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Yorodumi- EMDB-2501: Substrate Recruitment Pathways in the Yeast Exosome by Electron M... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-2501 | |||||||||
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Title | Substrate Recruitment Pathways in the Yeast Exosome by Electron Microscopy | |||||||||
Map data | Exosome with tRNA | |||||||||
Sample |
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Keywords | exosome / RNA degradation route | |||||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) / synthetic construct (others) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 24.0 Å | |||||||||
Authors | Liu J-J / Bratkowski MA / Liu XQ / Niu C-Y / Ke AL / Wang H-W | |||||||||
Citation | Journal: Nat Struct Mol Biol / Year: 2014 Title: Visualization of distinct substrate-recruitment pathways in the yeast exosome by EM. Authors: Jun-Jie Liu / Matthew A Bratkowski / Xueqi Liu / Chu-Ya Niu / Ailong Ke / Hong-Wei Wang / Abstract: The eukaryotic exosome is a multisubunit complex typically composed of a catalytically inactive core and the Rrp44 protein, which contains 3'-to-5' exo- and endo-RNase activities. RNA substrates have ...The eukaryotic exosome is a multisubunit complex typically composed of a catalytically inactive core and the Rrp44 protein, which contains 3'-to-5' exo- and endo-RNase activities. RNA substrates have been shown to be recruited through the core to reach Rrp44's exo-RNase (EXO) site. Using single-particle EM and biochemical analysis, we provide visual evidence that two distinct substrate-recruitment pathways exist. In the through-core route, channeling of the single-stranded substrates from the core to Rrp44 induces a characteristic conformational change in Rrp44. In the alternative direct-access route, this conformational change does not take place, and the RNA substrate is visualized to avoid the core and enter Rrp44's EXO site directly. Our results provide mechanistic explanations for several RNA processing scenarios by the eukaryotic exosome and indicate substrate-specific modes of degradation by this complex. | |||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_2501.map.gz | 2.6 MB | EMDB map data format | |
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Header (meta data) | emd-2501-v30.xml emd-2501.xml | 16.9 KB 16.9 KB | Display Display | EMDB header |
Images | 2501-Cryo-tRNA-RE.png | 55.7 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-2501 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-2501 | HTTPS FTP |
-Validation report
Summary document | emd_2501_validation.pdf.gz | 206.3 KB | Display | EMDB validaton report |
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Full document | emd_2501_full_validation.pdf.gz | 205.4 KB | Display | |
Data in XML | emd_2501_validation.xml.gz | 4.8 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-2501 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-2501 | HTTPS FTP |
-Related structure data
Related structure data | 2491C 2492C 2493C 2494C 2495C 2496C 2497C 2498C 2499C 2500C 2502C 2522C C: citing same article (ref.) |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_2501.map.gz / Format: CCP4 / Size: 6.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Exosome with tRNA | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 3 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
+Entire : Rrp44-Exosome with tRNA by Cryo-EMtRNA-RE
+Supramolecule #1000: Rrp44-Exosome with tRNA by Cryo-EMtRNA-RE
+Macromolecule #1: Rrp44
+Macromolecule #2: Rrp43
+Macromolecule #3: Rrp4
+Macromolecule #4: Csl4
+Macromolecule #5: Rrp45
+Macromolecule #6: Rrp46-TAP
+Macromolecule #7: Rrp41
+Macromolecule #8: Rrp42
+Macromolecule #9: Mtr3
+Macromolecule #10: Rrp40
+Macromolecule #11: methionine tRNA
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 2 mg/mL |
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Buffer | pH: 8 / Details: 150mM NaCl, 50mM Tris-HCL,1mM DTT, 2mM MgCl2 |
Grid | Details: Quantifoil grids (2/2) with2~3 nm thin carbon on top |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 80 K / Instrument: FEI VITROBOT MARK IV Method: 4 ul of the reaction solution was then applied to glow-discharged C-flat grids (1.2/1.3) covered with a layer of continuous carbon with a thickness of ~4nm. The grids were then blotted and ...Method: 4 ul of the reaction solution was then applied to glow-discharged C-flat grids (1.2/1.3) covered with a layer of continuous carbon with a thickness of ~4nm. The grids were then blotted and plunged into liquid ethane in a FEI Vitrobot Mark IV |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Temperature | Min: 80 K / Max: 85 K / Average: 82 K |
Date | Jun 10, 2012 |
Image recording | Category: CCD / Film or detector model: GENERIC GATAN (4k x 4k) / Number real images: 1200 / Average electron dose: 20 e/Å2 |
Electron beam | Acceleration voltage: 120 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Calibrated magnification: 59000 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: -3.5 µm / Nominal defocus min: -0.5 µm / Nominal magnification: 59000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Details | Micrographs of RE were collected using the AutoEMation software (Lei and Frank, 2005) installed on the microscope at low-dose condition with a dose of ~20 electron/A2 and a defocus value ranging from -1.2 to -4 um. The micrographs were collected on a FEI Eagle CCD camera with a pixel size of 1.5 A. |
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CTF correction | Details: both each particle and micrograph |
Final reconstruction | Applied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 24.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: eman, imagic, relion / Number images used: 28800 |
Final angle assignment | Details: RELION: theta 45 degrees, phi 180 degrees |
-Atomic model buiding 1
Initial model | PDB ID: |
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Software | Name: Chimera |
Refinement | Space: REAL / Protocol: RIGID BODY FIT |