[English] 日本語
Yorodumi- PDB-9rhu: Rabbit 80S ribosome in complex with eRF1-AAQ, stalled at the Stop... -
+
Open data
-
Basic information
| Entry | Database: PDB / ID: 9rhu | |||||||||||||||||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Title | Rabbit 80S ribosome in complex with eRF1-AAQ, stalled at the Stop codon in mutated F2A sequence | |||||||||||||||||||||||||||||||||
Components |
| |||||||||||||||||||||||||||||||||
Keywords | RIBOSOME / Translation / Recoding / Nascent peptide / Foot-and-mouth disease virus / F2A / StopGo | |||||||||||||||||||||||||||||||||
| Function / homology | Function and homology information[histone H4]-N-methyl-L-lysine20 N-methyltransferase / histone H4K20me methyltransferase activity / regulation of macromolecule metabolic process / L-peptidase / [histone H4]-lysine20 N-methyltransferase / histone H4K20 monomethyltransferase activity / translation termination factor activity / translation release factor complex / cytoplasmic translational termination / symbiont-mediated perturbation of host chromatin organization ...[histone H4]-N-methyl-L-lysine20 N-methyltransferase / histone H4K20me methyltransferase activity / regulation of macromolecule metabolic process / L-peptidase / [histone H4]-lysine20 N-methyltransferase / histone H4K20 monomethyltransferase activity / translation termination factor activity / translation release factor complex / cytoplasmic translational termination / symbiont-mediated perturbation of host chromatin organization / regulation of translational termination / protein methylation / ribosomal subunit / translation release factor activity, codon specific / S-adenosyl-L-methionine binding / translation release factor activity / sequence-specific mRNA binding / peptidyl-tRNA hydrolase activity / nuclear-transcribed mRNA catabolic process, nonsense-mediated decay / positive regulation of double-strand break repair via nonhomologous end joining / laminin receptor activity / Protein hydroxylation / Eukaryotic Translation Termination / ubiquitin ligase inhibitor activity / 90S preribosome / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / positive regulation of signal transduction by p53 class mediator / pericentric heterochromatin / translational termination / phagocytic cup / protein-RNA complex assembly / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / rough endoplasmic reticulum / laminin binding / ribosomal small subunit export from nucleus / translation regulator activity / gastrulation / MDM2/MDM4 family protein binding / cytosolic ribosome / class I DNA-(apurinic or apyrimidinic site) endonuclease activity / DNA-(apurinic or apyrimidinic site) lyase / ribosomal large subunit biogenesis / 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) / picornain 3C / maturation of SSU-rRNA / T=pseudo3 icosahedral viral capsid / small-subunit processome / host cell cytoplasmic vesicle membrane / spindle / Regulation of expression of SLITs and ROBOs / cytoplasmic ribonucleoprotein granule / ribonucleoside triphosphate phosphatase activity / rRNA processing / positive regulation of canonical Wnt signaling pathway / rhythmic process / antimicrobial humoral immune response mediated by antimicrobial peptide / nucleoside-triphosphate phosphatase / heparin binding / regulation of translation / large ribosomal subunit / channel activity / ribosome binding / virus receptor activity / ribosomal small subunit biogenesis / ribosomal small subunit assembly / ribosomal large subunit assembly / 5S rRNA binding / small ribosomal subunit / small ribosomal subunit rRNA binding / cytosolic small ribosomal subunit / large ribosomal subunit rRNA binding / monoatomic ion transmembrane transport / methylation / clathrin-dependent endocytosis of virus by host cell / cytosolic large ribosomal subunit / killing of cells of another organism / defense response to Gram-negative bacterium / perikaryon / cytoplasmic translation / cell differentiation / tRNA binding / RNA helicase activity / mitochondrial inner membrane / negative regulation of translation / rRNA binding / postsynaptic density / structural constituent of ribosome / viral protein processing / host cell endoplasmic reticulum membrane / ribosome / translation / ribonucleoprotein complex / cell division / RNA-directed RNA polymerase / cysteine-type endopeptidase activity / viral RNA genome replication / DNA repair / RNA-directed RNA polymerase activity Similarity search - Function | |||||||||||||||||||||||||||||||||
| Biological species | Homo sapiens (human) Foot-and-mouth disease virus SAT 2![]() | |||||||||||||||||||||||||||||||||
| Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.65 Å | |||||||||||||||||||||||||||||||||
Authors | Li, X. / Zuber, P.K. / Loughran, G. / Bhatt, P.R. / Alquraish, F. / Ramakrishnan, V. / Firth, A.E. / Atkins, J.F. | |||||||||||||||||||||||||||||||||
| Funding support | United Kingdom, European Union, 4items
| |||||||||||||||||||||||||||||||||
Citation | Journal: Proc Natl Acad Sci U S A / Year: 2026Title: Molecular architecture and diversity of StopGo/2A translational recoding. Authors: Xueyan Li / Philipp K Zuber / Gary Loughran / Pramod R Bhatt / Fatema Alquraish / V Ramakrishnan / Andrew E Firth / John F Atkins / ![]() Abstract: Viral 2A sequences trigger a cotranslational peptide bond formation "skipping" event, termed "StopGo," to generate two separate proteins from a single open reading frame without classical termination. ...Viral 2A sequences trigger a cotranslational peptide bond formation "skipping" event, termed "StopGo," to generate two separate proteins from a single open reading frame without classical termination. To investigate the mechanism of StopGo, we determined the cryo-EM structure of a mammalian ribosome positioned at the foot-and-mouth disease virus 2A (F2A) site. The structure shows how interactions between the F2A nascent chain (NC) and the ribosomal exit tunnel induce a conformational change in the peptidyl transferase center that precludes further translation elongation but instead pre-exposes the P-tRNA:F2A-NC ester bond for hydrolysis and NC release. Additionally, we bioinformatically characterized variation and host association across nearly 10,000 StopGo sequences identified in virus genomes. We expanded the canonical core motif to (D/G/C/N)(V/I)ExNPGP and identified additional rare but functional variants. We also revealed several distinct upstream motifs that we showed biochemically to be important for StopGo activity. Interestingly, although StopGo is known to be functionally active in plants, we found no evidence for natural utilization of StopGo by plant viruses. Overall, these findings provide valuable insights into a unique translation recoding mechanism, and lay foundations for further optimization of multigene expression in biotechnology. | |||||||||||||||||||||||||||||||||
| History |
|
-
Structure visualization
| Structure viewer | Molecule: Molmil Jmol/JSmol |
|---|
-
Downloads & links
-
Download
| PDBx/mmCIF format | 9rhu.cif.gz | 5.8 MB | Display | PDBx/mmCIF format |
|---|---|---|---|---|
| PDB format | pdb9rhu.ent.gz | Display | PDB format | |
| PDBx/mmJSON format | 9rhu.json.gz | Tree view | PDBx/mmJSON format | |
| Others | Other downloads |
