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Yorodumi- PDB-3nyb: Structure and function of the polymerase core of TRAMP, a RNA sur... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3nyb | ||||||
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Title | Structure and function of the polymerase core of TRAMP, a RNA surveillance complex | ||||||
Components |
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Keywords | TRANSFERASE/RNA BINDING PROTEIN / polyA RNA polymerase / zinc knuckle protein / RNA surveillance / Mtr4p binds to Trf4p/Air2p heterodimer / TRANSFERASE-RNA BINDING PROTEIN complex | ||||||
Function / homology | Function and homology information polyadenylation-dependent mRNA catabolic process / nuclear mRNA surveillance of mRNA 3'-end processing / nuclear polyadenylation-dependent antisense transcript catabolic process / nuclear polyadenylation-dependent snoRNA catabolic process / nuclear polyadenylation-dependent snRNA catabolic process / TRAMP complex / meiotic DNA double-strand break formation / nuclear polyadenylation-dependent CUT catabolic process / nuclear polyadenylation-dependent mRNA catabolic process / RNA 3'-end processing ...polyadenylation-dependent mRNA catabolic process / nuclear mRNA surveillance of mRNA 3'-end processing / nuclear polyadenylation-dependent antisense transcript catabolic process / nuclear polyadenylation-dependent snoRNA catabolic process / nuclear polyadenylation-dependent snRNA catabolic process / TRAMP complex / meiotic DNA double-strand break formation / nuclear polyadenylation-dependent CUT catabolic process / nuclear polyadenylation-dependent mRNA catabolic process / RNA 3'-end processing / TRAMP-dependent tRNA surveillance pathway / RNA fragment catabolic process / U4 snRNA 3'-end processing / nuclear polyadenylation-dependent rRNA catabolic process / poly(A)-dependent snoRNA 3'-end processing / polynucleotide adenylyltransferase / histone mRNA catabolic process / poly(A) RNA polymerase activity / negative regulation of DNA recombination / tRNA modification / 5'-deoxyribose-5-phosphate lyase activity / localization / base-excision repair / protein-macromolecule adaptor activity / molecular adaptor activity / cell division / mRNA binding / nucleolus / RNA binding / zinc ion binding / metal ion binding / nucleus / cytosol Similarity search - Function | ||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.7007 Å | ||||||
Authors | Reinisch, K.M. / Hamill, S. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2010 Title: Structure and function of the polymerase core of TRAMP, a RNA surveillance complex. Authors: Hamill, S. / Wolin, S.L. / Reinisch, K.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3nyb.cif.gz | 171.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3nyb.ent.gz | 135.5 KB | Display | PDB format |
PDBx/mmJSON format | 3nyb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ny/3nyb ftp://data.pdbj.org/pub/pdb/validation_reports/ny/3nyb | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 36459.453 Da / Num. of mol.: 1 Fragment: central and catalytic domains of Trf4p (UNP residues 161-481) Mutation: D293A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Gene: PAP2, TRF4, YOL115W, O0716, HRC584 / Production host: Escherichia coli (E. coli) References: UniProt: P53632, Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases | ||
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#2: Protein | Mass: 9399.759 Da / Num. of mol.: 1 Fragment: fourth and fifth zinc knuckles of Air2p (UNP residues 118-198) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Gene: AIR2, YDL175C / Production host: Escherichia coli (E. coli) / References: UniProt: Q12476 | ||
#3: Chemical | #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: 2.8 Å3/Da / Density % sol: 56.13 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.8 Details: 100 mM sodium citrate at pH 5.8, 200 mM sodium acetate, 11% PEG 4000, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 110 K | |||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 1.28215 Å | |||||||||||||||
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 19, 2009 | |||||||||||||||
Radiation | Monochromator: cryogenically cooled Si double crystal (111) monochromator Protocol: SAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||
Radiation wavelength | Wavelength: 1.28215 Å / Relative weight: 1 | |||||||||||||||
Reflection | Resolution: 2.6→25 Å / Num. all: 16163 / Num. obs: 16163 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 10.6 % / Rmerge(I) obs: 0.077 | |||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.7007→24.656 Å / SU ML: 0.37 / σ(F): 0.14 / Phase error: 27.04 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 39.544 Å2 / ksol: 0.315 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 2.7007→24.656 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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