- EMDB-24652: Structure of ribosomal complex bound with Rbg1/Tma46 -
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Basic information
Entry
Database: EMDB / ID: EMD-24652
Title
Structure of ribosomal complex bound with Rbg1/Tma46
Map data
Sample
Complex: Ribosomal complex with Rbg1/Tma46
Complex: 60S subunit
RNA: x 3 types
Protein or peptide: x 44 types
Complex: 40S subunit
RNA: x 1 types
Protein or peptide: x 33 types
Complex: Rbg1/Tma46
Protein or peptide: x 2 types
Complex: A-tRNA
RNA: x 1 types
Complex: P-tRNA
RNA: x 1 types
Complex: eIF5A
Protein or peptide: x 1 types
Complex: mRNA
RNA: x 1 types
Ligand: x 3 types
Keywords
Rbg1 / Tma46 / RIBOSOME
Function / homology
Function and homology information
positive regulation of translational termination / ribosomal subunit / positive regulation of translational elongation / pre-mRNA 5'-splice site binding / cytosolic large ribosomal subunit assembly / Ribosome Quality Control (RQC) complex extracts and degrades nascent peptide / Formation of the ternary complex, and subsequently, the 43S complex / Translation initiation complex formation / Ribosomal scanning and start codon recognition / Major pathway of rRNA processing in the nucleolus and cytosol ...positive regulation of translational termination / ribosomal subunit / positive regulation of translational elongation / pre-mRNA 5'-splice site binding / cytosolic large ribosomal subunit assembly / Ribosome Quality Control (RQC) complex extracts and degrades nascent peptide / Formation of the ternary complex, and subsequently, the 43S complex / Translation initiation complex formation / Ribosomal scanning and start codon recognition / Major pathway of rRNA processing in the nucleolus and cytosol / PELO:HBS1L and ABCE1 dissociate a ribosome on a non-stop mRNA / SRP-dependent cotranslational protein targeting to membrane / GTP hydrolysis and joining of the 60S ribosomal subunit / 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) / L13a-mediated translational silencing of Ceruloplasmin expression / negative regulation of mRNA splicing, via spliceosome / endonucleolytic cleavage to generate mature 3'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / translation elongation factor activity / maturation of LSU-rRNA / protein-RNA complex assembly / 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) / positive regulation of apoptotic signaling pathway / translation initiation factor activity / macroautophagy / ribosomal large subunit biogenesis / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of SSU-rRNA / modification-dependent protein catabolic process / protein tag activity / rRNA processing / large ribosomal subunit / ribosomal small subunit assembly / ribosome binding / ribosome biogenesis / 5S rRNA binding / ribosomal large subunit assembly / small ribosomal subunit / cytosolic small ribosomal subunit / large ribosomal subunit rRNA binding / cytosolic large ribosomal subunit / cytoplasmic translation / protein ubiquitination / rRNA binding / ribosome / translation / structural constituent of ribosome / ubiquitin protein ligase binding / mRNA binding / nucleolus / GTP binding / RNA binding / zinc ion binding / metal ion binding / nucleus / cytosol / cytoplasm Similarity search - Function
