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- PDB-9rhu: Rabbit 80S ribosome in complex with eRF1-AAQ, stalled at the Stop... -

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Basic information

Entry
Database: PDB / ID: 9rhu
TitleRabbit 80S ribosome in complex with eRF1-AAQ, stalled at the Stop codon in mutated F2A sequence
Components
  • (40S ribosomal protein ...) x 9
  • (60S ribosomal protein ...) x 20
  • (Large ribosomal subunit protein ...) x 11
  • (Ribosomal protein ...) x 10
  • (Small ribosomal subunit protein ...) x 22
  • (Ubiquitin-ribosomal protein ...) x 2
  • 18S rRNA
  • 28S rRNA
  • 5.8S rRNA
  • 5S rRNA
  • ATP binding cassette subfamily E member 1
  • Choriogonadotropin subunit beta variant 1,Genome polyprotein,Genome polyprotein
  • E-site tRNA-Pro
  • Eukaryotic peptide chain release factor subunit 1
  • P-site tRNA-Gly
  • [histone H4]-N-methyl-L-lysine20 N-methyltransferase KMT5B
  • eL18
  • eS10
  • eS26
  • mRNA containing F2A sequence
KeywordsRIBOSOME / 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 / regulation of macromolecule metabolic process / L-peptidase / [histone H4]-lysine20 N-methyltransferase / translation termination factor activity / histone H4K20 methyltransferase activity / translation release factor complex / cytoplasmic translational termination / symbiont-mediated perturbation of host chromatin organization / regulation of translational termination ...[histone H4]-N-methyl-L-lysine20 N-methyltransferase / regulation of macromolecule metabolic process / L-peptidase / [histone H4]-lysine20 N-methyltransferase / translation termination factor activity / histone H4K20 methyltransferase activity / translation release factor complex / cytoplasmic translational termination / symbiont-mediated perturbation of host chromatin organization / regulation of translational termination / protein methylation / translation release factor activity, codon specific / ribosomal subunit / translation release factor activity / S-adenosyl-L-methionine binding / 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 / positive regulation of signal transduction by p53 class mediator / 90S preribosome / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / pericentric heterochromatin / translational termination / phagocytic cup / protein-RNA complex assembly / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / laminin binding / rough endoplasmic reticulum / translation regulator activity / ribosomal small subunit export from nucleus / 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 / small-subunit processome / T=pseudo3 icosahedral viral capsid / ribonucleoside triphosphate phosphatase activity / host cell cytoplasmic vesicle membrane / spindle / Regulation of expression of SLITs and ROBOs / cytoplasmic ribonucleoprotein granule / rRNA processing / antimicrobial humoral immune response mediated by antimicrobial peptide / positive regulation of canonical Wnt signaling pathway / rhythmic process / heparin binding / regulation of translation / nucleoside-triphosphate phosphatase / large ribosomal subunit / channel activity / ribosome binding / virus receptor activity / ribosomal small subunit biogenesis / ribosomal small subunit assembly / 5S rRNA binding / ribosomal large subunit assembly / small ribosomal subunit / small ribosomal subunit rRNA binding / large ribosomal subunit rRNA binding / cytosolic small ribosomal subunit / monoatomic ion transmembrane transport / methylation / defense response to Gram-negative bacterium / perikaryon / clathrin-dependent endocytosis of virus by host cell / cytosolic large ribosomal subunit / killing of cells of another organism / cytoplasmic translation / cell differentiation / tRNA binding / RNA helicase activity / negative regulation of translation / mitochondrial inner membrane / postsynaptic density / rRNA binding / viral protein processing / structural constituent of ribosome / 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 / mRNA binding
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. / Peptide chain release factor eRF1/aRF1 / eRF1, domain 1 / Foot-and-mouth disease virus VP1 coat / 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, Picornavirus / Viral protein VP4 subunit / 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 / Ribosomal protein L6, N-terminal / Ribosomal protein L6, N-terminal domain / 40S ribosomal protein SA, C-terminal domain / 40S ribosomal protein SA C-terminus / Ubiquitin-like protein FUBI / Ribosomal protein L30e / SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain / Ribosomal L15/L27a, N-terminal / 50S ribosomal protein L10, insertion domain superfamily / SET domain / SET domain profile. / SET domain superfamily / SET domain / 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 / metallochaperone-like domain / Ribosomal protein L1, conserved site / TRASH domain / Ribosomal protein L1 signature. / Ribosomal protein L1 / : / 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 S26e / Ribosomal protein S26e superfamily / Ribosomal protein S26e / : / Ribosomal protein S12e signature. / Ribosomal protein L29e / Ribosomal L29e protein family / Ribosomal protein S12e / Ribosomal protein L27e, conserved site / Small (40S) ribosomal subunit Asc1/RACK1 / Ribosomal protein L27e signature. / Ribosomal protein S5, eukaryotic/archaeal / Ribosomal protein L22e / Ribosomal