+Open data
-Basic information
Entry | Database: PDB / ID: 2wp8 | ||||||
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Title | yeast rrp44 nuclease | ||||||
Components |
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Keywords | HYDROLASE / EXOSOME / NUCLEUS / NUCLEASE / RNA-BINDING / EXONUCLEASE / RNA BINDING / MITOCHONDRION / RRNA PROCESSING | ||||||
Function / homology | Function and homology information Butyrate Response Factor 1 (BRF1) binds and destabilizes mRNA / Tristetraprolin (TTP, ZFP36) binds and destabilizes mRNA / mRNA decay by 3' to 5' exoribonuclease / nuclear polyadenylation-dependent CUT catabolic process / nuclear mRNA surveillance of mRNA 3'-end processing / regulatory ncRNA 3'-end processing / U1 snRNA 3'-end processing / TRAMP-dependent tRNA surveillance pathway / U5 snRNA 3'-end processing / cytoplasmic exosome (RNase complex) ...Butyrate Response Factor 1 (BRF1) binds and destabilizes mRNA / Tristetraprolin (TTP, ZFP36) binds and destabilizes mRNA / mRNA decay by 3' to 5' exoribonuclease / nuclear polyadenylation-dependent CUT catabolic process / nuclear mRNA surveillance of mRNA 3'-end processing / regulatory ncRNA 3'-end processing / U1 snRNA 3'-end processing / TRAMP-dependent tRNA surveillance pathway / U5 snRNA 3'-end processing / cytoplasmic exosome (RNase complex) / exosome (RNase complex) / nuclear polyadenylation-dependent rRNA catabolic process / nuclear-transcribed mRNA catabolic process, 3'-5' exonucleolytic nonsense-mediated decay / U4 snRNA 3'-end processing / nuclear exosome (RNase complex) / poly(A)-dependent snoRNA 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) / nuclear mRNA surveillance / rRNA catabolic process / mRNA 3'-UTR AU-rich region binding / Hydrolases; Acting on ester bonds; Endoribonucleases producing 5'-phosphomonoesters / RNA catabolic process / nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / nonfunctional rRNA decay / Major pathway of rRNA processing in the nucleolus and cytosol / nuclear-transcribed mRNA catabolic process / RNA processing / RNA endonuclease activity / mRNA processing / Hydrolases; Acting on ester bonds; Exoribonucleases producing 5'-phosphomonoesters / 3'-5'-RNA exonuclease activity / endonuclease activity / tRNA binding / nucleolus / mitochondrion / RNA binding / nucleus Similarity search - Function | ||||||
Biological species | SACCHAROMYCES CEREVISIAE (brewer's yeast) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å | ||||||
Authors | Basquin, J. / Bonneau, F. / Ebert, J. / Lorentzen, E. / Conti, E. | ||||||
Citation | Journal: Cell(Cambridge,Mass.) / Year: 2009 Title: The Yeast Exosome Functions as a Macromolecular Cage to Channel RNA Substrates for Degradation. Authors: Bonneau, F. / Basquin, J. / Ebert, J. / Lorentzen, E. / Conti, E. | ||||||
History |
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Remark 700 | SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2wp8.cif.gz | 283.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2wp8.ent.gz | 221.7 KB | Display | PDB format |
PDBx/mmJSON format | 2wp8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2wp8_validation.pdf.gz | 465.4 KB | Display | wwPDB validaton report |
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Full document | 2wp8_full_validation.pdf.gz | 492.6 KB | Display | |
Data in XML | 2wp8_validation.xml.gz | 49.5 KB | Display | |
Data in CIF | 2wp8_validation.cif.gz | 68 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wp/2wp8 ftp://data.pdbj.org/pub/pdb/validation_reports/wp/2wp8 | HTTPS FTP |
-Related 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: 34001.859 Da / Num. of mol.: 1 Fragment: EXOSOME NON-CATALYTIC CORE COMPONENT RRP45, RIBOSOMAL RNA-PROCESSING PROTEIN 45 Source method: isolated from a genetically manipulated source Source: (gene. exp.) SACCHAROMYCES CEREVISIAE (brewer's yeast) Plasmid: PETM-11 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) References: UniProt: Q05636, Hydrolases; Acting on ester bonds; Exoribonucleases producing 5'-phosphomonoesters |
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#2: Protein | Mass: 27612.725 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) SACCHAROMYCES CEREVISIAE (brewer's yeast) Plasmid: PETMCN / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) References: UniProt: P46948, Hydrolases; Acting on ester bonds; Exoribonucleases producing 5'-phosphomonoesters |
#3: Protein | Mass: 111228.594 Da / Num. of mol.: 1 / Fragment: RESIDUES 25-1001 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) SACCHAROMYCES CEREVISIAE (brewer's yeast) Plasmid: PETMCN / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) References: UniProt: Q08162, Hydrolases; Acting on ester bonds; Exoribonucleases producing 5'-phosphomonoesters |
#4: Chemical | ChemComp-CL / |
#5: Chemical | ChemComp-GOL / |
Compound details | ENGINEERED |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.86 Å3/Da / Density % sol: 57.03 % / Description: NONE |
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Crystal grow | pH: 8 Details: 7.5 % (W/V) OF PEG 20.000, 50 MM TRIS PH 8.0 AND 10% (W/V) GLYCEROL |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.978 |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Mar 26, 2009 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.978 Å / Relative weight: 1 |
Reflection | Resolution: 3→20 Å / Num. obs: 39670 / % possible obs: 100 % / Observed criterion σ(I): 2 / Redundancy: 10 % / Biso Wilson estimate: 0 Å2 / Rmerge(I) obs: 0.01 / Net I/σ(I): 21 |
Reflection shell | Resolution: 3→3.2 Å / Rmerge(I) obs: 0.05 / Mean I/σ(I) obs: 5.6 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRIES 2NN6, 2VNU Resolution: 3→19.99 Å / Cor.coef. Fo:Fc: 0.919 / Cor.coef. Fo:Fc free: 0.848 / SU B: 40.476 / SU ML: 0.345 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0 / ESU R Free: 0.439 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
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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 mean: 24.452 Å2
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Refinement step | Cycle: LAST / Resolution: 3→19.99 Å
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Refine LS restraints |
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