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Yorodumi- PDB-5k36: Structure of an eleven component nuclear RNA exosome complex boun... -
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-Basic information
Entry | Database: PDB / ID: 5k36 | |||||||||
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Title | Structure of an eleven component nuclear RNA exosome complex bound to RNA | |||||||||
Components |
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Keywords | Hydrolase/RNA / Exoribonuclease / Complex / RNA / STRUCTURAL PROTEIN / Hydrolase-RNA complex | |||||||||
Function / homology | Function and homology information Butyrate Response Factor 1 (BRF1) binds and destabilizes mRNA / Tristetraprolin (TTP, ZFP36) binds and destabilizes mRNA / nuclear polyadenylation-dependent antisense transcript catabolic process / nuclear polyadenylation-dependent snoRNA catabolic process / nuclear polyadenylation-dependent snRNA catabolic process / mRNA decay by 3' to 5' exoribonuclease / U1 snRNA 3'-end processing / nuclear polyadenylation-dependent CUT catabolic process / nuclear polyadenylation-dependent mRNA catabolic process / U5 snRNA 3'-end processing ...Butyrate Response Factor 1 (BRF1) binds and destabilizes mRNA / Tristetraprolin (TTP, ZFP36) binds and destabilizes mRNA / nuclear polyadenylation-dependent antisense transcript catabolic process / nuclear polyadenylation-dependent snoRNA catabolic process / nuclear polyadenylation-dependent snRNA catabolic process / mRNA decay by 3' to 5' exoribonuclease / U1 snRNA 3'-end processing / nuclear polyadenylation-dependent CUT catabolic process / nuclear polyadenylation-dependent mRNA catabolic process / U5 snRNA 3'-end processing / regulatory ncRNA 3'-end processing / cytoplasmic exosome (RNase complex) / TRAMP-dependent tRNA surveillance pathway / CUT catabolic process / U4 snRNA 3'-end processing / nuclear polyadenylation-dependent rRNA catabolic process / nuclear-transcribed mRNA catabolic process, 3'-5' exonucleolytic nonsense-mediated decay / : / poly(A)-dependent snoRNA 3'-end processing / exosome (RNase complex) / nuclear exosome (RNase complex) / nuclear-transcribed mRNA catabolic process, non-stop decay / exonucleolytic trimming to generate mature 3'-end of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / : / rRNA catabolic process / post-transcriptional tethering of RNA polymerase II gene DNA at nuclear periphery / histone mRNA catabolic process / nuclear mRNA surveillance / nonfunctional rRNA decay / rRNA primary transcript binding / Hydrolases; Acting on ester bonds; Endoribonucleases producing 5'-phosphomonoesters / RNA catabolic process / rRNA metabolic process / Major pathway of rRNA processing in the nucleolus and cytosol / mRNA catabolic process / RNA processing / RNA endonuclease activity / mRNA processing / Hydrolases; Acting on ester bonds; Exoribonucleases producing 5'-phosphomonoesters / manganese ion binding / 3'-5'-RNA exonuclease activity / endonuclease activity / tRNA binding / single-stranded RNA binding / nucleotide binding / nucleolus / mitochondrion / RNA binding / nucleoplasm / nucleus / cytoplasm Similarity search - Function | |||||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) synthetic construct (others) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.1 Å | |||||||||
Authors | Lima, C.D. / Zinder, J.C. | |||||||||
Funding support | United States, 2items
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Citation | Journal: Mol.Cell / Year: 2016 Title: Nuclear RNA Exosome at 3.1 angstrom Reveals Substrate Specificities, RNA Paths, and Allosteric Inhibition of Rrp44/Dis3. Authors: Zinder, J.C. / Wasmuth, E.V. / Lima, C.D. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5k36.cif.gz | 787.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5k36.ent.gz | 619 KB | Display | PDB format |
PDBx/mmJSON format | 5k36.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/k3/5k36 ftp://data.pdbj.org/pub/pdb/validation_reports/k3/5k36 | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Details | Asymmetric unit is the biological assembly according to gel filtration chromatography and activity assays |
-Components
-Exosome complex component ... , 9 types, 9 molecules ABCDEFGHI
#1: Protein | Mass: 34001.859 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Strain: ATCC 204508 / S288c / Gene: RRP45, YDR280W, D9954.1 / Plasmid: pRSFduet / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) RIL / References: UniProt: Q05636 |
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#2: Protein | Mass: 28007.129 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Strain: ATCC 204508 / S288c / Gene: SKI6, ECM20, RRP41, YGR195W, G7587 / Plasmid: pRSFduet / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) RIL / References: UniProt: P46948 |
#3: Protein | Mass: 44060.934 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Strain: ATCC 204508 / S288c / Gene: RRP43, YCR035C, YCR35C, YCR522 / Plasmid: pRSFduet / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) RIL / References: UniProt: P25359 |