protein L22e superfamily / Ribosomal L22e protein family / Ribosomal protein S21e / Ribosomal protein S21e superfamily / Ribosomal protein S21e / Ribosomal protein S19e, conserved site / Ribosomal protein S19e signature. / Ribosomal protein S2, eukaryotic / Ribosomal protein L38e / Ribosomal protein L1-like / Ribosomal protein L1/ribosomal biogenesis protein / Ribosomal protein L38e superfamily / Ribosomal protein L1p/L10e family / Ribosomal L38e protein family / Ribosomal protein L13e / Ribosomal protein L13e / Ribosomal protein L19, eukaryotic / Ribosomal protein L10e, conserved site / Ribosomal protein L10e signature. / S27a-like superfamily / Ribosomal protein L44e signature. / Ribosomal protein L19/L19e conserved site / 40S Ribosomal protein S10 / Ribosomal protein L19e signature. / Ribosomal protein L24e, conserved site
Similarity search - Domain/homology
GUANOSINE-5'-TRIPHOSPHATE / : / IRON/SULFUR CLUSTER / SPERMIDINE / : / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) ...GUANOSINE-5'-TRIPHOSPHATE / : / IRON/SULFUR CLUSTER / SPERMIDINE / : / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / 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 speciesHomo sapiens (human)
Foot-and-mouth disease virus SAT 2
Oryctolagus cuniculus (rabbit)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.65 Å
AuthorsLi, 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
OrganizationGrant numberCountry
Medical Research Council (MRC, United Kingdom)MC_U105184332 United Kingdom
Wellcome TrustWT096570 United Kingdom
European Molecular Biology Organization (EMBO)ALTF 937-2022European Union
European Molecular Biology Organization (EMBO)ALTF 778-2021European Union
CitationJournal: To Be Published
Title: Molecular architecture and diversity of StopGo/2A translational recoding
Authors: Li, X. / Zuber, P.K. / Loughran, G. / Bhatt, P.R. / Alquraish, F. / Ramakrishnan, V. / Firth, A.E. / Atkins, J.F.
History
DepositionJun 10, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 21, 2026Provider: repository / Type: Initial release
Revision 1.0Jan 21, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
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Revision 1.0Jan 21, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
MB: 60S ribosomal protein L34
A1: 18S rRNA
A2: 60S ribosomal protein L6
A3: 28S rRNA
B1: Small ribosomal subunit protein eS27
B2: 60S ribosomal protein L7
B3: 5S rRNA
C1: Small ribosomal subunit protein eS28
C2: Large ribosomal subunit protein eL8
C3: 5.8S rRNA
D1: Ubiquitin-ribosomal protein eS31 fusion protein
D2: 60S ribosomal protein L9
D3: Large ribosomal subunit protein uL2
E1: 40S ribosomal protein eS30
E2: 60S ribosomal protein L10
E3: Ribosomal protein L3
F1: eS26
F2: 60S ribosomal protein L11
F3: Large ribosomal subunit protein uL4
G1: Small ribosomal subunit protein RACK1
G2: Choriogonadotropin subunit beta variant 1,Genome polyprotein,Genome polyprotein
G3: Large ribosomal subunit protein uL18
H1: Small ribosomal subunit protein uS14
H2: Large ribosomal subunit protein eL13
I1: mRNA containing F2A sequence
I2: 60S ribosomal protein L14
J1: E-site tRNA-Pro
J2: Ribosomal protein L15
K1: P-site tRNA-Gly
K2: Large ribosomal subunit protein uL13
L1: Small ribosomal subunit protein uS2
L2: Large ribosomal subunit protein uL22
M1: 40S ribosomal protein S3a
M2: eL18
N1: 40S ribosomal protein S2
N2: Ribosomal protein L19
O1: Small ribosomal subunit protein uS3
O2: Large ribosomal subunit protein eL20
P1: 40S ribosomal protein S4
P2: 60S ribosomal protein L21
Q1: Small ribosomal subunit protein uS7
Q2: 60S ribosomal protein L22
R1: 40S ribosomal protein S6
R2: Ribosomal protein L23
S1: Small ribosomal subunit protein eS7
S2: Ribosomal protein L24
T1: 40S ribosomal protein S8
T2: Large ribosomal subunit protein uL23
U1: Small ribosomal subunit protein uS4
U2: Ribosomal protein L26
V1: eS10
V2: 60S ribosomal protein L27
W1: Small ribosomal subunit protein uS17
W2: 60S ribosomal protein L27a
X1: Small ribosomal subunit protein eS12
X2: 60S ribosomal protein L29
Y1: Small ribosomal subunit protein uS15
Y2: 60S ribosomal protein L30
Z1: Small ribosomal subunit protein uS11
Z2: 60S ribosomal protein L31
a1: Small ribosomal subunit protein uS19
a2: Ribosomal protein L32
b1: Small ribosomal subunit protein uS9
b2: 60S ribosomal protein L35a
c1: Small ribosomal subunit protein eS17
d1: Small ribosomal subunit protein uS13
d2: 60S ribosomal protein L35
e1: 40S ribosomal protein eS19
e2: Large ribosomal subunit protein eL36
f1: Small ribosomal subunit protein uS10
f2: Ribosomal protein L37
g1: Small ribosomal subunit protein eS21
g2: 60S ribosomal protein L38
h1: Small ribosomal subunit protein uS8
h2: 60S ribosomal protein L39-like
i1: 40S ribosomal protein S23
i2: Ubiquitin-ribosomal protein eL40 fusion protein
j1: 40S ribosomal protein S24
j2: Ribosomal protein L36a
k1: Small ribosomal subunit protein eS25
k2: 60S ribosomal protein L37a
l1: Small ribosomal subunit protein eS32
l2: [histone H4]-N-methyl-L-lysine20 N-methyltransferase KMT5B
m2: Large ribosomal subunit protein uL10
n2: 60S ribosomal protein L12
o2: Ribosomal protein uL1
p2: Eukaryotic peptide chain release factor subunit 1
q2: ATP binding cassette subfamily E member 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)4,184,112505
Polymers4,171,70588
Non-polymers12,407417
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

