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Open data
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Basic information
Entry | Database: PDB / ID: 2je6 | ||||||
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Title | Structure of a 9-subunit archaeal exosome | ||||||
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![]() | HYDROLASE / NUCLEASE / RNA-BINDING / EXONUCLEASE / PHOSPHOROLYTIC / EXORIBONUCLEASE / RNA DEGRADATION / RNA / RRP4 / RRP42 / RRP41 / EXOSOME / ARCHAEAL / RNASE PH | ||||||
Function / homology | ![]() CUT catabolic process / exosome (RNase complex) / U1 snRNA 3'-end processing / nuclear polyadenylation-dependent mRNA catabolic process / U5 snRNA 3'-end processing / cytoplasmic exosome (RNase complex) / 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) ...CUT catabolic process / exosome (RNase complex) / U1 snRNA 3'-end processing / nuclear polyadenylation-dependent mRNA catabolic process / U5 snRNA 3'-end processing / cytoplasmic exosome (RNase complex) / 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) / : / rRNA catabolic process / poly(A) binding / Hydrolases; Acting on ester bonds; Exoribonucleases producing 5'-phosphomonoesters / 3'-5'-RNA exonuclease activity / RNA binding Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Lorentzen, E. / Conti, E. | ||||||
![]() | ![]() Title: RNA Channelling by the Archaeal Exosome. Authors: Lorentzen, E. / Dziembowski, A. / Lindner, D. / Seraphin, B. / Conti, E. | ||||||
History |
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Remark 700 | SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "IC" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "IC" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 6-STRANDED BARREL THIS IS REPRESENTED BY A 7-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED. |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 162 KB | Display | ![]() |
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PDB format | ![]() | 124.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 403.8 KB | Display | ![]() |
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Full document | ![]() | 410.3 KB | Display | |
Data in XML | ![]() | 15.4 KB | Display | |
Data in CIF | ![]() | 26.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2jeaC ![]() 2jebC ![]() 2br2S S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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Unit cell |
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Components
-EXOSOME COMPLEX EXONUCLEASE ... , 2 types, 2 molecules AB
#1: Protein | Mass: 30422.824 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: Q9UXC0, Hydrolases; Acting on ester bonds; Exoribonucleases producing 5'-phosphomonoesters |
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#2: Protein | Mass: 27764.125 Da / Num. of mol.: 1 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: Q9UXC2, Hydrolases; Acting on ester bonds; Exoribonucleases producing 5'-phosphomonoesters |
-Protein , 1 types, 1 molecules I
#3: Protein | Mass: 28225.320 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: Q9UXC4, Hydrolases; Acting on ester bonds; Exoribonucleases producing 5'-phosphomonoesters |
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-Non-polymers , 4 types, 401 molecules ![](data/chem/img/1PE.gif)
![](data/chem/img/PEG.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/PEG.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/HOH.gif)
#4: Chemical | ChemComp-1PE / |
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#5: Chemical | ChemComp-PEG / |
#6: Chemical | ChemComp-CL / |
#7: Water | ChemComp-HOH / |
-Details
Compound details | ENGINEERED |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.3 Å3/Da / Density % sol: 46 % |
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Crystal grow | pH: 8 / Details: 40% PEG 400, 50 MM TRIS-HCL PH 8.0 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Jul 15, 2006 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→50 Å / Num. obs: 106599 / % possible obs: 100 % / Redundancy: 7.9 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 11.7 |
Reflection shell | Resolution: 1.6→1.7 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.68 / Mean I/σ(I) obs: 2.2 / % possible all: 99.9 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 2BR2 Resolution: 1.6→45.18 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.938 / SU B: 2.488 / SU ML: 0.086 / Cross valid method: THROUGHOUT / ESU R: 0.092 / ESU R Free: 0.094 / 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: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 36.53 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.6→45.18 Å
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Refine LS restraints |
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