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Yorodumi- EMDB-10009: Cryo-EM structures of Lsg1-TAP pre-60S ribosomal particles (State... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-10009 | |||||||||
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Title | Cryo-EM structures of Lsg1-TAP pre-60S ribosomal particles (State III - subclass 1) | |||||||||
Map data | ||||||||||
Sample |
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Biological species | Saccharomyces cerevisiae (brewer's yeast) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.5 Å | |||||||||
Authors | Kargas V / Warren AJ | |||||||||
Funding support | United Kingdom, 2 items
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Citation | Journal: To Be Published Title: Cryo-EM structures of Lsg1-TAP pre-60S ribosomal particles Authors: Kargas V / Warren AJ | |||||||||
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_10009.map.gz | 155.7 MB | EMDB map data format | |
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Header (meta data) | emd-10009-v30.xml emd-10009.xml | 15 KB 15 KB | Display Display | EMDB header |
Images | emd_10009.png | 76.9 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-10009 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-10009 | HTTPS FTP |
-Validation report
Summary document | emd_10009_validation.pdf.gz | 261 KB | Display | EMDB validaton report |
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Full document | emd_10009_full_validation.pdf.gz | 260.1 KB | Display | |
Data in XML | emd_10009_validation.xml.gz | 7 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-10009 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-10009 | HTTPS FTP |
-Related structure data
Related structure data | |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_10009.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Voxel size | X=Y=Z: 1.065 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 : Lsg1-TAP 60s ribosomal subunit
Entire | Name: Lsg1-TAP 60s ribosomal subunit |
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Components |
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-Supramolecule #1: Lsg1-TAP 60s ribosomal subunit
Supramolecule | Name: Lsg1-TAP 60s ribosomal subunit / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#48 |
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Source (natural) | Organism: Saccharomyces cerevisiae (brewer's yeast) |
-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: FEI FALCON III (4k x 4k) / Average electron dose: 63.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
CTF correction | Software: (Name: Gctf (ver. 1.06), CTFFIND (ver. 4.1)) |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 2.1) / Number images used: 27769 |
Initial angle assignment | Type: ANGULAR RECONSTITUTION / Software - Name: RELION |
Final angle assignment | Type: ANGULAR RECONSTITUTION |
-Atomic model buiding 1
Initial model | PDB ID: |
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Refinement | Protocol: FLEXIBLE FIT |