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60S ribosomal protein ... , 20 types, 20 molecules MBA2B2D2E2F2I2P2Q2V2W2X2Y2Z2b2d2g2h2k2n2

#1: Protein 60S ribosomal protein L34


Mass: 13326.074 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TXG5
#3: Protein 60S ribosomal protein L6


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 60S ribosomal protein L7 / uL30


Mass: 29514.250 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SV32
#12: Protein 60S ribosomal protein L9


Mass: 21871.418 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SWI6
#15: Protein 60S ribosomal protein L10 / Ribosomal protein L10


Mass: 24643.057 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: B7NZQ2
#18: Protein 60S ribosomal protein L11


Mass: 20288.465 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TUB8
#26: Protein 60S ribosomal protein L14


Mass: 23870.549 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SZ12
#40: Protein 60S ribosomal protein L21 / eL21


Mass: 18609.988 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SHQ2
#42: Protein 60S ribosomal protein L22


Mass: 14756.909 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TSG1
#52: Protein 60S ribosomal protein L27


Mass: 15835.831 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TXF6
#54: Protein 60S ribosomal protein L27a


Mass: 16635.551 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SNY0
#56: Protein 60S ribosomal protein L29


Mass: 26721.727 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SGR6
#58: Protein 60S ribosomal protein L30 / eL30


Mass: 12807.065 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TDL2
#60: Protein 60S ribosomal protein L31 / eL31


Mass: 14494.938 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SHG0
#64: Protein 60S ribosomal protein L35a / eL33


Mass: 12580.809 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SF08
#67: Protein 60S ribosomal protein L35 / uL29


Mass: 14566.599 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SIT5
#73: Protein 60S ribosomal protein L38 / eL38


Mass: 8238.948 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1U001
#75: Protein 60S ribosomal protein L39-like / eL39


