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Yorodumi- EMDB-10067: Cryo-EM structure of Lsg1-TAP ribosomal subunit (State I - subclass 2) -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-10067 | |||||||||
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Title | Cryo-EM structure of Lsg1-TAP ribosomal subunit (State I - subclass 2) | |||||||||
Map data | ||||||||||
Sample |
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Biological species | Saccharomyces cerevisiae (brewer's yeast) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.4 Å | |||||||||
Authors | Kargas V / Warren AJ | |||||||||
Funding support | United Kingdom, 2 items
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Citation | Journal: Elife / Year: 2019 Title: Mechanism of completion of peptidyltransferase centre assembly in eukaryotes. Authors: Vasileios Kargas / Pablo Castro-Hartmann / Norberto Escudero-Urquijo / Kyle Dent / Christine Hilcenko / Carolin Sailer / Gertrude Zisser / Maria J Marques-Carvalho / Simone Pellegrino / ...Authors: Vasileios Kargas / Pablo Castro-Hartmann / Norberto Escudero-Urquijo / Kyle Dent / Christine Hilcenko / Carolin Sailer / Gertrude Zisser / Maria J Marques-Carvalho / Simone Pellegrino / Leszek Wawiórka / Stefan Mv Freund / Jane L Wagstaff / Antonina Andreeva / Alexandre Faille / Edwin Chen / Florian Stengel / Helmut Bergler / Alan John Warren / Abstract: During their final maturation in the cytoplasm, pre-60S ribosomal particles are converted to translation-competent large ribosomal subunits. Here, we present the mechanism of peptidyltransferase ...During their final maturation in the cytoplasm, pre-60S ribosomal particles are converted to translation-competent large ribosomal subunits. Here, we present the mechanism of peptidyltransferase centre (PTC) completion that explains how integration of the last ribosomal proteins is coupled to release of the nuclear export adaptor Nmd3. Single-particle cryo-EM reveals that eL40 recruitment stabilises helix 89 to form the uL16 binding site. The loading of uL16 unhooks helix 38 from Nmd3 to adopt its mature conformation. In turn, partial retraction of the L1 stalk is coupled to a conformational switch in Nmd3 that allows the uL16 P-site loop to fully accommodate into the PTC where it competes with Nmd3 for an overlapping binding site (base A2971). Our data reveal how the central functional site of the ribosome is sculpted and suggest how the formation of translation-competent 60S subunits is disrupted in leukaemia-associated ribosomopathies. | |||||||||
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_10067.map.gz | 88.9 MB | EMDB map data format | |
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Header (meta data) | emd-10067-v30.xml emd-10067.xml | 16 KB 16 KB | Display Display | EMDB header |
Images | emd_10067.png | 75.3 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-10067 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-10067 | HTTPS FTP |
-Validation report
Summary document | emd_10067_validation.pdf.gz | 263.8 KB | Display | EMDB validaton report |
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Full document | emd_10067_full_validation.pdf.gz | 263 KB | Display | |
Data in XML | emd_10067_validation.xml.gz | 7.1 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-10067 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-10067 | HTTPS FTP |
-Related structure data
Related structure data | 4560C 4630C 4636C 4884C 6qikC 6qt0C 6qtzC 6ri5C 6rzzC 6s05C C: citing same article (ref.) |
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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_10067.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: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 2.1) / Number images used: 46631 |
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 |