+Open data
-Basic information
Entry | Database: PDB / ID: 8ip9 | ||||||
---|---|---|---|---|---|---|---|
Title | Wheat 40S ribosome in complex with a tRNAi | ||||||
Components |
| ||||||
Keywords | TRANSLATION / ribosome | ||||||
Function / homology | Function and homology information endonucleolytic cleavage to generate mature 3'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / translation regulator 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) / rescue of stalled ribosome / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of SSU-rRNA / small-subunit processome / protein kinase C binding / rRNA processing / ribosomal small subunit biogenesis ...endonucleolytic cleavage to generate mature 3'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / translation regulator 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) / rescue of stalled ribosome / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of SSU-rRNA / small-subunit processome / protein kinase C binding / rRNA processing / ribosomal small subunit biogenesis / ribosome binding / ribosomal small subunit assembly / small ribosomal subunit / cytosolic small ribosomal subunit / cytoplasmic translation / rRNA binding / ribosome / structural constituent of ribosome / ribonucleoprotein complex / positive regulation of protein phosphorylation / translation / mRNA binding / RNA binding / zinc ion binding / nucleus / metal ion binding / cytosol Similarity search - Function | ||||||
Biological species | Triticum aestivum (bread wheat) Oryza sativa (Asian cultivated rice) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3 Å | ||||||
Authors | Yokoyama, T. / Tanaka, M. / Saito, H. / Nishimoto, M. / Tsuda, K. / Sotta, N. / Shigematsu, H. / Shirouzu, M. / Iwasaki, S. / Ito, T. / Fujiwara, T. | ||||||
Funding support | Japan, 1items
| ||||||
Citation | Journal: Nat Chem Biol / Year: 2024 Title: Boric acid intercepts 80S ribosome migration from AUG-stop by stabilizing eRF1. Authors: Mayuki Tanaka / Takeshi Yokoyama / Hironori Saito / Madoka Nishimoto / Kengo Tsuda / Naoyuki Sotta / Hideki Shigematsu / Mikako Shirouzu / Shintaro Iwasaki / Takuhiro Ito / Toru Fujiwara / Abstract: In response to environmental changes, cells flexibly and rapidly alter gene expression through translational controls. In plants, the translation of NIP5;1, a boric acid diffusion facilitator, is ...In response to environmental changes, cells flexibly and rapidly alter gene expression through translational controls. In plants, the translation of NIP5;1, a boric acid diffusion facilitator, is downregulated in response to an excess amount of boric acid in the environment through upstream open reading frames (uORFs) that consist of only AUG and stop codons. However, the molecular details of how this minimum uORF controls translation of the downstream main ORF in a boric acid-dependent manner have remained unclear. Here, by combining ribosome profiling, translation complex profile sequencing, structural analysis with cryo-electron microscopy and biochemical assays, we show that the 80S ribosome assembled at AUG-stop migrates into the subsequent RNA segment, followed by downstream translation initiation, and that boric acid impedes this process by the stable confinement of eukaryotic release factor 1 on the 80S ribosome on AUG-stop. Our results provide molecular insight into translation regulation by a minimum and environment-responsive uORF. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 8ip9.cif.gz | 1.6 MB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb8ip9.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 8ip9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8ip9_validation.pdf.gz | 1.9 MB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 8ip9_full_validation.pdf.gz | 2 MB | Display | |
Data in XML | 8ip9_validation.xml.gz | 152.9 KB | Display | |
Data in CIF | 8ip9_validation.cif.gz | 252.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ip/8ip9 ftp://data.pdbj.org/pub/pdb/validation_reports/ip/8ip9 | HTTPS FTP |
-Related structure data
Related structure data | 35635MC 8ip8C 8ipaC 8ipbC M: map data used to model this data C: citing same article (ref.) |
---|---|
Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
|
---|---|
1 |
|
-Components
-RNA chain , 3 types, 3 molecules aaalcl
#1: RNA chain | Mass: 583613.562 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Triticum aestivum (bread wheat) / References: GenBank: 2123606567 |
---|---|
#34: RNA chain | Mass: 2229.403 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Triticum aestivum (bread wheat) |
#35: RNA chain | Mass: 24446.926 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Triticum aestivum (bread wheat) |
+40S ribosomal protein ... , 30 types, 30 molecules bacadagaiajakalamanaoapaqarasatauavawaxayazabbcbdbebfbgbhbib
-Protein / Protein/peptide , 2 types, 2 molecules haIB
#33: Protein/peptide | Mass: 3445.437 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryza sativa (Asian cultivated rice) / References: UniProt: P62125 |
---|---|
#6: Protein | Mass: 36200.527 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Triticum aestivum (bread wheat) / References: UniProt: W5D4F5 |
-Non-polymers , 2 types, 86 molecules
#36: Chemical | ChemComp-MG / #37: Chemical | |
---|
-Details
Has ligand of interest | N |
---|
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
---|---|
EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: Wheat 40S ribosome in complex with a tRNAi / Type: RIBOSOME / Entity ID: #1-#35 / Source: NATURAL |
---|---|
Source (natural) | Organism: Triticum aestivum (bread wheat) |
Buffer solution | pH: 7 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Grid material: COPPER / Grid mesh size: 200 divisions/in. / Grid type: Quantifoil R1.2/1.3 |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy imaging
Microscopy | Model: JEOL CRYO ARM 300 |
---|---|
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 60000 X / Nominal defocus max: 3000 nm / Nominal defocus min: 500 nm / Cs: 2.7 mm |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: JEOL CRYOSPECPORTER |
Image recording | Electron dose: 40 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) |
-Processing
EM software |
| ||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 41361 / Symmetry type: POINT |