Mass: 6455.775 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TTN1
#81: Protein 60S ribosomal protein L37a / eL43


Mass: 10299.350 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SY53
#85: Protein 60S ribosomal protein L12


Mass: 17847.619 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SMR7

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RNA chain , 7 types, 7 molecules A1A3B3C3I1J1K1

#2: RNA chain 18S rRNA


Mass: 603928.250 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#4: RNA chain 28S rRNA


Mass: 1557519.500 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: GenBank: GBCN01009604.1
#7: RNA chain 5S rRNA


Mass: 38346.707 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: GenBank: GBCM01014045.1
#10: RNA chain 5.8S rRNA


Mass: 50809.047 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: GenBank: GBCN01009604.1
#25: RNA chain mRNA containing F2A sequence


Mass: 211439.672 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Foot-and-mouth disease virus SAT 2
#27: RNA chain E-site tRNA-Pro


Mass: 24102.275 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#29: RNA chain P-site tRNA-Gly


Mass: 23896.344 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)

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Small ribosomal subunit protein ... , 22 types, 22 molecules B1C1G1H1L1O1Q1S1U1W1X1Y1Z1a1b1c1d1f1g1h1k1l1

#5: Protein Small ribosomal subunit protein eS27


Mass: 9480.186 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TZ76
#8: Protein Small ribosomal subunit protein eS28


Mass: 7855.052 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TIB4
#20: Protein Small ribosomal subunit protein RACK1 / RACK1


Mass: 35115.652 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SJB4
#23: Protein Small ribosomal subunit protein uS14 / uS14


Mass: 6690.821 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1U7M4
#31: Protein Small ribosomal subunit protein uS2 / 37 kDa laminin receptor precursor / 37LRP / 37/67 kDa laminin receptor / LRP/LR / 67 kDa laminin ...37 kDa laminin receptor precursor / 37LRP / 37/67 kDa laminin receptor / LRP/LR / 67 kDa laminin receptor / 67LR / Laminin receptor 1 / LamR / Laminin-binding protein precursor p40 / LBP/p40


Mass: 32822.828 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TLT8
#37: Protein Small ribosomal subunit protein uS3


Mass: 26715.344 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TNM3
#41: Protein Small ribosomal subunit protein uS7


Mass: 22913.453 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TFM5
#45: Protein Small ribosomal subunit protein eS7


Mass: 22168.914 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SVB0
#49: Protein Small ribosomal subunit protein uS4


Mass: 22641.564 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: B7NZS8
#53: Protein Small ribosomal subunit protein uS17


Mass: 18468.826 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TRM4
#55: Protein Small ribosomal subunit protein eS12


Mass: 14538.987 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SFR8
#57: Protein Small ribosomal subunit protein uS15 / uS15


Mass: 17259.389 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SP51
#59: Protein Small ribosomal subunit protein uS11


Mass: 16302.772 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1T1F0
#61: Protein Small ribosomal subunit protein uS19


Mass: 17049.182 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1U0Q2
#63: Protein Small ribosomal subunit protein uS9


Mass: 16477.377 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SGX4
#65: Protein Small ribosomal subunit protein eS17


Mass: 15552.119 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TU13
#66: Protein Small ribosomal subunit protein uS13 / 40S ribosomal protein S18


Mass: 17654.619 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TPG3
#70: Protein Small ribosomal subunit protein uS10


Mass: 13398.763 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SIZ2
#72: Protein Small ribosomal subunit protein eS21 / 40S ribosomal protein S21


Mass: 9165.375 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TM82
#74: Protein Small ribosomal subunit protein uS8


Mass: 14865.555 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TG89
#80: Protein Small ribosomal subunit protein eS25


Mass: 13645.028 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TDB3
#82: Protein/peptide Small ribosomal subunit protein eS32


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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Large ribosomal subunit protein ... , 11 types, 11 molecules C2D3F3G3H2K2L2O2T2e2m2

#9: Protein Large ribosomal subunit protein eL8 / 60S ribosomal protein L7a


Mass: 36193.461 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1STW0
#13: Protein Large ribosomal subunit protein uL2 / 60S ribosomal protein L8


Mass: 28103.855 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TT27
#19: Protein Large ribosomal subunit protein uL4 / 60S ribosomal protein L4


