation / perinucleolar chromocenter / PET complex / pi-body / retrotransposon silencing by mRNA destabilization / secondary piRNA processing / piRNA-mediated retrotransposon silencing by heterochromatin formation / retrotransposon silencing by heterochromatin formation / P granule organization / positive regulation of meiosis I / piRNA binding / piRNA processing / germ-line stem cell population maintenance / negative regulation of circadian rhythm / chromatoid body / dense body / positive regulation of cytoplasmic translation / regulatory ncRNA-mediated gene silencing / P granule / Hydrolases; Acting on ester bonds; Endoribonucleases producing 5'-phosphomonoesters / oogenesis / germ cell development / RNA endonuclease activity / meiotic cell cycle / rhythmic process / spermatogenesis / ribonucleoprotein complex / mRNA binding / synapse / nucleus / metal ion binding / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | MUS MUSCULUS (house mouse) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.1 Å | ||||||
Authors | Mathioudakis, N. / Palencia, A. / Kadlec, J. / Round, A. / Tripsianes, K. / Sattler, M. / Pillai, R.S. / Cusack, S. | ||||||
Citation | Journal: Rna / Year: 2012 Title: The multiple Tudor domain-containing protein TDRD1 is a molecular scaffold for mouse Piwi proteins and piRNA biogenesis factors. Authors: Mathioudakis, N. / Palencia, A. / Kadlec, J. / Round, A. / Tripsianes, K. / Sattler, M. / Pillai, R.S. / Cusack, S. | ||||||
History |
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Remark 700 | SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 5-STRANDED BARREL THIS IS REPRESENTED BY A 6-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "BA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 5-STRANDED BARREL THIS IS REPRESENTED BY A 6-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4b9w.cif.gz | 91 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4b9w.ent.gz | 74.2 KB | Display | PDB format |
PDBx/mmJSON format | 4b9w.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4b9w_validation.pdf.gz | 467.9 KB | Display | wwPDB validaton report |
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Full document | 4b9w_full_validation.pdf.gz | 471.7 KB | Display | |
Data in XML | 4b9w_validation.xml.gz | 18.9 KB | Display | |
Data in CIF | 4b9w_validation.cif.gz | 26.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/b9/4b9w ftp://data.pdbj.org/pub/pdb/validation_reports/b9/4b9w | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper:
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-Components
#1: Protein | Mass: 22578.844 Da / Num. of mol.: 2 / Fragment: EXTENDED TUDOR DOMAIN TD3, RESIDUES 692-892 Source method: isolated from a genetically manipulated source Source: (gene. exp.) MUS MUSCULUS (house mouse) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q99MV1 #2: Protein/peptide | Mass: 1343.582 Da / Num. of mol.: 2 Fragment: N-TERMINAL PEPTIDE CONTAINING METHYLATED ARG45, RESIDUES 38-50 Source method: obtained synthetically / Details: ARG45 IS SYMMETRICALLY DIMETHYLATED / Source: (synth.) MUS MUSCULUS (house mouse) / References: UniProt: Q8CDG1 #3: Chemical | #4: Water | ChemComp-HOH / | Nonpolymer details | GLYCEROL (GOL): FROM CRYOPROTEC | |
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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: 2.65 Å3/Da / Density % sol: 53.6 % / Description: NONE |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: PROTEIN:PEPTIDE 1:5 RATIO, 0.2 M AMMONIUM ACETATE, 0.05 M SODIUM CACODYLATE PH 6.5, 30 % PEG8000, 0.01 M MAGNESIUM ACETATE TETRAHYDRATE |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.939 |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 18, 2011 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.939 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→50 Å / Num. obs: 25755 / % possible obs: 95.5 % / Observed criterion σ(I): 0 / Redundancy: 2.4 % / Rmerge(I) obs: 0.11 / Net I/σ(I): 7.28 |
Reflection shell | Resolution: 2.1→2.2 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.39 / Mean I/σ(I) obs: 2.55 / % possible all: 95.8 |
-Processing
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Refinement | Method to determine structure: SAD Starting model: NONE Resolution: 2.1→36.94 Å / Cor.coef. Fo:Fc: 0.916 / Cor.coef. Fo:Fc free: 0.859 / SU B: 6.314 / SU ML: 0.166 / Cross valid method: THROUGHOUT / ESU R: 0.268 / ESU R Free: 0.23 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 15.793 Å2
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Refinement step | Cycle: LAST / Resolution: 2.1→36.94 Å
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