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Yorodumi- EMDB-20905: Yeast RTP Interacts with Extended Termini of Clinet Protein Nop58p -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-20905 | ||||||||||||
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Title | Yeast RTP Interacts with Extended Termini of Clinet Protein Nop58p | ||||||||||||
Map data | Yeast RTP | ||||||||||||
Sample |
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Biological species | Saccharomyces cerevisiae (brewer's yeast) | ||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 8.9 Å | ||||||||||||
Authors | Yu G / Zhao Y / Rai J / Stagg SM / Li H | ||||||||||||
Funding support | United States, 3 items
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Citation | Journal: Sci Rep / Year: 2019 Title: Yeast R2TP Interacts with Extended Termini of Client Protein Nop58p. Authors: Ge Yu / Yu Zhao / Shaoxiong Tian / Jay Rai / Huan He / John Spear / Duncan Sousa / Jinbo Fan / Hong-Guo Yu / Scott M Stagg / Hong Li / Abstract: The AAA + ATPase R2TP complex facilitates assembly of a number of ribonucleoprotein particles (RNPs). Although the architecture of R2TP is known, its molecular basis for acting upon multiple RNPs ...The AAA + ATPase R2TP complex facilitates assembly of a number of ribonucleoprotein particles (RNPs). Although the architecture of R2TP is known, its molecular basis for acting upon multiple RNPs remains unknown. In yeast, the core subunit of the box C/D small nucleolar RNPs, Nop58p, is the target for R2TP function. In the recently observed U3 box C/D snoRNP as part of the 90 S small subunit processome, the unfolded regions of Nop58p are observed to form extensive interactions, suggesting a possible role of R2TP in stabilizing the unfolded region of Nop58p prior to its assembly. Here, we analyze the interaction between R2TP and a Maltose Binding Protein (MBP)-fused Nop58p by biophysical and yeast genetics methods. We present evidence that R2TP interacts largely with the unfolded termini of Nop58p. Our results suggest a general mechanism for R2TP to impart specificity by recognizing unfolded regions in its clients. | ||||||||||||
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_20905.map.gz | 5.9 MB | EMDB map data format | |
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Header (meta data) | emd-20905-v30.xml emd-20905.xml | 8.3 KB 8.3 KB | Display Display | EMDB header |
Images | emd_20905.png | 31.5 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-20905 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-20905 | HTTPS FTP |
-Validation report
Summary document | emd_20905_validation.pdf.gz | 78.6 KB | Display | EMDB validaton report |
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Full document | emd_20905_full_validation.pdf.gz | 77.8 KB | Display | |
Data in XML | emd_20905_validation.xml.gz | 494 B | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-20905 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-20905 | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_20905.map.gz / Format: CCP4 / Size: 8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Yeast RTP | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 2.02 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 : Yeast -R2TP
Entire | Name: Yeast -R2TP |
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Components |
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-Supramolecule #1: Yeast -R2TP
Supramolecule | Name: Yeast -R2TP / type: complex / ID: 1 / Parent: 0 |
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Source (natural) | Organism: Saccharomyces cerevisiae (brewer's yeast) |
Recombinant expression | Organism: Escherichia coli (E. coli) |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.5 |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: DIRECT ELECTRON DE-64 (8k x 8k) / Detector mode: INTEGRATING / Average electron dose: 60.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: OTHER / Imaging mode: BRIGHT FIELD |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 8.9 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 179483 |
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Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: OTHER |