-Validation report
| Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rh/9rhu ftp://data.pdbj.org/pub/pdb/validation_reports/rh/9rhu | HTTPS FTP |
|---|
-Related structure data
| Related structure data | ![]() 53976MC M: map data used to model this data C: citing same article ( |
|---|---|
| Similar structure data | Similarity search - Function & homology F&H Search |
-
Links
-
Assembly
| Deposited unit | ![]()
|
|---|---|
| 1 |
|
-
Components
-60S ribosomal protein ... , 20 types, 20 molecules MBA2B2D2E2F2I2P2Q2V2W2X2Y2Z2b2d2g2h2k2n2
| #1: Protein | Mass: 13326.074 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
|---|---|
| #3: Protein | Mass: 33028.336 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
| #6: Protein | Mass: 29514.250 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
| #12: Protein | Mass: 21871.418 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
| #15: Protein | Mass: 24643.057 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
| #18: Protein | Mass: 20288.465 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
| #26: Protein | Mass: 23870.549 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
| #40: Protein | Mass: 18609.988 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
| #42: Protein | Mass: 14756.909 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
| #52: Protein | Mass: 15835.831 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
| #54: Protein | Mass: 16635.551 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
| #56: Protein | Mass: 26721.727 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
| #58: Protein | Mass: 12807.065 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
| #60: Protein | Mass: 14494.938 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
| #64: Protein | Mass: 12580.809 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
| #67: Protein | Mass: 14566.599 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
| #73: Protein | Mass: 8238.948 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
| #75: Protein | Mass: 6455.775 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
| #81: Protein | Mass: 10299.350 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
| #85: Protein | Mass: 17847.619 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
-RNA chain , 7 types, 7 molecules A1A3B3C3I1J1K1
| #2: RNA chain | Mass: 603928.250 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
|---|---|
| #4: RNA chain | Mass: 1557519.500 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
| #7: RNA chain | Mass: 38346.707 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
| #10: RNA chain | Mass: 50809.047 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
| #25: RNA chain | Mass: 211439.672 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Foot-and-mouth disease virus SAT 2 |
| #27: RNA chain | Mass: 24102.275 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
| #29: RNA chain | Mass: 23896.344 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
+Small ribosomal subunit protein ... , 22 types, 22 molecules B1C1G1H1L1O1Q1S1U1W1X1Y1Z1a1b1c1d1f1g1h1k1l1
-Large ribosomal subunit protein ... , 11 types, 11 molecules C2D3F3G3H2K2L2O2T2e2m2
| #9: Protein | Mass: 36193.461 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
|---|---|
| #13: Protein | Mass: 28103.855 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
| #19: Protein | Mass: 46283.703 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
| #22: Protein | Mass: 34424.777 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
| #24: Protein | Mass: 24331.723 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
| #30: Protein | Mass: 23533.299 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
| #32: Protein | Mass: 21444.221 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
| #38: Protein | Mass: 20749.391 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
| #48: Protein | Mass: 17768.246 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
| #69: Protein | Mass: 12263.834 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
| #84: Protein | Mass: 34380.504 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
-Ubiquitin-ribosomal protein ... , 2 types, 2 molecules D1i2
| #11: Protein | Mass: 9445.211 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
|---|---|
| #77: Protein | Mass: 6241.654 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
-40S ribosomal protein ... , 9 types, 9 molecules E1M1N1P1R1T1e1i1j1
| #14: Protein | Mass: 6741.048 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
|---|---|
| #33: Protein | Mass: 30002.061 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
| #35: Protein | Mass: 31285.426 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
| #39: Protein | Mass: 29654.869 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
| #43: Protein | Mass: 28751.906 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
| #47: Protein | Mass: 24263.387 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
| #68: Protein | Mass: 15966.432 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
| #76: Protein | Mass: 15860.666 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
| #78: Protein | Mass: 15463.333 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
-Ribosomal protein ... , 10 types, 10 molecules E3J2N2R2S2U2a2f2j2o2
| #16: Protein | Mass: 46120.996 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
|---|---|
| #28: Protein | Mass: 24207.285 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
| #36: Protein | Mass: 23535.281 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
| #44: Protein | Mass: 14892.505 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
| #46: Protein | Mass: 17825.111 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
| #50: Protein | Mass: 17303.363 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
| #62: Protein | Mass: 15898.932 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
| #71: Protein | Mass: 11111.032 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
| #79: Protein | Mass: 16143.188 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
| #86: Protein | Mass: 24875.410 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
-Protein , 7 types, 7 molecules F1G2M2V1l2p2q2
| #17: Protein | Mass: 13047.532 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
|---|---|
| #21: Protein | Mass: 20020.877 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human), (gene. exp.) Foot-and-mouth disease virus SAT 2Gene: CGB1 / Production host: ![]() |
| #34: Protein | Mass: 21699.688 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
| #51: Protein | Mass: 18933.846 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
| #83: Protein | [ Mass: 15697.503 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() References: UniProt: A0A8C0DF35, [histone H4]-lysine20 N-methyltransferase, [histone H4]-N-methyl-L-lysine20 N-methyltransferase |
| #87: Protein | Mass: 49143.770 Da / Num. of mol.: 1 / Mutation: G183A, G184A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: ETF1, ERF1, RF1, SUP45L1 / Production host: ![]() |
| #88: Protein | Mass: 67405.234 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
-Non-polymers , 6 types, 417 molecules 