ZC3H15/TMA46 family, C-terminal / DRG Family Regulatory Proteins, Tma46 / GTP binding protein, second domain / C-terminal region of MMR_HSR1 domain / GTP1/OBG, conserved site / GTP1/OBG family signature. / Translation elongation factor, IF5A, hypusine site / Eukaryotic initiation factor 5A hypusine signature. / Eukaryotic elongation factor 5A hypusine, DNA-binding OB fold / Translation elongation factor, IF5A C-terminal ...ZC3H15/TMA46 family, C-terminal / DRG Family Regulatory Proteins, Tma46 / GTP binding protein, second domain / C-terminal region of MMR_HSR1 domain / GTP1/OBG, conserved site / GTP1/OBG family signature. / Translation elongation factor, IF5A, hypusine site / Eukaryotic initiation factor 5A hypusine signature. / Eukaryotic elongation factor 5A hypusine, DNA-binding OB fold / Translation elongation factor, IF5A C-terminal / Eukaryotic elongation factor 5A hypusine, DNA-binding OB fold / TGS domain / Translation elongation factor IF5A-like / Zinc finger, CCCH-type superfamily / zinc finger / OBG-type guanine nucleotide-binding (G) domain / OBG-type guanine nucleotide-binding (G) domain profile. / Zinc finger, CCCH-type / Zinc finger C3H1-type profile. / TGS-like / TGS domain profile. / TGS / 50S ribosome-binding GTPase / 60S acidic ribosomal protein P0 / GTP binding domain / 50S ribosomal protein L10, insertion domain superfamily / 60S ribosomal protein L10P, insertion domain / Insertion domain in 60S ribosomal protein L10P / : / Beta-grasp domain superfamily / : / Ribosomal protein S26e signature. / Ribosomal protein L41 / Ribosomal protein L41 / Ribosomal protein L13e, conserved site / Ribosomal protein L13e signature. / Ribosomal protein S21e, conserved site / Ribosomal protein S21e signature. / : / Ribosomal protein S12e signature. / Ribosomal protein L29e / Ribosomal L29e protein family / Ribosomal protein S26e / Ribosomal protein S26e superfamily / Ribosomal protein S26e / Ribosomal protein S12e / Ribosomal protein L27e, conserved site / Ribosomal protein L27e signature. / Ribosomal protein L22e / Ribosomal protein L22e superfamily / Ribosomal L22e protein family / Ribosomal protein L13e / Ribosomal protein L13e / Ribosomal protein L38e / Ribosomal protein L38e superfamily / Ribosomal L38e protein family / Ribosomal protein L6e signature. / Ribosomal protein S5, eukaryotic/archaeal / Ribosomal protein S21e / Ribosomal protein S21e superfamily / Ribosomal protein S21e / Ribosomal protein L19, eukaryotic / Ribosomal protein S19e, conserved site / Ribosomal protein S19e signature. / Ribosomal protein S2, eukaryotic / 60S ribosomal protein L18a/ L20, eukaryotes / Ribosomal protein L10e, conserved site / 40S Ribosomal protein S10 / Ribosomal protein L10e signature. / Ribosomal protein L18/L18-A/B/e, conserved site / Ribosomal protein L18e signature. / Ribosomal protein L44e signature. / Plectin/S10, N-terminal / Ribosomal protein L24e, conserved site / Ribosomal protein L19/L19e conserved site / Plectin/S10 domain / Ribosomal protein L19e signature. / Ribosomal protein L24e signature. / S27a-like superfamily / Ribosomal protein L5 eukaryotic, C-terminal / Ribosomal L18 C-terminal region / Ribosomal protein L23/L25, N-terminal / Ribosomal protein L23, N-terminal domain / Ribosomal protein L10e / Ribosomal protein L34e, conserved site / Ribosomal protein L34e signature. / Ribosomal protein S30 / Ribosomal protein S30 / Ribosomal L40e family / Ribosomal protein L36e signature. / Ribosomal protein S10, eukaryotic/archaeal / Ribosomal protein L30e signature 1. / Eukaryotic Ribosomal Protein L27, KOW domain / Ribosomal protein S25 / S25 ribosomal protein / Ribosomal protein L27e / Ribosomal protein L27e superfamily / Ribosomal L27e protein family / Ribosomal Protein L6, KOW domain / 50S ribosomal protein L18Ae/60S ribosomal protein L20 and L18a Similarity search - Domain/homology
