- EMDB-53976: Rabbit 80S ribosome in complex with eRF1-AAQ, stalled at the Stop... -
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Basic information
Entry
Database: EMDB / ID: EMD-53976
Title
Rabbit 80S ribosome in complex with eRF1-AAQ, stalled at the Stop codon in mutated F2A sequence
Map data
Sharpened, masked map (using B-factor of -10 and provided mask)
Sample
Complex: Rabbit 80S ribosome stalled at the stop codon of a PGX mutant of the foot-and-mooth disease virus F2A sequence using dominant negative release factor eRF1-AAQ (human)
Complex: 40S subunit
Complex: 40S subunit proteins
Protein or peptide: x 34 types
Complex: 18S rRNA
RNA: x 1 types
Complex: 60S subunit
Complex: 60 subunit proteins
Protein or peptide: x 44 types
Complex: 5S, 5.8S, 28S rRNAs
RNA: x 2 types
Complex: P- and E-site tRNAs and nascent polypeptide chain
[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
Suv4-20 family, animal / Histone-lysine N-methyltransferase Suv4-20/Set9 / Histone-lysine N-methyltransferase, N-terminal domain / Histone-lysine N-methyltransferase (EC 2.1.1.43) family profile. / RLI, domain 1 / RLI1 / RNase L inhibitor RLI-like, possible metal-binding domain / Possible Fer4-like domain in RNase L inhibitor, RLI / Peptidase C28, foot-and-mouth virus L-proteinase / Foot-and-mouth virus L-proteinase ...Suv4-20 family, animal / Histone-lysine N-methyltransferase Suv4-20/Set9 / Histone-lysine N-methyltransferase, N-terminal domain / Histone-lysine N-methyltransferase (EC 2.1.1.43) family profile. / RLI, domain 1 / RLI1 / RNase L inhibitor RLI-like, possible metal-binding domain / Possible Fer4-like domain in RNase L inhibitor, RLI / Peptidase C28, foot-and-mouth virus L-proteinase / Foot-and-mouth virus L-proteinase / Aphthovirus leader protease (L(pro)) domain profile. / Foot-and-mouth disease virus VP1 coat / Capsid protein VP4, Picornavirus / Viral protein VP4 subunit / Peptide chain release factor eRF1/aRF1 / eRF1, domain 1 / eRF1 domain 2 / eRF1 domain 2 / eRF1 domain 1/Pelota-like / eRF1 domain 3 / eRF1, domain 2 superfamily / eRF1 domain 1 / eRF1 domain 3 / eRF1_1 / Capsid protein VP4 superfamily, Picornavirus / 4Fe-4S binding domain / Helicase/polymerase/peptidase polyprotein, Calicivirus-type / 60s Acidic ribosomal protein / 60S acidic ribosomal protein P0 / : / 40S ribosomal protein SA / 40S ribosomal protein SA, C-terminal domain / 40S ribosomal protein SA C-terminus / Ribosomal protein L6, N-terminal / Ribosomal protein L6, N-terminal domain / Ubiquitin-like protein FUBI / SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain / SET domain / Ribosomal protein L30e / 50S ribosomal protein L10, insertion domain superfamily / SET domain profile. / SET domain superfamily / SET domain / Ribosomal L15/L27a, N-terminal / 60S ribosomal protein L10P, insertion domain / Insertion domain in 60S ribosomal protein L10P / Ribosomal protein L23 / Ribosomal protein L2, archaeal-type / Ribosomal L28e/Mak16 / Ribosomal L28e protein family / Ribosomal protein L1, conserved site / Ribosomal protein L1 signature. / Ribosomal protein L1 / metallochaperone-like domain / TRASH domain / : / Ribosomal protein S26e signature. / Ribosomal protein L41 / Ribosomal protein L41 / Ribosomal protein S21e, conserved site / Ribosomal protein S21e signature. / Ribosomal protein L1, 3-layer alpha/beta-sandwich / : / Ribosomal protein S12e signature. / Ribosomal protein S26e / Ribosomal protein S26e superfamily / Ribosomal protein S26e / Ribosomal protein S12e / Ribosomal protein L29e / Ribosomal L29e protein family / Small (40S) ribosomal subunit Asc1/RACK1 / Ribosomal protein S5, eukaryotic/archaeal / Ribosomal protein L27e, conserved