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Yorodumi- EMDB-1439: Architecture of the yeast Rrp44 exosome complex suggests routes o... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-1439 | |||||||||
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Title | Architecture of the yeast Rrp44 exosome complex suggests routes of RNA recruitment for 3' end processing. | |||||||||
Map data | This is the 3D map of yeast exosome core complex | |||||||||
Sample |
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Biological species | Saccharomyces cerevisiae (brewer's yeast) | |||||||||
Method | single particle reconstruction / cryo EM / negative staining / Resolution: 23.0 Å | |||||||||
Authors | Wang H-W / Wang J / Ding F / Callahan K / Bratkowski MA / Butler JS / Nogales E / Ke A | |||||||||
Citation | Journal: Proc Natl Acad Sci U S A / Year: 2007 Title: Architecture of the yeast Rrp44 exosome complex suggests routes of RNA recruitment for 3' end processing. Authors: Hong-Wei Wang / Jianjun Wang / Fang Ding / Kevin Callahan / Matthew A Bratkowski / J Scott Butler / Eva Nogales / Ailong Ke / Abstract: The eukaryotic core exosome (CE) is a conserved nine-subunit protein complex important for 3' end trimming and degradation of RNA. In yeast, the Rrp44 protein constitutively associates with the CE ...The eukaryotic core exosome (CE) is a conserved nine-subunit protein complex important for 3' end trimming and degradation of RNA. In yeast, the Rrp44 protein constitutively associates with the CE and provides the sole source of processive 3'-to-5' exoribonuclease activity. Here we present EM reconstructions of the core and Rrp44-bound exosome complexes. The two-lobed Rrp44 protein binds to the RNase PH domain side of the exosome and buttresses the bottom of the exosome-processing chamber. The Rrp44 C-terminal body part containing an RNase II-type active site is anchored to the exosome through a conserved set of interactions mainly to the Rrp45 and Rrp43 subunit, whereas the Rrp44 N-terminal head part is anchored to the Rrp41 subunit and may function as a roadblock to restrict access of RNA to the active site in the body region. The Rrp44-exosome (RE) architecture suggests an active site sequestration mechanism for strict control of 3' exoribonuclease activity in the RE 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_1439.map.gz | 1.2 MB | EMDB map data format | |
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Header (meta data) | emd-1439-v30.xml emd-1439.xml | 15.9 KB 15.9 KB | Display Display | EMDB header |
Images | 1439.gif | 30.6 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-1439 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-1439 | HTTPS FTP |
-Validation report
Summary document | emd_1439_validation.pdf.gz | 198.7 KB | Display | EMDB validaton report |
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Full document | emd_1439_full_validation.pdf.gz | 197.9 KB | Display | |
Data in XML | emd_1439_validation.xml.gz | 5.2 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-1439 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-1439 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_1439.map.gz / Format: CCP4 / Size: 1.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | This is the 3D map of yeast exosome core complex | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 5.18 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 : exosome core complex
+Supramolecule #1000: exosome core complex
+Macromolecule #1: Rrp43
+Macromolecule #2: Rrp4
+Macromolecule #3: Cls4
+Macromolecule #4: Rrp45
+Macromolecule #5: Rrp46-TAP
+Macromolecule #6: Rrp41
+Macromolecule #7: Rrp42
+Macromolecule #8: Mtr3
+Macromolecule #9: Rrp40
-Experimental details
-Structure determination
Method | negative staining, cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.03 mg/mL |
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Buffer | pH: 7.5 Details: 25 mM Tris-HCl, 50 mM NaCl, 2 mM DTT, and 10 uM ZnCl2 |
Staining | Type: NEGATIVE Details: Four microliters of the protein solution was negatively stained with 2% uranyl formate solution between two thin layers of carbon on a copper grid by using the sandwich method. |
Grid | Details: 400 mesh copper grid |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TECNAI 12 |
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Temperature | Average: 300 K |
Alignment procedure | Legacy - Astigmatism: objective lens astigmatism was corrected at 100,000 times magnification |
Details | Low dose mode was used for taking pictures |
Date | Aug 1, 2006 |
Image recording | Category: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: OTHER / Digitization - Sampling interval: 12.7 µm / Number real images: 50 / Average electron dose: 20 e/Å2 Details: The micrographs were scanned on a Nikon Super Coolscan 8000 scanner Od range: 1.4 / Bits/pixel: 14 |
Tilt angle min | 0 |
Tilt angle max | 0 |
Electron beam | Acceleration voltage: 120 kV / Electron source: LAB6 |
Electron optics | Calibrated magnification: 49000 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 6.6 mm / Nominal defocus max: 0.9 µm / Nominal defocus min: 0.7 µm / Nominal magnification: 49000 |
Sample stage | Specimen holder: normal single-tilt holder / Specimen holder model: OTHER |
-Image processing
Final reconstruction | Applied symmetry - Point group: C1 (asymmetric) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 23.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: SPIDER / Details: Final map were calculated from all the particles. / Number images used: 2980 |
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Final angle assignment | Details: SPIDER: theta 90 degrees, phi 90 degrees |
Final two d classification | Number classes: 50 |
-Atomic model buiding 1
Initial model | PDB ID: |
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Software | Name: Situs |
Details | Protocol: Rigid Body. The docking was performed by automatic rigid body docking in Situs. |
Refinement | Space: REAL / Protocol: RIGID BODY FIT |