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Yorodumi- PDB-4u4c: The molecular architecture of the TRAMP complex reveals the organ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4u4c | ||||||
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Title | The molecular architecture of the TRAMP complex reveals the organization and interplay of its two catalytic activities | ||||||
Components |
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Keywords | HYDROLASE / helicase / ATPase / poly(A)polymerase / RNA degradation / exosome | ||||||
Function / homology | Function and homology information polyadenylation-dependent mRNA catabolic process / nuclear mRNA surveillance of mRNA 3'-end processing / nuclear polyadenylation-dependent snoRNA catabolic process / nuclear polyadenylation-dependent snRNA catabolic process / TRAMP complex / nuclear polyadenylation-dependent antisense transcript catabolic process / nuclear polyadenylation-dependent CUT catabolic process / RNA 3'-end processing / meiotic DNA double-strand break formation / TRAMP-dependent tRNA surveillance pathway ...polyadenylation-dependent mRNA catabolic process / nuclear mRNA surveillance of mRNA 3'-end processing / nuclear polyadenylation-dependent snoRNA catabolic process / nuclear polyadenylation-dependent snRNA catabolic process / TRAMP complex / nuclear polyadenylation-dependent antisense transcript catabolic process / nuclear polyadenylation-dependent CUT catabolic process / RNA 3'-end processing / meiotic DNA double-strand break formation / TRAMP-dependent tRNA surveillance pathway / RNA fragment catabolic process / nuclear polyadenylation-dependent rRNA catabolic process / nuclear polyadenylation-dependent mRNA catabolic process / U5 snRNA 3'-end processing / poly(A)-dependent snoRNA 3'-end processing / U4 snRNA 3'-end processing / exonucleolytic trimming to generate mature 3'-end of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / 3'-5' RNA helicase activity / histone mRNA catabolic process / nuclear mRNA surveillance / rRNA catabolic process / tRNA modification / negative regulation of DNA recombination / poly(A) binding / polynucleotide adenylyltransferase / poly(A) RNA polymerase activity / RNA catabolic process / maturation of 5.8S rRNA / Major pathway of rRNA processing in the nucleolus and cytosol / 5'-deoxyribose-5-phosphate lyase activity / localization / base-excision repair / mRNA processing / protein-macromolecule adaptor activity / molecular adaptor activity / RNA helicase activity / oxidoreductase activity / RNA helicase / cell division / mRNA binding / nucleolus / ATP hydrolysis activity / DNA binding / RNA binding / zinc ion binding / ATP binding / nucleus / metal ion binding / cytosol Similarity search - Function | ||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å | ||||||
Authors | Falk, S. / Weir, J.R. / Hentschel, J. / Reichelt, P. / Bonneau, F. / Conti, E. | ||||||
Citation | Journal: Mol.Cell / Year: 2014 Title: The Molecular Architecture of the TRAMP Complex Reveals the Organization and Interplay of Its Two Catalytic Activities. Authors: Falk, S. / Weir, J.R. / Hentschel, J. / Reichelt, P. / Bonneau, F. / Conti, E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4u4c.cif.gz | 219.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4u4c.ent.gz | 168.6 KB | Display | PDB format |
PDBx/mmJSON format | 4u4c.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4u4c_validation.pdf.gz | 483.5 KB | Display | wwPDB validaton report |
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Full document | 4u4c_full_validation.pdf.gz | 496.2 KB | Display | |
Data in XML | 4u4c_validation.xml.gz | 38 KB | Display | |
Data in CIF | 4u4c_validation.cif.gz | 53.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/u4/4u4c ftp://data.pdbj.org/pub/pdb/validation_reports/u4/4u4c | HTTPS FTP |
-Related structure data
Related structure data | 2xgjS 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
-Protein , 2 types, 2 molecules AB
#1: Protein | Mass: 113579.922 Da / Num. of mol.: 1 / Fragment: UNP residues 81-1073 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Strain: ATCC 204508 / S288c / Gene: MTR4, DOB1, YJL050W, J1158 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): pLysS / References: UniProt: P47047, RNA helicase |
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#2: Protein | Mass: 12830.835 Da / Num. of mol.: 1 Fragment: UNP residues 1-62,UNP residues 111-160,UNP residues 1-62,UNP residues 111-160 Source method: isolated from a genetically manipulated source Details: Fusion of Air2 residues 1-62 to Trf4 residues 111-160 Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Strain: ATCC 204508 / S288c / Gene: AIR2, YDL175C, PAP2, TRF4, YOL115W, HRC584, O0716 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): pLysS References: UniProt: Q12476, UniProt: P53632, Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases |
-Non-polymers , 6 types, 235 molecules
#3: Chemical | ChemComp-SO4 / #4: Chemical | #5: Chemical | #6: Chemical | #7: Chemical | ChemComp-PEG / | #8: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 3.38 Å3/Da / Density % sol: 63.62 % |
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Crystal grow | Temperature: 285.15 K / Method: vapor diffusion, sitting drop / pH: 8.2 / Details: 0.1 M Tris pH 8.2, 0.15 M Li2SO4, 32% PEG 400 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å |
Detector | Type: PSI PILATUS 6M / Detector: PIXEL / Date: Sep 26, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→86 Å / Num. obs: 67064 / % possible obs: 99.61 % / Redundancy: 5.6 % / Net I/σ(I): 15.6 |
Reflection shell | Resolution: 2.397→2.483 Å / Redundancy: 4.5 % / Rmerge(I) obs: 1.075 / Mean I/σ(I) obs: 1.16 / % possible all: 96.52 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2XGJ Resolution: 2.4→49.696 Å / SU ML: 0.41 / Cross valid method: FREE R-VALUE / σ(F): 1.05 / Phase error: 28.8 / 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 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.4→49.696 Å
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Refine LS restraints |
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LS refinement shell |
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