site / Ribosomal protein L1-like / Ribosomal protein L1/ribosomal biogenesis protein / Ribosomal protein L1p/L10e family / Ribosomal protein L27e signature. / Ribosomal protein L22e / Ribosomal protein L22e superfamily / Ribosomal L22e protein family / Ribosomal protein S21e / Ribosomal protein S21e superfamily / Ribosomal protein S21e / Ribosomal protein L13e / Ribosomal protein L13e / Ribosomal protein S2, eukaryotic / Ribosomal protein S19e, conserved site / Ribosomal protein S19e signature. / Ribosomal protein L38e / Ribosomal protein L38e superfamily / Ribosomal L38e protein family / Ribosomal protein L19, eukaryotic / S27a-like superfamily / Ribosomal protein L10e, conserved site / : / Ribosomal protein L10e signature. / Ribosomal protein L6e signature. / Ribosomal protein L44e signature. / 40S Ribosomal protein S10 / Ribosomal protein L19/L19e conserved site Similarity search - Domain/homology
Small ribosomal subunit protein eS32 / 40S ribosomal protein S26 / Small ribosomal subunit protein eS24 / Ribosomal protein L36a / Large ribosomal subunit protein eL28 / Ribosomal protein L32 / Small ribosomal subunit protein eS19 / Large ribosomal subunit protein uL16 / Small ribosomal subunit protein uS4 / Ribosomal protein L18 ...Small ribosomal subunit protein eS32 / 40S ribosomal protein S26 / Small ribosomal subunit protein eS24 / Ribosomal protein L36a / Large ribosomal subunit protein eL28 / Ribosomal protein L32 / Small ribosomal subunit protein eS19 / Large ribosomal subunit protein uL16 / Small ribosomal subunit protein uS4 / Ribosomal protein L18 / Large ribosomal subunit protein uL22 / Large ribosomal subunit protein eL24 / Large ribosomal subunit protein uL23 / Large ribosomal subunit protein eL33 / Small ribosomal subunit protein eS12 / ATP-binding cassette sub-family E member 1 / Large ribosomal subunit protein eL29 / Small ribosomal subunit protein uS9 / Large ribosomal subunit protein eL31 / Large ribosomal subunit protein eL21 / Large ribosomal subunit protein uL29 / Small ribosomal subunit protein uS10 / Small ribosomal subunit protein RACK1 / Ubiquitin-ribosomal protein eS31 fusion protein / Large ribosomal subunit protein eL6 / Large ribosomal subunit protein uL1 / Large ribosomal subunit protein uL11 / Large ribosomal subunit protein uL15 / Small ribosomal subunit protein uS15 / Large ribosomal subunit protein uL10 / Large ribosomal subunit protein uL24 / Small ribosomal subunit protein eS1 / Large ribosomal subunit protein eL8 / Large ribosomal subunit protein uL30 / Small ribosomal subunit protein eS7 / Large ribosomal subunit protein uL4 / Large ribosomal subunit protein uL6 / Large ribosomal subunit protein eL43 / Large ribosomal subunit protein eL14 / Small ribosomal subunit protein uS12 / Large ribosomal subunit protein eL15 / Small ribosomal subunit protein eS10 / Small ribosomal subunit protein uS11 / Large ribosomal subunit protein uL14 / Ubiquitin-like FUBI-ribosomal protein eS30 fusion protein / Small ribosomal subunit protein eS25 / Large ribosomal subunit protein eL30 / Small ribosomal subunit protein uS7 / Small ribosomal subunit protein uS8 / Small ribosomal subunit protein eS28 / Small ribosomal subunit protein eS8 / Small ribosomal subunit protein eS4 / Large ribosomal subunit protein eL13 / Large ribosomal subunit protein uL3 / Small ribosomal subunit protein uS2 / Small ribosomal subunit protein eS6 / Small ribosomal subunit protein eS21 / Small ribosomal subunit protein uS3 / Small ribosomal subunit protein uS13 / Small ribosomal subunit protein uS17 / Large ribosomal subunit protein eL22 / Large ribosomal subunit protein uL2 / Large ribosomal subunit protein eL39 / Large ribosomal subunit protein eL36 / Large ribosomal subunit protein eL20 / Small ribosomal subunit protein eS17 / Large ribosomal subunit protein uL5 / Large ribosomal subunit protein uL13 / Large ribosomal subunit protein eL27 / Large ribosomal subunit protein eL34 / Large ribosomal subunit protein eL19 / Small ribosomal subunit protein eS27 / Large ribosomal subunit protein eL38 / Small ribosomal subunit protein uS19 / Small ribosomal subunit protein uS14 / Small ribosomal subunit protein uS5 / Ubiquitin-ribosomal protein eL40 fusion protein / Large ribosomal subunit protein uL18 / Eukaryotic peptide chain release factor subunit 1 / Genome polyprotein / Large ribosomal subunit protein eL37 Similarity search - Component
Biological species
Oryctolagus cuniculus (rabbit) / Foot-and-mouth disease virus SAT 2 / Homo sapiens (human)
Method
single particle reconstruction / cryo EM / Resolution: 2.65 Å
Journal: Proc Natl Acad Sci U S A / Year: 2026 Title: 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.
Entire : Rabbit 80S ribosome stalled at the stop codon of a PGX mutant of ...
Entire
Name: Rabbit 80S ribosome stalled at the stop codon of a PGX mutant of the foot-and-mooth disease virus F2A sequence using dominant negative release factor eRF1-AAQ (human)
Components
Complex: Rabbit 80S ribosome stalled at the stop codon of a PGX mutant of the foot-and-mooth disease virus F2A sequence using dominant negative release factor eRF1-AAQ (human)
Complex: 40S subunit
Complex: 40S subunit proteins
Protein or peptide: Small ribosomal subunit protein eS27
Protein or peptide: Small ribosomal subunit protein eS28
Protein or peptide: Ubiquitin-ribosomal protein eS31 fusion protein
Protein or peptide: 40S ribosomal protein eS30
Protein or peptide: eS26
Protein or peptide: Small ribosomal subunit protein RACK1
Protein or peptide: Small ribosomal subunit protein uS14
Protein or peptide: Small ribosomal subunit protein uS2
Protein or peptide: 40S ribosomal protein S3a
Protein or peptide: 40S ribosomal protein S2
Protein or peptide: Small ribosomal subunit protein uS3
Protein or peptide: 40S ribosomal protein S4
Protein or peptide: Small ribosomal subunit protein uS7
Protein or peptide: 40S ribosomal protein S6
Protein or peptide: Small ribosomal subunit protein eS7
Protein or peptide: 40S ribosomal protein S8
Protein or peptide: Small ribosomal subunit protein uS4
Protein or peptide: eS10
Protein or peptide: Small ribosomal subunit protein uS17
Protein or peptide: Small ribosomal subunit protein eS12
Protein or peptide: Small ribosomal subunit protein uS15
Protein or peptide: Small ribosomal subunit protein uS11
Protein or peptide: Small ribosomal subunit protein uS19
Protein or peptide: Small ribosomal subunit protein uS9
Protein or peptide: Small ribosomal subunit protein eS17
Protein or peptide: Small ribosomal subunit protein uS13
Protein or peptide: 40S ribosomal protein eS19
Protein or peptide: Small ribosomal subunit protein uS10
Protein or peptide: Small ribosomal subunit protein eS21
Protein or peptide: Small ribosomal subunit protein uS8
Protein or peptide: 40S ribosomal protein S23
Protein or peptide: 40S ribosomal protein S24
Protein or peptide: Small ribosomal subunit protein eS25
Protein or peptide: Small ribosomal subunit protein eS32
Complex: 18S rRNA
RNA: 18S rRNA
Complex: 60S subunit
Complex: 60 subunit proteins
Protein or peptide: 60S ribosomal protein L6
Protein or peptide: 60S ribosomal protein L7
Protein or peptide: Large ribosomal subunit protein eL8
Protein or peptide: 60S ribosomal protein L9
Protein or peptide: Large ribosomal subunit protein uL2
Protein or peptide: 60S ribosomal protein L10
