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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-4630 | |||||||||
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Title | Cryo-EM structures of Lsg1-TAP pre-60S ribosomal particles | |||||||||
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![]() | 60S subunit / eIF6 / Nmd3 / Lsg1 / RIBOSOME | |||||||||
Function / homology | ![]() maturation of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / pre-mRNA 5'-splice site binding / cleavage in ITS2 between 5.8S rRNA and LSU-rRNA of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / response to cycloheximide / maturation of 5.8S rRNA / SRP-dependent cotranslational protein targeting to membrane / GTP hydrolysis and joining of the 60S ribosomal subunit / ribosomal large subunit binding / Formation of a pool of free 40S subunits / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) ...maturation of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / pre-mRNA 5'-splice site binding / cleavage in ITS2 between 5.8S rRNA and LSU-rRNA of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / response to cycloheximide / maturation of 5.8S rRNA / SRP-dependent cotranslational protein targeting to membrane / GTP hydrolysis and joining of the 60S ribosomal subunit / ribosomal large subunit binding / Formation of a pool of free 40S subunits / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / negative regulation of mRNA splicing, via spliceosome / L13a-mediated translational silencing of Ceruloplasmin expression / preribosome, large subunit precursor / translational elongation / ribosomal large subunit export from nucleus / protein-RNA complex assembly / regulation of translational fidelity / ribosomal subunit export from nucleus / translational termination / translation initiation factor activity / maturation of LSU-rRNA / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / assembly of large subunit precursor of preribosome / cytosolic ribosome assembly / ribosomal large subunit biogenesis / translational initiation / macroautophagy / maintenance of translational fidelity / modification-dependent protein catabolic process / rRNA processing / protein tag activity / ribosome biogenesis / 5S rRNA binding / large ribosomal subunit rRNA binding / cytosolic large ribosomal subunit / cytoplasmic translation / rRNA binding / negative regulation of translation / ribosome / protein ubiquitination / structural constituent of ribosome / translation / response to antibiotic / mRNA binding / ubiquitin protein ligase binding / nucleolus / RNA binding / nucleus / metal ion binding / cytosol / cytoplasm Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.4 Å | |||||||||
![]() | Kargas V / Warren AJ | |||||||||
Funding support | ![]()
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![]() | ![]() 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 |
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 16.7 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 60.2 KB 60.2 KB | Display Display | ![]() |
Images | ![]() | 63.3 KB | ||
Filedesc metadata | ![]() | 13.3 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6qt0MC ![]() 4560C ![]() 4636C ![]() 4884C ![]() 6qikC ![]() 6qtzC ![]() 6ri5C ![]() 6rzzC ![]() 6s05C C: citing same article ( M: atomic model generated by this map |
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Similar structure data |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
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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
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Sample components
+Entire : Lsg1-TAP 60s ribosomal subunit
+Supramolecule #1: Lsg1-TAP 60s ribosomal subunit
+Macromolecule #1: 25S rRNA
+Macromolecule #44: 5S rRNA
+Macromolecule #45: 5.8S rRNA
+Macromolecule #2: 60S ribosomal protein L2-A
+Macromolecule #3: 60S ribosomal protein L3
+Macromolecule #4: 60S ribosomal protein L4-A
+Macromolecule #5: 60S ribosomal protein L11-A
+Macromolecule #6: 60S ribosomal protein L9-A
+Macromolecule #7: 60S ribosomal protein L6-A
+Macromolecule #8: 60S ribosomal protein L8-A
+Macromolecule #9: 60S ribosomal protein L10
+Macromolecule #10: 60S ribosomal protein L16-B
+Macromolecule #11: 60S ribosomal protein L13-A
+Macromolecule #12: 60S ribosomal protein L23-A
+Macromolecule #13: 60S ribosomal protein L14-A
+Macromolecule #14: 60S ribosomal protein L28
+Macromolecule #15: 60S ribosomal protein L15-A
+Macromolecule #16: 60S ribosomal protein L5
+Macromolecule #17: 60S ribosomal protein L18-A
+Macromolecule #18: 60S ribosomal protein L19-A
+Macromolecule #19: 60S ribosomal protein L20-A
+Macromolecule #20: 60S ribosomal protein L21-A
+Macromolecule #21: 60S ribosomal protein L17-A
+Macromolecule #22: 60S ribosomal protein L22-A
+Macromolecule #23: 60S ribosomal protein L25
+Macromolecule #24: 60S ribosomal protein L26-A
+Macromolecule #25: 60S ribosomal protein L27-A
+Macromolecule #26: 60S ribosomal protein L35-A
+Macromolecule #27: 60S ribosomal protein L29
+Macromolecule #28: 60S ribosomal protein L7-A
+Macromolecule #29: 60S ribosomal protein L30
+Macromolecule #30: 60S ribosomal protein L31-A
+Macromolecule #31: 60S ribosomal protein L32
+Macromolecule #32: 60S ribosomal protein L33-A
+Macromolecule #33: 60S ribosomal protein L34-A
+Macromolecule #34: 60S ribosomal protein L36-A
+Macromolecule #35: 60S ribosomal protein L37-A
+Macromolecule #36: 60S ribosomal protein L38
+Macromolecule #37: 60S ribosomal protein L39
+Macromolecule #38: 60S ribosomal protein L42-A
+Macromolecule #39: 60S ribosomal protein L43-A
+Macromolecule #40: Eukaryotic translation initiation factor 6
+Macromolecule #41: Ubiquitin-60S ribosomal protein L40
+Macromolecule #42: 60S ribosomal protein L24-A
+Macromolecule #43: Cytoplasmic 60S subunit biogenesis factor REH1
+Macromolecule #46: ZINC ION
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Buffer | pH: 7.5 |
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Vitrification | Cryogen name: ETHANE |
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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: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Image processing
Startup model | Type of model: OTHER |
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Final reconstruction | Applied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 2.1) / Number images used: 46734 |
Initial angle assignment | Type: ANGULAR RECONSTITUTION / Software - Name: RELION |
Final angle assignment | Type: ANGULAR RECONSTITUTION |