[English] 日本語
Yorodumi- EMDB-11097: Cryo-EM structure of yeast reconstituted Lso2 bound to 80S ribosomes -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-11097 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Cryo-EM structure of yeast reconstituted Lso2 bound to 80S ribosomes | |||||||||
Map data | ||||||||||
Sample |
| |||||||||
Function / homology | Function and homology information cytoplasmic translational elongation / : / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, LSU-rRNA,5S) / negative regulation of glucose mediated signaling pathway / negative regulation of translational frameshifting / Protein methylation / RMTs methylate histone arginines / positive regulation of translational fidelity / mTORC1-mediated signalling / ribosome-associated ubiquitin-dependent protein catabolic process ...cytoplasmic translational elongation / : / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, LSU-rRNA,5S) / negative regulation of glucose mediated signaling pathway / negative regulation of translational frameshifting / Protein methylation / RMTs methylate histone arginines / positive regulation of translational fidelity / mTORC1-mediated signalling / ribosome-associated ubiquitin-dependent protein catabolic process / Protein hydroxylation / GDP-dissociation inhibitor activity / : / pre-mRNA 5'-splice site binding / positive regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / Formation of the ternary complex, and subsequently, the 43S complex / Translation initiation complex formation / cleavage in ITS2 between 5.8S rRNA and LSU-rRNA of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / Ribosomal scanning and start codon recognition / preribosome, small subunit precursor / response to cycloheximide / mRNA destabilization / Major pathway of rRNA processing in the nucleolus and cytosol / SRP-dependent cotranslational protein targeting to membrane / 90S preribosome / GTP hydrolysis and joining of the 60S ribosomal subunit / Formation of a pool of free 40S subunits / endonucleolytic cleavage to generate mature 3'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / 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 / protein-RNA complex assembly / ribosomal small subunit export from nucleus / preribosome, large subunit precursor / L13a-mediated translational silencing of Ceruloplasmin expression / translation regulator activity / ribosomal large subunit export from nucleus / G-protein alpha-subunit binding / endonucleolytic cleavage in ITS1 to separate SSU-rRNA from 5.8S rRNA and LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / regulation of translational fidelity / positive regulation of protein kinase activity / rescue of stalled ribosome / translational termination / maturation of SSU-rRNA / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of LSU-rRNA / ribosomal large subunit biogenesis / DNA-(apurinic or apyrimidinic site) endonuclease activity / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / cellular response to amino acid starvation / ribosome assembly / small-subunit processome / protein kinase C binding / maintenance of translational fidelity / macroautophagy / modification-dependent protein catabolic process / ribosomal small subunit biogenesis / small ribosomal subunit rRNA binding / protein tag activity / rRNA processing / ribosomal small subunit assembly / cytoplasmic stress granule / ribosomal large subunit assembly / cytosolic small ribosomal subunit / large ribosomal subunit rRNA binding / ribosome binding / ribosome biogenesis / small ribosomal subunit / 5S rRNA binding / cytoplasmic translation / cytosolic large ribosomal subunit / negative regulation of translation / rRNA binding / protein ubiquitination / ribosome / structural constituent of ribosome / positive regulation of protein phosphorylation / translation / G protein-coupled receptor signaling pathway / response to antibiotic / negative regulation of gene expression / mRNA binding / ubiquitin protein ligase binding / nucleolus / mitochondrion / RNA binding / zinc ion binding / nucleoplasm / metal ion binding / nucleus / cytosol / cytoplasm Similarity search - Function | |||||||||
