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Open data
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Basic information
Entry | Database: PDB / ID: 8pel | ||||||
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Title | Structure of C. thermophilum RNA exosome core | ||||||
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![]() | RNA BINDING PROTEIN / nuclease / RNA degradation / RNA metabolism / RNA binding | ||||||
Function / homology | ![]() TRAMP-dependent tRNA surveillance pathway / CUT catabolic process / nuclear polyadenylation-dependent rRNA catabolic process / U1 snRNA 3'-end processing / nuclear polyadenylation-dependent mRNA catabolic process / U5 snRNA 3'-end processing / cytoplasmic exosome (RNase complex) / nuclear exosome (RNase complex) / poly(A)-dependent snoRNA 3'-end processing / U4 snRNA 3'-end processing ...TRAMP-dependent tRNA surveillance pathway / CUT catabolic process / nuclear polyadenylation-dependent rRNA catabolic process / U1 snRNA 3'-end processing / nuclear polyadenylation-dependent mRNA catabolic process / U5 snRNA 3'-end processing / cytoplasmic exosome (RNase complex) / nuclear 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) / : / nuclear mRNA surveillance / rRNA catabolic process / RNA processing / rRNA processing / nucleolus / RNA binding / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Lazzaretti, D. / Holdermann, I. / Sprangers, R. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Beyond static structures: quantitative dynamics in the eukaryotic RNA exosome complex Authors: Liebau, J. / Lazzaretti, D. / Bichler, A. / Pilsl, M. / Sprangers, R. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 896.5 KB | Display | ![]() |
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PDB format | ![]() | 690 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 501 KB | Display | ![]() |
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Full document | ![]() | 543.7 KB | Display | |
Data in XML | ![]() | 79.3 KB | Display | |
Data in CIF | ![]() | 106 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8r1oC C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
-Protein , 4 types, 4 molecules ACFG
#1: Protein | Mass: 32470.098 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Gene: CTHT_0027490 / Production host: ![]() ![]() |
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#3: Protein | Mass: 39553.035 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Gene: CTHT_0014300 / Production host: ![]() ![]() |
#6: Protein | Mass: 30541.703 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Gene: MTR3, CTHT_0115690 / Production host: ![]() ![]() |
#7: Protein | Mass: 27955.145 Da / Num. of mol.: 1 / Mutation: G-1, A0 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Gene: CTHT_0008000 / Production host: ![]() ![]() |
-Exoribonuclease phosphorolytic domain-containing ... , 3 types, 3 molecules BDE
#2: Protein | Mass: 29986.879 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Gene: CTHT_0055610 / Production host: ![]() ![]() |
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#4: Protein | Mass: 27979.668 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Gene: CTHT_0056790 / Production host: ![]() ![]() |
#5: Protein | Mass: 43949.383 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Gene: CTHT_0002870 / Production host: ![]() ![]() |
-Putative exosome ... , 2 types, 2 molecules HI
#8: Protein | Mass: 38403.348 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Gene: CTHT_0045080 / Production host: ![]() ![]() |
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#9: Protein | Mass: 23886.416 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Gene: CTHT_0062250 / Production host: ![]() ![]() |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.47 Å3/Da / Density % sol: 50.28 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 5.5 Details: 0.2M Ammonium Sulphate 0.1M Sodium Acetate pH 5.5 10% PEG MME 2000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Mar 13, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.99994 Å / Relative weight: 1 |
Reflection | Resolution: 3.81→48.9 Å / Num. obs: 29143 / % possible obs: 99.57 % / Redundancy: 13.5 % / Biso Wilson estimate: 74.733 Å2 / CC1/2: 0.984 / CC star: 0.996 / Net I/σ(I): 5.01 |
Reflection shell | Resolution: 3.81→3.946 Å / Redundancy: 13.5 % / Mean I/σ(I) obs: 1.19 / Num. unique obs: 2793 / CC1/2: 0.586 / CC star: 0.86 / % possible all: 97.14 |
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Processing
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Refinement | Method to determine structure: ![]() Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 103.52 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.81→48.9 Å
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Refine LS restraints |
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LS refinement shell |
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