+Open data
-Basic information
Entry | Database: PDB / ID: 8scb | ||||||||||||
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Title | Terminating ribosome with SRI-41315 | ||||||||||||
Components |
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Keywords | RIBOSOME / termination / SRI-41315 | ||||||||||||
Function / homology | Function and homology information translation termination factor activity / translation release factor complex / cytoplasmic translational termination / translation release factor activity / regulation of translational termination / translation release factor activity, codon specific / protein methylation / sequence-specific mRNA binding / aminoacyl-tRNA hydrolase activity / regulation of G1 to G0 transition ...translation termination factor activity / translation release factor complex / cytoplasmic translational termination / translation release factor activity / regulation of translational termination / translation release factor activity, codon specific / protein methylation / sequence-specific mRNA binding / aminoacyl-tRNA hydrolase activity / regulation of G1 to G0 transition / laminin receptor activity / exit from mitosis / nuclear-transcribed mRNA catabolic process, nonsense-mediated decay / positive regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / regulation of translation involved in cellular response to UV / protein-DNA complex disassembly / positive regulation of DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator / optic nerve development / retinal ganglion cell axon guidance / mammalian oogenesis stage / G1 to G0 transition / activation-induced cell death of T cells / Protein hydroxylation / positive regulation of signal transduction by p53 class mediator / Eukaryotic Translation Termination / phagocytic cup / ubiquitin ligase inhibitor activity / ribosomal small subunit binding / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / TOR signaling / endonucleolytic cleavage to generate mature 3'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / 90S preribosome / T cell proliferation involved in immune response / protein-RNA complex assembly / erythrocyte development / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / negative regulation of ubiquitin-dependent protein catabolic process / ribosomal subunit export from nucleus / translation regulator activity / cellular response to actinomycin D / ribosomal small subunit export from nucleus / translational termination / cytosolic ribosome / laminin 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) / rough endoplasmic reticulum / gastrulation / MDM2/MDM4 family protein binding / DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest / maturation of LSU-rRNA / class I DNA-(apurinic or apyrimidinic site) endonuclease activity / DNA-(apurinic or apyrimidinic site) lyase / rescue of stalled ribosome / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / positive regulation of apoptotic signaling pathway / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / ribosomal large subunit biogenesis / cellular response to leukemia inhibitory factor / maturation of SSU-rRNA / placenta development / small-subunit processome / positive regulation of translation / translational initiation / protein kinase C binding / positive regulation of protein-containing complex assembly / G1/S transition of mitotic cell cycle / cellular response to gamma radiation / transcription coactivator binding / mRNA 5'-UTR binding / Regulation of expression of SLITs and ROBOs / modification-dependent protein catabolic process / spindle / cytoplasmic ribonucleoprotein granule / positive regulation of canonical Wnt signaling pathway / rhythmic process / rRNA processing / protein tag activity / antimicrobial humoral immune response mediated by antimicrobial peptide / glucose homeostasis / virus receptor activity / ribosome biogenesis / ribosome binding / retina development in camera-type eye / regulation of translation / heparin binding / ribosomal small subunit biogenesis / ribosomal small subunit assembly / small ribosomal subunit / small ribosomal subunit rRNA binding / cell body / T cell differentiation in thymus / 5S rRNA binding / large ribosomal subunit rRNA binding / cytosolic small ribosomal subunit / perikaryon / defense response to Gram-negative bacterium / cytosolic large ribosomal subunit / killing of cells of another organism / cytoplasmic translation / cell differentiation Similarity search - Function | ||||||||||||
Biological species | Homo sapiens (human) Oryctolagus cuniculus (rabbit) | ||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.5 Å | ||||||||||||
Authors | Yip, M.C.J. / Coelho, J.P.L. / Oltion, K. / Tauton, J. / Shao, S. | ||||||||||||
Funding support | United States, 3items
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Citation | Journal: Nat Chem Biol / Year: 2024 Title: The eRF1 degrader SRI-41315 acts as a molecular glue at the ribosomal decoding center. Authors: João P L Coelho / Matthew C J Yip / Keely Oltion / Jack Taunton / Sichen Shao / Abstract: Translation termination is an essential cellular process, which is also of therapeutic interest for diseases that manifest from premature stop codons. In eukaryotes, translation termination requires ...Translation termination is an essential cellular process, which is also of therapeutic interest for diseases that manifest from premature stop codons. In eukaryotes, translation termination requires eRF1, which recognizes stop codons, catalyzes the release of nascent proteins from ribosomes and facilitates ribosome recycling. The small molecule SRI-41315 triggers eRF1 degradation and enhances translational readthrough of premature stop codons. However, the mechanism of action of SRI-41315 on eRF1 and translation is not known. Here we report cryo-EM structures showing that SRI-41315 acts as a metal-dependent molecular glue between the N domain of eRF1 responsible for stop codon recognition and the ribosomal subunit interface near the decoding center. Retention of eRF1 on ribosomes by SRI-41315 leads to ribosome collisions, eRF1 ubiquitylation and a higher frequency of translation termination at near-cognate stop codons. Our findings reveal a new mechanism of release factor inhibition and additional implications for pharmacologically targeting eRF1. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8scb.cif.gz | 4.9 MB | Display | PDBx/mmCIF format |
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PDB format | pdb8scb.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 8scb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8scb_validation.pdf.gz | 2.2 MB | Display | wwPDB validaton report |
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Full document | 8scb_full_validation.pdf.gz | 2.5 MB | Display | |
Data in XML | 8scb_validation.xml.gz | 379.4 KB | Display | |
Data in CIF | 8scb_validation.cif.gz | 661.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/sc/8scb ftp://data.pdbj.org/pub/pdb/validation_reports/sc/8scb | HTTPS FTP |
-Related structure data
Related structure data | 40344MC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
-Ribosomal protein ... , 8 types, 8 molecules ABNQRVjDD
#1: Protein | Mass: 28088.863 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TT27 |
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#2: Protein | Mass: 46107.977 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TL06 |
#13: Protein | Mass: 24207.285 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1T0C1 |
#16: Protein | Mass: 21699.688 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TFE0 |
#17: Protein | Mass: 23535.281 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TJR3 |
#21: Protein | Mass: 14892.505 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1T6D1 |
#35: Protein | Mass: 11111.032 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: U3KPD5 |
#55: Protein | Mass: 26715.344 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) References: UniProt: G1TNM3, DNA-(apurinic or apyrimidinic site) lyase |
-60S ribosomal protein ... , 16 types, 16 molecules CEFGHIJMWZabgikt
#3: Protein | Mass: 46388.855 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SVW5 |
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#5: Protein | Mass: 33028.336 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SKF7 |
#6: Protein | Mass: 29201.836 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TUB1 |
#7: Protein | Mass: 36221.516 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1STW0 |
#8: Protein | Mass: 21871.418 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SWI6 |
#9: Protein | Mass: 24643.057 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: B7NZQ2 |
#10: Protein | Mass: 20288.465 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TUB8 |
#12: Protein | Mass: 23870.549 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SZ12 |
#22: Protein | Mass: 17825.111 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SE28 |
#25: Protein | Mass: 15835.831 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TXF6 |
#26: Protein | Mass: 16620.561 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SNY0 |
#27: Protein | Mass: 26708.707 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SGR6 |
#32: Protein | Mass: 13326.074 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TXG5 |
#34: Protein | Mass: 12263.834 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TTQ5 |
#36: Protein | Mass: 8238.948 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1U001 |
#44: Protein | Mass: 17847.619 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SMR7 |
+Protein , 53 types, 53 molecules DLOPSTUXYcdefhlmoprs1AABBCCEEFFGGHHIIJJ...
-Protein/peptide , 1 types, 1 molecules n
#39: Protein/peptide | Mass: 3473.451 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: A0A087WNH4 |
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-RNA chain , 7 types, 7 molecules 235789hh
#46: RNA chain | Mass: 24436.551 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) |
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#47: RNA chain | Mass: 24102.275 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) |
#48: RNA chain | Mass: 1149054.125 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) |
#49: RNA chain | Mass: 38691.914 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: GenBank: X06789.1 |
#50: RNA chain | Mass: 50157.676 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) |
#51: RNA chain | Mass: 603440.875 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) |
#85: RNA chain | Mass: 63720.914 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) |
-40S ribosomal protein ... , 2 types, 2 molecules YYaa
#76: Protein | Mass: 15107.924 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1T3D8 |
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#78: Protein | Mass: 13047.532 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TFE8 |
-Non-polymers , 5 types, 1281 molecules
#88: Chemical | ChemComp-MG / #89: Chemical | ChemComp-ZN / #90: Chemical | ChemComp-ZVM / ( | #91: Chemical | #92: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: terminating rabbit ribosome / Type: RIBOSOME / Entity ID: #1-#87 / Source: NATURAL |
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Molecular weight | Value: 4 MDa / Experimental value: NO |
Source (natural) | Organism: Oryctolagus cuniculus (rabbit) |
Buffer solution | pH: 7.5 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 800 nm |
Image recording | Electron dose: 53.8 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) |
-Processing
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION |
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3D reconstruction | Resolution: 2.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 90190 / Symmetry type: POINT |