+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-24652 | |||||||||
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Title | Structure of ribosomal complex bound with Rbg1/Tma46 | |||||||||
Map data | ||||||||||
Sample |
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Function / homology | Function and homology information positive regulation of translational termination / positive regulation of translational elongation / ribosomal subunit / pre-mRNA 5'-splice site binding / Formation of the ternary complex, and subsequently, the 43S complex / Translation initiation complex formation / Ribosomal scanning and start codon recognition / SRP-dependent cotranslational protein targeting to membrane / GTP hydrolysis and joining of the 60S ribosomal subunit / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) ...positive regulation of translational termination / positive regulation of translational elongation / ribosomal subunit / pre-mRNA 5'-splice site binding / Formation of the ternary complex, and subsequently, the 43S complex / Translation initiation complex formation / Ribosomal scanning and start codon recognition / SRP-dependent cotranslational protein targeting to membrane / GTP hydrolysis and joining of the 60S ribosomal subunit / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / Formation of a pool of free 40S subunits / negative regulation of mRNA splicing, via spliceosome / L13a-mediated translational silencing of Ceruloplasmin expression / endonucleolytic cleavage to generate mature 3'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / protein-RNA complex assembly / translation elongation factor activity / 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) / maturation of LSU-rRNA / translation initiation factor activity / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / ribosomal large subunit biogenesis / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of SSU-rRNA / macroautophagy / positive regulation of apoptotic signaling pathway / modification-dependent protein catabolic process / protein tag activity / rRNA processing / large ribosomal subunit / ribosome biogenesis / ribosome binding / ribosomal small subunit assembly / small ribosomal subunit / 5S rRNA binding / large ribosomal subunit rRNA binding / cytosolic small ribosomal subunit / ribosomal large subunit assembly / cytoplasmic translation / cytosolic large ribosomal subunit / rRNA binding / ribosome / protein ubiquitination / structural constituent of ribosome / translation / mRNA binding / ubiquitin protein ligase binding / GTP binding / nucleolus / RNA binding / zinc ion binding / nucleus / metal ion binding / cytosol / cytoplasm Similarity search - Function | |||||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) / Baker's yeast (brewer's yeast) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.23 Å | |||||||||
Authors | Zeng F / Li X / Pires-Alves M / Chen X / Hawk CW / Jin H | |||||||||
Funding support | United States, 1 items
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Citation | Journal: Cell Rep / Year: 2021 Title: Conserved heterodimeric GTPase Rbg1/Tma46 promotes efficient translation in eukaryotic cells. Authors: Fuxing Zeng / Xin Li / Melissa Pires-Alves / Xin Chen / Christopher W Hawk / Hong Jin / Abstract: Conserved developmentally regulated guanosine triphosphate (GTP)-binding proteins (Drgs) and their binding partner Drg family regulatory proteins (Dfrps) are important for embryonic development, ...Conserved developmentally regulated guanosine triphosphate (GTP)-binding proteins (Drgs) and their binding partner Drg family regulatory proteins (Dfrps) are important for embryonic development, cellular growth control, differentiation, and proliferation. Here, we report that the yeast Drg1/Dfrp1 ortholog Rbg1/Tma46 facilitates translational initiation, elongation, and termination by suppressing prolonged ribosome pausing. Consistent with the genome-wide observations, deletion of Rbg1 exacerbates the growth defect resulting from translation stalling, and Rbg1 stabilizes mRNAs against no-go decay. Furthermore, we provide a cryoelectron microscopy (cryo-EM) structure of the 80S ribosome bound with Rbg1/Tma46 that reveals the molecular interactions responsible for Rbg1/Tma46 function. The Rbg1 subunit binds to the GTPase association center of the ribosome and the A-tRNA, and the N-terminal zinc finger domain of the Tma46 subunit binds to the 40S, establishing an interaction critical for the ribosomal association. Our results answer the fundamental question of how a paused ribosome resumes translation and show that Drg1/Dfrp1 play a critical role in ensuring orderly translation. | |||||||||
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_24652.map.gz | 46.3 MB | EMDB map data format | |
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Header (meta data) | emd-24652-v30.xml emd-24652.xml | 111.5 KB 111.5 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_24652_fsc.xml | 15.9 KB | Display | FSC data file |
Images | emd_24652.png | 80.1 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-24652 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-24652 | HTTPS FTP |
-Validation report
Summary document | emd_24652_validation.pdf.gz | 430.9 KB | Display | EMDB validaton report |