Biological species | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.4 Å | |||||||||
Authors | Wells JN / Buschauer R / Mackens-Kiani T / Best K / Kratzat H / Berninghausen O / Becker T / Cheng J / Beckmann R | |||||||||
Citation | Journal: PLoS Biol / Year: 2020 Title: Structure and function of yeast Lso2 and human CCDC124 bound to hibernating ribosomes. Authors: Jennifer N Wells / Robert Buschauer / Timur Mackens-Kiani / Katharina Best / Hanna Kratzat / Otto Berninghausen / Thomas Becker / Wendy Gilbert / Jingdong Cheng / Roland Beckmann / Abstract: Cells adjust to nutrient deprivation by reversible translational shutdown. This is accompanied by maintaining inactive ribosomes in a hibernation state, in which they are bound by proteins with ...Cells adjust to nutrient deprivation by reversible translational shutdown. This is accompanied by maintaining inactive ribosomes in a hibernation state, in which they are bound by proteins with inhibitory and protective functions. In eukaryotes, such a function was attributed to suppressor of target of Myb protein 1 (Stm1; SERPINE1 mRNA-binding protein 1 [SERBP1] in mammals), and recently, late-annotated short open reading frame 2 (Lso2; coiled-coil domain containing short open reading frame 124 [CCDC124] in mammals) was found to be involved in translational recovery after starvation from stationary phase. Here, we present cryo-electron microscopy (cryo-EM) structures of translationally inactive yeast and human ribosomes. We found Lso2/CCDC124 accumulating on idle ribosomes in the nonrotated state, in contrast to Stm1/SERBP1-bound ribosomes, which display a rotated state. Lso2/CCDC124 bridges the decoding sites of the small with the GTPase activating center (GAC) of the large subunit. This position allows accommodation of the duplication of multilocus region 34 protein (Dom34)-dependent ribosome recycling system, which splits Lso2-containing, but not Stm1-containing, ribosomes. We propose a model in which Lso2 facilitates rapid translation reactivation by stabilizing the recycling-competent state of inactive ribosomes. | |||||||||
History |
|
-Structure visualization
Movie |
Movie viewer |
---|---|
Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_11097.map.gz | 23.1 MB | EMDB map data format | |
---|---|---|---|---|
Header (meta data) | emd-11097-v30.xml emd-11097.xml | 100.3 KB 100.3 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_11097_fsc.xml | 14.2 KB | Display | FSC data file |
Images | emd_11097.png | 237 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-11097 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-11097 | HTTPS FTP |
-Related structure data
Related structure data | 6z6kMC 6z6jC 6z6lC 6z6mC 6z6nC M: atomic model generated by this map C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
---|---|
Related items in Molecule of the Month |
-Map
File | Download / File: emd_11097.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Voxel size | X=Y=Z: 1.084 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
|
-Supplemental data
-Sample components
+Entire : Lso2-80S ribosome
+Supramolecule #1: Lso2-80S ribosome
+Supramolecule #2: 80S ribosome
+Supramolecule #3: Lso2
+Macromolecule #1: 18S rRNA
+Macromolecule #3: 25S rRNA
+Macromolecule #4: 5S rRNA
+Macromolecule #5: 5.8S rRNA
+Macromolecule #2: Protein LSO2
+Macromolecule #6: 40S ribosomal protein S0-A
+Macromolecule #7: 40S ribosomal protein S1-A
+Macromolecule #8: 40S ribosomal protein S2
+Macromolecule #9: 40S ribosomal protein S3
+Macromolecule #10: 40S ribosomal protein S4-A