| #89: Chemical | ChemComp-MG / #90: Chemical | ChemComp-ZN / #91: Chemical | ChemComp-K / #92: Chemical | #93: Chemical | ChemComp-GTP / | #94: Chemical | |
|---|
-Details
| Has ligand of interest | N |
|---|---|
| Has protein modification | Y |
-Experimental details
-Experiment
| Experiment | Method: ELECTRON MICROSCOPY |
|---|---|
| EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-
Sample preparation
| Component |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Molecular weight |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Source (natural) |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Buffer solution | pH: 7.4 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Buffer component |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Specimen | Conc.: 0.4 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Specimen support | Grid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Vitrification | Instrument: FEI VITROBOT MARK II / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K |
-
Electron microscopy imaging
| Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
|---|---|
| Microscopy | Model: TFS KRIOS |
| Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
| Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 105000 X / Nominal defocus max: 2200 nm / Nominal defocus min: 1000 nm / Cs: 2.7 mm / C2 aperture diameter: 50 µm |
| Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
| Image recording | Average exposure time: 1.2 sec. / Electron dose: 40 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) / Num. of grids imaged: 2 / Num. of real images: 22565 |
-
Processing
| EM software |
| ||||||||||||||||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||
| Particle selection | Num. of particles selected: 544139 / Details: Particle picking using 2D template matching | ||||||||||||||||||||||||||||||||
| Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||||||||||||||||||||||
| 3D reconstruction | Resolution: 2.65 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 49964 / Symmetry type: POINT | ||||||||||||||||||||||||||||||||
| Atomic model building | Protocol: FLEXIBLE FIT / Space: REAL | ||||||||||||||||||||||||||||||||
| Atomic model building | PDB-ID: 7O80 Accession code: 7O80 / Source name: PDB / Type: experimental model |
Movie
Controller
About Yorodumi



Homo sapiens (human)
Foot-and-mouth disease virus SAT 2

United Kingdom, European Union, 4items
Citation

PDBj














































FIELD EMISSION GUN