Mass: 46283.703 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SVW5
#22: Protein Large ribosomal subunit protein uL18 / 60S ribosomal protein L5


Mass: 34424.777 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: P19949
#24: Protein Large ribosomal subunit protein eL13 / 60S ribosomal protein L13


Mass: 24331.723 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TKB3
#30: Protein Large ribosomal subunit protein uL13 / 60S ribosomal protein L13a


Mass: 23533.299 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TVS8
#32: Protein Large ribosomal subunit protein uL22 / 60S ribosomal protein L17


Mass: 21444.221 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SCJ6
#38: Protein Large ribosomal subunit protein eL20 / 60S ribosomal protein L18a


Mass: 20749.391 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TTY7
#48: Protein Large ribosomal subunit protein uL23 / uL23


Mass: 17768.246 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SE76
#69: Protein Large ribosomal subunit protein eL36 / 60S ribosomal protein L36


Mass: 12263.834 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TTQ5
#84: Protein Large ribosomal subunit protein uL10 / uL10


Mass: 34380.504 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SPK4

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Ubiquitin-ribosomal protein ... , 2 types, 2 molecules D1i2

#11: Protein Ubiquitin-ribosomal protein eS31 fusion protein


Mass: 9445.211 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SK22
#77: Protein Ubiquitin-ribosomal protein eL40 fusion protein / Ubiquitin A-52 residue ribosomal protein fusion product 1


Mass: 6241.654 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: P0DXC2

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40S ribosomal protein ... , 9 types, 9 molecules E1M1N1P1R1T1e1i1j1

#14: Protein 40S ribosomal protein eS30


Mass: 6741.048 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1T8A2
#33: Protein 40S ribosomal protein S3a / RPS3A


Mass: 30002.061 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SS70
#35: Protein 40S ribosomal protein S2


Mass: 31285.426 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: O18789
#39: Protein 40S ribosomal protein S4


Mass: 29654.869 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TK17
#43: Protein 40S ribosomal protein S6


Mass: 28751.906 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TM55
#47: Protein 40S ribosomal protein S8


Mass: 24263.387 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TJW1
#68: Protein 40S ribosomal protein eS19


Mass: 15966.432 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: A0ABF7PQ95
#76: Protein 40S ribosomal protein S23


Mass: 15860.666 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SZ47
#78: Protein 40S ribosomal protein S24


Mass: 15463.333 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: A0A5F9D2E6

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Ribosomal protein ... , 10 types, 10 molecules E3J2N2R2S2U2a2f2j2o2

#16: Protein Ribosomal protein L3


Mass: 46120.996 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TL06
#28: Protein Ribosomal protein L15


Mass: 24207.285 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1T0C1
#36: Protein Ribosomal protein L19


Mass: 23535.281 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TYL6
#44: Protein Ribosomal protein L23


Mass: 14892.505 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1T6D1
#46: Protein Ribosomal protein L24 / eL24


Mass: 17825.111 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SE28
#50: Protein Ribosomal protein L26


Mass: 17303.363 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SQH0
#62: Protein Ribosomal protein L32


Mass: 15898.932 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: A0AAA9WVN6
#71: Protein Ribosomal protein L37


Mass: 11111.032 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: U3KPD5
#79: Protein Ribosomal protein L36a


Mass: 16143.188 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: A0A5F9D391
#86: Protein Ribosomal protein uL1


Mass: 24875.410 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SKZ8

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Protein , 7 types, 7 molecules F1G2M2V1l2p2q2

#17: Protein eS26


Mass: 13047.532 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: A0A2K5LQY6
#21: Protein Choriogonadotropin subunit beta variant 1,Genome polyprotein,Genome polyprotein


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 2
Gene: CGB1 / Production host: Oryctolagus cuniculus (rabbit) / References: UniProt: Q9Q2N9
#34: Protein eL18


Mass: 21699.688 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: F6QKI9
#51: Protein eS10


Mass: 18933.846 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1T168
#83: Protein [histone H4]-N-methyl-L-lysine20 N-methyltransferase KMT5B / [histone H4]-lysine20 N-methyltransferase KMT5B


Mass: 15697.503 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
References: UniProt: A0A8C0DF35, [histone H4]-lysine20 N-methyltransferase, [histone H4]-N-methyl-L-lysine20 N-methyltransferase
#87: Protein Eukaryotic peptide chain release factor subunit 1 / Eukaryotic release factor 1 / eRF1 / Protein Cl1 / TB3-1