Rps5p / Small ribosomal subunit protein eS1 / RPS22A isoform 1 / 60S acidic ribosomal protein P0 / RPS31 isoform 1 / RPL38 isoform 1 / RPL10 isoform 1 / RPS29A isoform 1 / RPS20 isoform 1 / RPS2 isoform 1 ...Rps5p / Small ribosomal subunit protein eS1 / RPS22A isoform 1 / 60S acidic ribosomal protein P0 / RPS31 isoform 1 / RPL38 isoform 1 / RPL10 isoform 1 / RPS29A isoform 1 / RPS20 isoform 1 / RPS2 isoform 1 / 60S ribosomal protein L29 / BJ4_G0051200.mRNA.1.CDS.1 / Eukaryotic translation initiation factor 5A / RPL24A isoform 1 / RPL11B isoform 1 / 40S ribosomal protein S25 / 40S ribosomal protein S26 / RPL5 isoform 1 / 40S ribosomal protein S8 / RPL32 isoform 1 / RPL12A isoform 1 / 40S ribosomal protein S3 / RPL4A isoform 1 / Large ribosomal subunit protein uL3 / RPS15 isoform 1 / RPS28A isoform 1 / BJ4_G0035820.mRNA.1.CDS.1 / 40S ribosomal protein S12 / 60S ribosomal protein L2-B / 40S ribosomal protein S13 / 60S ribosomal protein L31-A / 40S ribosomal protein S11-B / EM14S01-3B_G0023620.mRNA.1.CDS.1 / 60S ribosomal protein L25 / BJ4_G0018510.mRNA.1.CDS.1 / 40S ribosomal protein S4 / 40S ribosomal protein S14-B / 60S ribosomal protein L23-B / 60S ribosomal protein L16-A / 60S ribosomal protein L28 / 60S ribosomal protein L34-A / 40S ribosomal protein S10-A / 60S ribosomal protein L27 / 40S ribosomal protein S0 / 60S ribosomal protein L22-A / 40S ribosomal protein S30 / 60S ribosomal protein L18-B / 40S ribosomal protein S7 / 60S ribosomal protein L13 / 40S ribosomal protein S18-B / 40S ribosomal protein S6 / 60S ribosomal protein L39 / 40S ribosomal protein S24 / 40S ribosomal protein S23 / 60S ribosomal protein L42-B / 60S ribosomal protein L17-A / Ribosomal protein L37 / 60S ribosomal protein L6 / EM14S01-3B_G0023350.mRNA.1.CDS.1 / EM14S01-3B_G0022060.mRNA.1.CDS.1 / 40S ribosomal protein S19-A / EM14S01-3B_G0017920.mRNA.1.CDS.1 / 60S ribosomal protein L7-A / Ubiquitin / EM14S01-3B_G0041280.mRNA.1.CDS.1 / EM14S01-3B_G0018500.mRNA.1.CDS.1 / Large ribosomal subunit protein uL6A / Large ribosomal subunit protein uL24A / Large ribosomal subunit protein eL36A / Large ribosomal subunit protein eL15A / Small ribosomal subunit protein eS21A / Large ribosomal subunit protein eL20A / Large ribosomal subunit protein eL43A / Large ribosomal subunit protein eL19A / Small ribosomal subunit protein eS32A / Large ribosomal subunit protein eL30 / Large ribosomal subunit protein eL8A / Small ribosomal subunit protein eS27A / Large ribosomal subunit protein eL14A Similarity search - Component
Biological species
Saccharomyces cerevisiae (brewer's yeast)
Method
single particle reconstruction / cryo EM / Resolution: 3.23 Å
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)
R01-GM120552
United States
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
Deposition
Aug 9, 2021
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Header (metadata) release
Nov 10, 2021
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Map release
Nov 10, 2021
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Update
Nov 20, 2024
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Current status
Nov 20, 2024
Processing site: RCSB / Status: Released
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Structure visualization
Movie
Surface view with section colored by density value
Name: P-tRNA / type: rna / ID: 82 Details: Althrough the position 34 is G or A in NCBI database. But it can only be U base on the density. It might be a varient tRNA from the yeast. Number of copies: 1
Name: 60S ribosomal protein L1 / type: protein_or_peptide / ID: 87 Details: Only show the backbone of the protein due to the poor density Number of copies: 1 / Enantiomer: LEVO
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