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- PDB-5k36: Structure of an eleven component nuclear RNA exosome complex boun... -
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Open data
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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 | |||||||||
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![]() | Hydrolase/RNA / Exoribonuclease / Complex / RNA / STRUCTURAL PROTEIN / Hydrolase-RNA complex | |||||||||
Function / homology | ![]() nuclear polyadenylation-dependent snoRNA catabolic process / nuclear polyadenylation-dependent snRNA catabolic process / nuclear polyadenylation-dependent antisense transcript catabolic process / mRNA decay by 3' to 5' exoribonuclease / Butyrate Response Factor 1 (BRF1) binds and destabilizes mRNA / Tristetraprolin (TTP, ZFP36) binds and destabilizes mRNA / nuclear polyadenylation-dependent mRNA catabolic process / nuclear mRNA surveillance of mRNA 3'-end processing / regulatory ncRNA 3'-end processing / U1 snRNA 3'-end processing ...nuclear polyadenylation-dependent snoRNA catabolic process / nuclear polyadenylation-dependent snRNA catabolic process / nuclear polyadenylation-dependent antisense transcript catabolic process / mRNA decay by 3' to 5' exoribonuclease / Butyrate Response Factor 1 (BRF1) binds and destabilizes mRNA / Tristetraprolin (TTP, ZFP36) binds and destabilizes mRNA / nuclear polyadenylation-dependent mRNA catabolic process / nuclear mRNA surveillance of mRNA 3'-end processing / regulatory ncRNA 3'-end processing / U1 snRNA 3'-end processing / nuclear polyadenylation-dependent CUT catabolic process / U5 snRNA 3'-end processing / TRAMP-dependent tRNA surveillance pathway / CUT catabolic process / exosome (RNase complex) / U4 snRNA 3'-end processing / cytoplasmic exosome (RNase complex) / nuclear polyadenylation-dependent rRNA catabolic process / poly(A)-dependent snoRNA 3'-end processing / nuclear exosome (RNase complex) / nuclear-transcribed mRNA catabolic process, non-stop decay / nuclear-transcribed mRNA catabolic process, 3'-5' exonucleolytic nonsense-mediated decay / exonucleolytic trimming to generate mature 3'-end of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / histone mRNA catabolic process / nuclear mRNA surveillance / post-transcriptional tethering of RNA polymerase II gene DNA at nuclear periphery / rRNA catabolic process / mRNA 3'-UTR AU-rich region binding / rRNA primary transcript binding / Hydrolases; Acting on ester bonds; Endoribonucleases producing 5'-phosphomonoesters / RNA catabolic process / regulation of telomere maintenance / nonfunctional rRNA decay / rRNA metabolic process / Major pathway of rRNA processing in the nucleolus and cytosol / mRNA catabolic process / nuclear-transcribed mRNA catabolic process / RNA processing / RNA endonuclease activity / mRNA processing / manganese ion binding / Hydrolases; Acting on ester bonds; Exoribonucleases producing 5'-phosphomonoesters / 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 | ![]() ![]() synthetic construct (others) | |||||||||
Method | ![]() ![]() ![]() ![]() | |||||||||
![]() | Lima, C.D. / Zinder, J.C. | |||||||||
Funding support | ![]()
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![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 787.1 KB | Display | ![]() |
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PDB format | ![]() | 619 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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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 |
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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.) ![]() ![]() Strain: ATCC 204508 / S288c / Gene: RRP45, YDR280W, D9954.1 / Plasmid: pRSFduet / Production host: ![]() ![]() |
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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.) ![]() ![]() Strain: ATCC 204508 / S288c / Gene: SKI6, ECM20, RRP41, YGR195W, G7587 / Plasmid: pRSFduet / Production host: ![]() ![]() |
#3: Protein | Mass: 44060.934 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: ATCC 204508 / S288c / Gene: RRP43, YCR035C, YCR35C, YCR522 / Plasmid: pRSFduet / Production host: ![]() ![]() |
#4: Protein | Mass: 24574.324 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: ATCC 204508 / S288c / Gene: RRP46, YGR095C / Plasmid: pRSFduet / Production host: ![]() ![]() |
#5: Protein | Mass: 29492.574 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: ATCC 204508 / S288c / Gene: RRP42, YDL111C / Plasmid: pRSFduet / Production host: ![]() ![]() |
#6: Protein | Mass: 27603.988 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: ATCC 204508 / S288c / Gene: MTR3, YGR158C, G6676 / Plasmid: pRSFduet / Production host: ![]() ![]() |
#7: Protein | Mass: 26990.756 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: ATCC 204508 / S288c / Gene: RRP40, YOL142W / Plasmid: pTOPO-Smt3 / Production host: ![]() ![]() |
#8: Protein | Mass: 39877.574 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: ATCC 204508 / S288c / Gene: RRP4, YHR069C / Plasmid: pTOPO-Smt3 / Production host: ![]() ![]() |
#9: Protein | Mass: 32026.684 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: ATCC 204508 / S288c / Gene: CSL4, SKI4, YNL232W, N1154 / Plasmid: pTOPO-Smt3 / Production host: ![]() ![]() |
-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.) ![]() ![]() Strain: ATCC 204508 / S288c / Gene: RRP6, UNC733, YOR001W / Plasmid: pTOPO-Smt3 / Production host: ![]() ![]() 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.) ![]() ![]() Strain: ATCC 204508 / S288c / Gene: DIS3, RRP44, YOL021C, O2197 / Plasmid: pTOPO-Smt3 / Production host: ![]() ![]() 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: ![]() |
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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: ![]() ![]() ![]() |
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: ![]() |
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Processing
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Refinement | Method to determine structure: ![]() 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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