Protein or peptide: Ribosomal protein L3
Protein or peptide: 60S ribosomal protein L11
Protein or peptide: Large ribosomal subunit protein uL4
Protein or peptide: Large ribosomal subunit protein uL18
Protein or peptide: Large ribosomal subunit protein eL13
Protein or peptide: 60S ribosomal protein L14
Protein or peptide: Ribosomal protein L15
Protein or peptide: Large ribosomal subunit protein uL13
Protein or peptide: Large ribosomal subunit protein uL22
Protein or peptide: eL18
Protein or peptide: 60S ribosomal protein L34
Protein or peptide: Ribosomal protein L19
Protein or peptide: Large ribosomal subunit protein eL20
Protein or peptide: 60S ribosomal protein L21
Protein or peptide: 60S ribosomal protein L22
Protein or peptide: Ribosomal protein L23
Protein or peptide: Ribosomal protein L24
Protein or peptide: Large ribosomal subunit protein uL23
Protein or peptide: Ribosomal protein L26
Protein or peptide: 60S ribosomal protein L27
Protein or peptide: 60S ribosomal protein L27a
Protein or peptide: 60S ribosomal protein L29
Protein or peptide: 60S ribosomal protein L30
Protein or peptide: 60S ribosomal protein L31
Protein or peptide: Ribosomal protein L32
Protein or peptide: 60S ribosomal protein L35a
Protein or peptide: 60S ribosomal protein L35
Protein or peptide: Large ribosomal subunit protein eL36
Protein or peptide: Ribosomal protein L37
Protein or peptide: 60S ribosomal protein L38
Protein or peptide: 60S ribosomal protein L39-like
Protein or peptide: Ubiquitin-ribosomal protein eL40 fusion protein
Protein or peptide: Ribosomal protein L36a
Protein or peptide: 60S ribosomal protein L37a
Protein or peptide: [histone H4]-N-methyl-L-lysine20 N-methyltransferase KMT5B
Protein or peptide: Large ribosomal subunit protein uL10
Protein or peptide: 60S ribosomal protein L12
Protein or peptide: Ribosomal protein uL1
Complex: 5S, 5.8S, 28S rRNAs
RNA: 5S rRNA
RNA: 5.8S rRNA
Complex: P- and E-site tRNAs and nascent polypeptide chain
Protein or peptide: Choriogonadotropin subunit beta variant 1,Genome polyprotein,Genome polyprotein
RNA: E-site tRNA-Pro
RNA: P-site tRNA-Gly
RNA: mRNA containing F2A sequence
Protein or peptide: Eukaryotic peptide chain release factor subunit 1
Protein or peptide: ATP binding cassette subfamily E member 1
RNA: 28S rRNA
Ligand: MAGNESIUM ION
Ligand: ZINC ION
Ligand: POTASSIUM ION
Ligand: SPERMIDINE
Ligand: GUANOSINE-5'-TRIPHOSPHATE
Ligand: IRON/SULFUR CLUSTER
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Supramolecule #1: Rabbit 80S ribosome stalled at the stop codon of a PGX mutant of ...
Supramolecule
Name: Rabbit 80S ribosome stalled at the stop codon of a PGX mutant of the foot-and-mooth disease virus F2A sequence using dominant negative release factor eRF1-AAQ (human) type: complex / ID: 1 / Parent: 0 / Macromolecule list: #2-#3, #5-#34, #1, #35-#88 Details: Sample generated by in vitro translation of an F2A PGX mRNA in rabbit reticulocyte lysate and subsequent affinity purification via a FLAG tag in the nascent poly peptide chain
Model: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Support film - Material: GRAPHENE OXIDE / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 45 sec. / Pretreatment - Atmosphere: AIR
Vitrification
Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK II
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Electron microscopy
Microscope
TFS KRIOS
Image recording
Film or detector model: GATAN K3 (6k x 4k) / Number grids imaged: 2 / Number real images: 22565 / Average exposure time: 1.2 sec. / Average electron dose: 40.0 e/Å2
Electron beam
Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
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