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: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P62495
#88: Protein ATP binding cassette subfamily E member 1


Mass: 67405.234 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SG72

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Non-polymers , 6 types, 417 molecules

#89: Chemical...
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 367 / Source method: obtained synthetically / Formula: Mg
#90: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Zn
#91: Chemical...
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 37 / Source method: obtained synthetically / Formula: K
#92: Chemical ChemComp-SPD / SPERMIDINE / N-(2-AMINO-PROPYL)-1,4-DIAMINOBUTANE / PA(34)


Mass: 145.246 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H19N3
#93: Chemical ChemComp-GTP / GUANOSINE-5'-TRIPHOSPHATE


Mass: 523.180 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O14P3 / Comment: GTP, energy-carrying molecule*YM
#94: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe4S4

-
Details

Has ligand of interestN
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

-
Sample preparation

Component
IDNameTypeDetailsEntity IDParent-IDSource
1Rabbit 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)RIBOSOMESample 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#2-#3, #5-#34, #1, #35-#880NATURAL
240S subunitCOMPLEX#2, #5, #8, #11, #14, #17, #20, #23, #31, #33, #35, #37, #39, #41, #43, #45, #47, #49, #51, #53, #55, #57, #59, #61, #63, #65-#66, #68, #70, #72, #74, #76, #78, #80, #821NATURAL
360S subunitCOMPLEX#3, #6-#7, #9-#10, #12-#13, #15-#16, #18-#19, #22, #24, #26, #28, #30, #32, #34, #1, #36, #38, #40, #42, #44, #46, #48, #50, #52, #54, #56, #58, #60, #62, #64, #67, #69, #71, #73, #75, #77, #79, #81, #83-#861NATURAL
4P- and E-site tRNAs and nascent polypeptide chainCOMPLEX#21, #27, #291NATURAL
540S subunit proteinsCOMPLEX#5, #8, #11, #14, #17, #20, #23, #31, #33, #35, #37, #39, #41, #43, #45, #47, #49, #51, #53, #55, #57, #59, #61, #63, #65-#66, #68, #70, #72, #74, #76, #78, #80, #822NATURAL
618S rRNACOMPLEX#22NATURAL
760 subunit proteinsCOMPLEX#3, #6, #9, #12-#13, #15-#16, #18-#19, #22, #24, #26, #28, #30, #32, #34, #1, #36, #38, #40, #42, #44, #46, #48, #50, #52, #54, #56, #58, #60, #62, #64, #67, #69, #71, #73, #75, #77, #79, #81, #83-#863NATURAL
85S, 5.8S, 28S rRNAsCOMPLEX#7, #103NATURAL
Molecular weight
IDEntity assembly-IDValue (°)Experimental value
113.8 MDaNO
21NO
31NO
41NO
51NO
61NO
71NO
81NO
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
21Oryctolagus cuniculus (rabbit)9986
32Oryctolagus cuniculus (rabbit)9986
43Oryctolagus cuniculus (rabbit)9986
54Oryctolagus cuniculus (rabbit)9986
65Oryctolagus cuniculus (rabbit)9986
76Oryctolagus cuniculus (rabbit)9986
87Oryctolagus cuniculus (rabbit)9986
98Oryctolagus cuniculus (rabbit)9986
Buffer solutionpH: 7.4
Buffer component
IDConc.NameFormulaBuffer-ID
150 mMHEPES1
2100 mMPotassium acetateKOAc1
35 mMMagnesium acetateMg(OAc)21
41 mMDTT1
SpecimenConc.: 0.4 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK II / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: 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 holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage 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

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Processing

EM software
IDNameVersionCategory
1RELION5particle selection
2PHENIX1.21.2_5419:model refinement
5CTFFIND4.1CTF correction
10RELION5initial Euler assignment
11RELION5final Euler assignment
12RELION5classification
13RELION53D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 544139 / Details: Particle picking using 2D template matching
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 2.65 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 49964 / Symmetry type: POINT
Atomic model buildingProtocol: FLEXIBLE FIT / Space: REAL
Atomic model buildingPDB-ID: 7O80

7o80


Accession code: 7O80 / Source name: PDB / Type: experimental model

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