#4: Protein | Mass: 24574.324 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Strain: ATCC 204508 / S288c / Gene: RRP46, YGR095C / Plasmid: pRSFduet / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) RIL / References: UniProt: P53256 |
#5: Protein | Mass: 29492.574 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Strain: ATCC 204508 / S288c / Gene: RRP42, YDL111C / Plasmid: pRSFduet / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) RIL / References: UniProt: Q12277 |
#6: Protein | Mass: 27603.988 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Strain: ATCC 204508 / S288c / Gene: MTR3, YGR158C, G6676 / Plasmid: pRSFduet / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) RIL / References: UniProt: P48240 |
#7: Protein | Mass: 26990.756 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Strain: ATCC 204508 / S288c / Gene: RRP40, YOL142W / Plasmid: pTOPO-Smt3 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) RIL / References: UniProt: Q08285 |
#8: Protein | Mass: 39877.574 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Strain: ATCC 204508 / S288c / Gene: RRP4, YHR069C / Plasmid: pTOPO-Smt3 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) RIL / References: UniProt: P38792 |
#9: Protein | Mass: 32026.684 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Strain: ATCC 204508 / S288c / Gene: CSL4, SKI4, YNL232W, N1154 / Plasmid: pTOPO-Smt3 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) RIL / References: UniProt: P53859 |
-Exosome complex exonuclease ... , 2 types, 2 molecules JK
#10: Protein | Mass: 64515.590 Da / Num. of mol.: 1 / Mutation: D238N Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Strain: ATCC 204508 / S288c / Gene: RRP6, UNC733, YOR001W / Plasmid: pTOPO-Smt3 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) RIL References: UniProt: Q12149, Hydrolases; Acting on ester bonds; Exoribonucleases producing 5'-phosphomonoesters |
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#11: Protein | Mass: 114056.008 Da / Num. of mol.: 1 / Mutation: D171N, D551N Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Strain: ATCC 204508 / S288c / Gene: DIS3, RRP44, YOL021C, O2197 / Plasmid: pTOPO-Smt3 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) RIL References: UniProt: Q08162, Hydrolases; Acting on ester bonds; Exoribonucleases producing 5'-phosphomonoesters, Hydrolases; Acting on ester bonds; Endoribonucleases producing 5'-phosphomonoesters |
-RNA chain , 1 types, 2 molecules ML
#12: RNA chain | Mass: 5321.142 Da / Num. of mol.: 2 / Source method: obtained synthetically Details: Original compound used for crystallization is 3'AAAAUUUUAUUUAUUAU5'-1,1'-(oxybis(ethane-2,1-diyl))bis(4-butyl-1H-1,2,3-triazole)-5'UAUUAUUUAUUUUAAAA3' Source: (synth.) synthetic construct (others) |
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-Non-polymers , 4 types, 298 molecules
#13: Chemical | ChemComp-SO4 / #14: Chemical | ChemComp-GOL / #15: Chemical | ChemComp-ZN / | #16: Water | ChemComp-HOH / | |
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-Details
Compound details | The RNA chain in the crystal is two 17-mers linked head to head by (oxybis(ethane-2,1-diyl))bis(4- ...The RNA chain in the crystal is two 17-mers linked head to head by (oxybis(ethane-2,1-diyl))bis(4-butyl-1H-1,2,3-triazole) at their 5' ends to generate an RNA with two available 3' ends, 3'AAAAUUUUAU |
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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: 3.42 Å3/Da / Density % sol: 64.07 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.6 Details: 100 mM sodium citrate pH 5.25, 7 mM sodium MES pH 6.5, 6.7% PEG 3350, 175 mM (NH4)2SO4, 0.5 mM MgCl2, 40 mM TRIS-Cl pH 8.0, 200 mM NaCl, 2 mM TCEP-HCl |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9795 Å |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jul 26, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 3.1→106.13 Å / Num. obs: 116037 / % possible obs: 98.8 % / Redundancy: 3.6 % / Biso Wilson estimate: 66.2 Å2 / Rmerge(I) obs: 0.116 / Net I/σ(I): 14.3 |
Reflection shell | Resolution: 3.1→3.21 Å / Redundancy: 3 % / Rmerge(I) obs: 0.534 / Mean I/σ(I) obs: 2.8 / % possible all: 97 |
-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4OO1, 2WP8 Resolution: 3.1→106.13 Å / SU ML: 0.42 / Cross valid method: THROUGHOUT / σ(F): 1 / Phase error: 26.22 Details: ITERATIVE ROUNDS OF REFINEMENT WERE ACCOMPLISHED USING PHENIX. RNA AND SIDE CHAINS WERE MANUALLY BUILT USING COOT. SIMULATED ANNEALING OMIT MAPS AND MAPS USED DURING BUILDING WERE ALSO ...Details: ITERATIVE ROUNDS OF REFINEMENT WERE ACCOMPLISHED USING PHENIX. RNA AND SIDE CHAINS WERE MANUALLY BUILT USING COOT. SIMULATED ANNEALING OMIT MAPS AND MAPS USED DURING BUILDING WERE ALSO GENERATED USING CNS. THE MODEL WAS REFINED USING POSITIONAL REFINEMENT, REAL-SPACE REFINEMENT AND INDIVIDUAL B-FACTOR REFINEMENT
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.1→106.13 Å
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Refine LS restraints |
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LS refinement shell |
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