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Full document | emd_24652_full_validation.pdf.gz | 430.5 KB | Display | |
Data in XML | emd_24652_validation.xml.gz | 14.9 KB | Display | |
Data in CIF | emd_24652_validation.cif.gz | 20.4 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-24652 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-24652 | HTTPS FTP |
-Related structure data
Related structure data | 7rr5MC M: atomic model generated by this map 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_24652.map.gz / Format: CCP4 / Size: 343 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.08 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 : Ribosomal complex with Rbg1/Tma46
+Supramolecule #1: Ribosomal complex with Rbg1/Tma46
+Supramolecule #2: 60S subunit
+Supramolecule #3: 40S subunit
+Supramolecule #4: Rbg1/Tma46
+Supramolecule #5: A-tRNA
+Supramolecule #6: P-tRNA
+Supramolecule #7: eIF5A
+Supramolecule #8: mRNA
+Macromolecule #1: 25S rRNA
+Macromolecule #2: 5S rRNA
+Macromolecule #3: 5.8S rRNA
+Macromolecule #47: 18S rRNA
+Macromolecule #81: A-tRNA
+Macromolecule #82: P-tRNA
+Macromolecule #83: mRNA
+Macromolecule #4: 60S ribosomal protein L2-B
+Macromolecule #5: RPL3 isoform 1
+Macromolecule #6: RPL4A isoform 1
+Macromolecule #7: RPL5 isoform 1
+Macromolecule #8: 60S ribosomal protein L6
+Macromolecule #9: 60S ribosomal protein L7-A
+Macromolecule #10: 60S ribosomal protein L8-A
+Macromolecule #11: 60S ribosomal protein L9-A
+Macromolecule #12: RPL10 isoform 1
+Macromolecule #13: RPL11B isoform 1
+Macromolecule #14: 60S ribosomal protein L13
+Macromolecule #15: 60S ribosomal protein L14-A
+Macromolecule #16: 60S ribosomal protein L15-A
+Macromolecule #17: 60S ribosomal protein L16-A
+Macromolecule #18: 60S ribosomal protein L17-A
+Macromolecule #19: 60S ribosomal protein L18-B
+Macromolecule #20: 60S ribosomal protein L19-A
+Macromolecule #21: 60S ribosomal protein L20-A
+Macromolecule #22: 60S ribosomal protein L21-A
+Macromolecule #23: 60S ribosomal protein L22-A
+Macromolecule #24: 60S ribosomal protein L23-B
+Macromolecule #25: RPL24A isoform 1
+Macromolecule #26: 60S ribosomal protein L25
+Macromolecule #27: 60S ribosomal protein L26-A
+Macromolecule #28: 60S ribosomal protein L27
+Macromolecule #29: 60S ribosomal protein L28
+Macromolecule #30: RPL29 isoform 1
+Macromolecule #31: 60S ribosomal protein L30
+Macromolecule #32: 60S ribosomal protein L31-A
+Macromolecule #33: RPL32 isoform 1
+Macromolecule #34: 60S ribosomal protein L33-A
+Macromolecule #35: 60S ribosomal protein L34-A
+Macromolecule #36: 60S ribosomal protein L35-A
+Macromolecule #37: 60S ribosomal protein L36-A
+Macromolecule #38: Ribosomal protein L37
+Macromolecule #39: RPL38 isoform 1
+Macromolecule #40: 60S ribosomal protein L39
+Macromolecule #41: Ubiquitin-60S ribosomal protein L40
+Macromolecule #42: 60S ribosomal protein L41-A
+Macromolecule #43: 60S ribosomal protein L42-A
+Macromolecule #44: 60S ribosomal protein L43-A
+Macromolecule #45: RPP0 isoform 1
+Macromolecule #46: RPL12A isoform 1
+Macromolecule #48: 40S ribosomal protein S0
+Macromolecule #49: RPS1A isoform 1
+Macromolecule #50: RPS2 isoform 1
+Macromolecule #51: RPS3 isoform 1
+Macromolecule #52: 40S ribosomal protein S4
+Macromolecule #53: Rps5p
+Macromolecule #54: 40S ribosomal protein S6
+Macromolecule #55: 40S ribosomal protein S7
+Macromolecule #56: RPS8A isoform 1
+Macromolecule #57: 40S ribosomal protein S9-A
+Macromolecule #58: 40S ribosomal protein S10-A
+Macromolecule #59: 40S ribosomal protein S11-B
+Macromolecule #60: 40S ribosomal protein S12
+Macromolecule #61: 40S ribosomal protein S13
+Macromolecule #62: 40S ribosomal protein S14-B
+Macromolecule #63: RPS15 isoform 1
+Macromolecule #64: 40S ribosomal protein S16-A
+Macromolecule #65: 40S ribosomal protein S17-A
+Macromolecule #66: 40S ribosomal protein S18-B
+Macromolecule #67: 40S ribosomal protein S19-A
+Macromolecule #68: RPS20 isoform 1
+Macromolecule #69: 40S ribosomal protein S21-A
+Macromolecule #70: RPS22A isoform 1
+Macromolecule #71: 40S ribosomal protein S23
+Macromolecule #72: 40S ribosomal protein S24
+Macromolecule #73: RPS25A isoform 1
+Macromolecule #74: RPS26B isoform 1
+Macromolecule #75: 40S ribosomal protein S27-A
+Macromolecule #76: RPS28A isoform 1
+Macromolecule #77: RPS29A isoform 1
+Macromolecule #78: 40S ribosomal protein S30
+Macromolecule #79: Ubiquitin-40S ribosomal protein S31
+Macromolecule #80: Guanine nucleotide-binding protein subunit beta-like protein
+Macromolecule #84: Eukaryotic translation initiation factor 5A
+Macromolecule #85: Ribosome-interacting GTPase 1
+Macromolecule #86: Translation machinery-associated protein 46
+Macromolecule #87: 60S ribosomal protein L1
+Macromolecule #88: MAGNESIUM ION
+Macromolecule #89: ASPARTIC ACID
+Macromolecule #90: ZINC ION
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 8 Component:
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Grid | Model: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE | ||||||||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Specialist optics | Phase plate: OTHER |
Image recording | Film or detector model: FEI FALCON III (4k x 4k) / Average electron dose: 30.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |