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Yorodumi- PDB-8wq4: Structural basis of translation inhibition by a valine tRNA-deriv... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8wq4 | ||||||
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Title | Structural basis of translation inhibition by a valine tRNA-derived fragment | ||||||
Components |
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Keywords | RIBOSOME / Sulfolobus acidocaldarius ribosome | ||||||
Function / homology | Function and homology information ribonuclease P activity / tRNA 5'-leader removal / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of SSU-rRNA / positive regulation of apoptotic signaling pathway / ribosomal small subunit biogenesis / small ribosomal subunit rRNA binding / ribosome biogenesis / ribosomal small subunit assembly / small ribosomal subunit ...ribonuclease P activity / tRNA 5'-leader removal / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of SSU-rRNA / positive regulation of apoptotic signaling pathway / ribosomal small subunit biogenesis / small ribosomal subunit rRNA binding / ribosome biogenesis / ribosomal small subunit assembly / small ribosomal subunit / cytosolic small ribosomal subunit / cytoplasmic translation / tRNA binding / rRNA binding / ribosome / structural constituent of ribosome / ribonucleoprotein complex / translation / mRNA binding / RNA binding / zinc ion binding / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Sulfolobus acidocaldarius DSM 639 (acidophilic) Haloferax volcanii (archaea) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.53 Å | ||||||
Authors | Wang, Y.H. / Zhou, J. | ||||||
Funding support | China, 1items
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Citation | Journal: Life Sci Alliance / Year: 2024 Title: Structural basis of translation inhibition by a valine tRNA-derived fragment. Authors: Yun Wu / Meng-Ting Ni / Ying-Hui Wang / Chen Wang / Hai Hou / Xing Zhang / Jie Zhou / Abstract: Translational regulation by non-coding RNAs is a mechanism commonly used by cells to fine-tune gene expression. A fragment derived from an archaeal valine tRNA (Val-tRF) has been previously ...Translational regulation by non-coding RNAs is a mechanism commonly used by cells to fine-tune gene expression. A fragment derived from an archaeal valine tRNA (Val-tRF) has been previously identified to bind the small subunit of the ribosome and inhibit translation in Here, we present three cryo-electron microscopy structures of Val-tRF bound to the small subunit of ribosomes at resolutions between 4.02 and 4.53 Å. Within these complexes, Val-tRF was observed to bind to conserved RNA-interacting sites, including the ribosomal decoding center. The binding of Val-tRF destabilizes helices h24, h44, and h45 and the anti-Shine-Dalgarno sequence of 16S rRNA. The binding position of this molecule partially overlaps with the translation initiation factor aIF1A and occludes the mRNA P-site codon. Moreover, we found that the binding of Val-tRF is associated with steric hindrance of the H69 base of 23S rRNA in the large ribosome subunit, thereby preventing 70S assembly. Our data exemplify how tRNA-derived fragments bind to ribosomes and provide new insights into the mechanisms underlying translation inhibition by Val-tRFs. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8wq4.cif.gz | 1.3 MB | Display | PDBx/mmCIF format |
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PDB format | pdb8wq4.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 8wq4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8wq4_validation.pdf.gz | 1.4 MB | Display | wwPDB validaton report |
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Full document | 8wq4_full_validation.pdf.gz | 1.5 MB | Display | |
Data in XML | 8wq4_validation.xml.gz | 104.8 KB | Display | |
Data in CIF | 8wq4_validation.cif.gz | 177.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wq/8wq4 ftp://data.pdbj.org/pub/pdb/validation_reports/wq/8wq4 | HTTPS FTP |
-Related structure data
Related structure data | 37734MC 8wkpC 8wq2C 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
-RNA chain , 2 types, 2 molecules A16SVTRF
#1: RNA chain | Mass: 486920.531 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Sulfolobus acidocaldarius DSM 639 (acidophilic) Production host: Sulfolobus acidocaldarius DSM 639 (acidophilic) References: GenBank: 2440479486 |
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#2: RNA chain | Mass: 8411.946 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Haloferax volcanii (archaea) / Production host: Haloferax volcanii (archaea) |
+30S ribosomal protein ... , 24 types, 24 molecules AS2PAS4EAS4PAS5PAS6EAS8ES11PS12PS15PS17PS24ES27ES3AEAS3PAS7PAS9PS10PS13PS14PS17ES19ES19PS27AS28E
-Protein , 2 types, 2 molecules SL7AAS8P
#27: Protein | Mass: 13351.481 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Sulfolobus acidocaldarius DSM 639 (acidophilic) Gene: rpl7ae, Saci_1520 Production host: Sulfolobus acidocaldarius DSM 639 (acidophilic) References: UniProt: Q4J8P1 |
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#28: Protein | Mass: 14624.191 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Sulfolobus acidocaldarius DSM 639 (acidophilic) Gene: rps8, Saci_0582 Production host: Sulfolobus acidocaldarius DSM 639 (acidophilic) References: UniProt: O05636 |
-Non-polymers , 1 types, 57 molecules
#29: Chemical | ChemComp-UNK / |
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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: 2D ARRAY / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: Sulfolobus acidocaldarius ribosome / Type: RIBOSOME / Entity ID: #2, #1, #3-#8, #28, #9-#28 / Source: NATURAL |
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Source (natural) | Organism: Sulfolobus acidocaldarius DSM 639 (acidophilic) |
Buffer solution | pH: 7.5 |
Specimen | Conc.: 5 mg/ml / 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: 3000 nm / Nominal defocus min: 1000 nm |
Image recording | Electron dose: 26.7 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
-Processing
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
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3D reconstruction | Resolution: 4.53 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 5281 / Symmetry type: POINT | ||||||||||||||||||||||||
Refinement | Cross valid method: NONE Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2 | ||||||||||||||||||||||||
Displacement parameters | Biso mean: 460.55 Å2 | ||||||||||||||||||||||||
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