+Macromolecule #11: Rps5p
+Macromolecule #12: 40S ribosomal protein S6-A
+Macromolecule #13: 40S ribosomal protein S7-A
+Macromolecule #14: 40S ribosomal protein S8-A
+Macromolecule #15: 40S ribosomal protein S9-A
+Macromolecule #16: 40S ribosomal protein S10-A
+Macromolecule #17: 40S ribosomal protein S11-A
+Macromolecule #18: 40S ribosomal protein S12
+Macromolecule #19: 40S ribosomal protein S13
+Macromolecule #20: 40S ribosomal protein S14-A
+Macromolecule #21: 40S ribosomal protein S15
+Macromolecule #22: 40S ribosomal protein S16-A
+Macromolecule #23: 40S ribosomal protein S17-A
+Macromolecule #24: 40S ribosomal protein S18-A
+Macromolecule #25: 40S ribosomal protein S19-A
+Macromolecule #26: 40S ribosomal protein S20
+Macromolecule #27: 40S ribosomal protein S21-A
+Macromolecule #28: 40S ribosomal protein S22-A
+Macromolecule #29: 40S ribosomal protein S23-A
+Macromolecule #30: 40S ribosomal protein S24-A
+Macromolecule #31: 40S ribosomal protein S25-A
+Macromolecule #32: 40S ribosomal protein S26-B
+Macromolecule #33: 40S ribosomal protein S27-A
+Macromolecule #34: 40S ribosomal protein S28-A
+Macromolecule #35: 40S ribosomal protein S29-A
+Macromolecule #36: 40S ribosomal protein S30-A
+Macromolecule #37: Ubiquitin-40S ribosomal protein S31
+Macromolecule #38: Guanine nucleotide-binding protein subunit beta-like protein
+Macromolecule #39: 60S ribosomal protein L2-A
+Macromolecule #40: 60S ribosomal protein L3
+Macromolecule #41: 60S ribosomal protein L4-A
+Macromolecule #42: 60S ribosomal protein L5
+Macromolecule #43: 60S ribosomal protein L6-A
+Macromolecule #44: 60S ribosomal protein L7-A
+Macromolecule #45: 60S ribosomal protein L8-A
+Macromolecule #46: 60S ribosomal protein L9-A
+Macromolecule #47: 60S ribosomal protein L10
+Macromolecule #48: 60S ribosomal protein L11-A
+Macromolecule #49: 60S ribosomal protein L13-A
+Macromolecule #50: 60S ribosomal protein L14-A
+Macromolecule #51: 60S ribosomal protein L15-A
+Macromolecule #52: 60S ribosomal protein L16-A
+Macromolecule #53: 60S ribosomal protein L17-A
+Macromolecule #54: 60S ribosomal protein L18-A
+Macromolecule #55: 60S ribosomal protein L19-A
+Macromolecule #56: 60S ribosomal protein L20-A
+Macromolecule #57: 60S ribosomal protein L21-A
+Macromolecule #58: 60S ribosomal protein L22-A
+Macromolecule #59: 60S ribosomal protein L23-A
+Macromolecule #60: 60S ribosomal protein L24-A
+Macromolecule #61: 60S ribosomal protein L25
+Macromolecule #62: 60S ribosomal protein L26-A
+Macromolecule #63: 60S ribosomal protein L27-A
+Macromolecule #64: 60S ribosomal protein L28
+Macromolecule #65: 60S ribosomal protein L29
+Macromolecule #66: 60S ribosomal protein L30
+Macromolecule #67: 60S ribosomal protein L31-A
+Macromolecule #68: 60S ribosomal protein L32
+Macromolecule #69: 60S ribosomal protein L33-A
+Macromolecule #70: 60S ribosomal protein L34-A
+Macromolecule #71: 60S ribosomal protein L35-A
+Macromolecule #72: 60S ribosomal protein L36-A
+Macromolecule #73: 60S ribosomal protein L37-A
+Macromolecule #74: 60S ribosomal protein L38
+Macromolecule #75: 60S ribosomal protein L39
+Macromolecule #76: Ubiquitin-60S ribosomal protein L40
+Macromolecule #77: 60S ribosomal protein L41-A
+Macromolecule #78: 60S ribosomal protein L42-A
+Macromolecule #79: 60S ribosomal protein L43-A
+Macromolecule #80: ZINC ION
-Experimental details
-Structure determination
Method | cryo EM |
---|---|
Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.4 |
---|---|
Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
---|---|
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy |
Image recording | Film or detector model: FEI FALCON II (4k x 4k) / Average electron dose: 28.0 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
-Atomic model buiding 1
Refinement | Space: REAL / Protocol: RIGID BODY FIT |
---|---|
Output model | PDB-6z6k: |