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- PDB-9ydd: Eukaryotic 80S ribosome with A/A, P/P tRNAs from uL16 P-site loop... -

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Basic information

Entry
Database: PDB / ID: 9ydd
TitleEukaryotic 80S ribosome with A/A, P/P tRNAs from uL16 P-site loop mutants in bypass condition
Components
  • (40S ribosomal protein ...) x 29
  • (60S ribosomal protein ...) x 37
  • (Large ribosomal subunit protein ...) x 3
  • (Small ribosomal subunit protein ...) x 2
  • 18S rRNA
  • 25S RNA
  • 5S RNA
  • 8S RNA
  • A site tRNA
  • Guanine nucleotide-binding protein subunit beta-like protein
  • P site tRNA
  • Ubiquitin-40S ribosomal protein S31
  • Ubiquitin-60S ribosomal protein L40
  • messenger RNA
KeywordsRIBOSOME / 80S ribosome / Rpl10 loop deletion
Function / homology
Function and homology information


maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, LSU-rRNA,5S) / regulation of amino acid metabolic process / negative regulation of glucose mediated signaling pathway / positive regulation of translational fidelity / RMTs methylate histone arginines / Protein methylation / response to cycloheximide / translational readthrough / mTORC1-mediated signalling / Protein hydroxylation ...maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, LSU-rRNA,5S) / regulation of amino acid metabolic process / negative regulation of glucose mediated signaling pathway / positive regulation of translational fidelity / RMTs methylate histone arginines / Protein methylation / response to cycloheximide / translational readthrough / mTORC1-mediated signalling / Protein hydroxylation / pre-mRNA 5'-splice site binding / GDP-dissociation inhibitor activity / Ribosome Quality Control (RQC) complex extracts and degrades nascent peptide / ascospore wall assembly / Formation of the ternary complex, and subsequently, the 43S complex / Translation initiation complex formation / cytosolic large ribosomal subunit assembly / Ribosomal scanning and start codon recognition / nonfunctional rRNA decay / positive regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / preribosome, small subunit precursor / mRNA destabilization / Major pathway of rRNA processing in the nucleolus and cytosol / PELO:HBS1L and ABCE1 dissociate a ribosome on a non-stop mRNA / SRP-dependent cotranslational protein targeting to membrane / GTP hydrolysis and joining of the 60S ribosomal subunit / protein-RNA complex assembly / Formation of a pool of free 40S subunits / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / preribosome, large subunit precursor / positive regulation of protein kinase activity / L13a-mediated translational silencing of Ceruloplasmin expression / negative regulation of mRNA splicing, via spliceosome / negative regulation of translational frameshifting / ribosomal large subunit export from nucleus / translational elongation / G-protein alpha-subunit binding / endonucleolytic cleavage to generate mature 3'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / 90S preribosome / ribosomal subunit export from nucleus / translational termination / cleavage in ITS2 between 5.8S rRNA and LSU-rRNA of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / regulation of translational fidelity / ribosome-associated ubiquitin-dependent protein catabolic process / maturation of LSU-rRNA / 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) / translation regulator activity / DNA-(apurinic or apyrimidinic site) endonuclease activity / ribosomal small subunit export from nucleus / cellular response to amino acid starvation / protein kinase C binding / macroautophagy / rescue of stalled cytosolic ribosome / ribosome assembly / ribosomal large subunit biogenesis / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of SSU-rRNA / small-subunit processome / translational initiation / maintenance of translational fidelity / modification-dependent protein catabolic process / cytoplasmic stress granule / protein tag activity / rRNA processing / cytosolic ribosome / ribosomal small subunit assembly / ribosome biogenesis / ribosome binding / ribosomal small subunit biogenesis / small ribosomal subunit rRNA binding / 5S rRNA binding / ribosomal large subunit assembly / small ribosomal subunit / cytosolic small ribosomal subunit / large ribosomal subunit rRNA binding / cytosolic large ribosomal subunit / cytoplasmic translation / rRNA binding / negative regulation of translation / protein ubiquitination / ribosome / translation / structural constituent of ribosome / response to antibiotic / G protein-coupled receptor signaling pathway / negative regulation of gene expression / mRNA binding / nucleolus / mitochondrion / RNA binding / zinc ion binding / nucleoplasm / nucleus / cytosol / cytoplasm
Similarity search - Function
: / : / Ribosomal protein S26e signature. / Ribosomal protein L41 / Ribosomal protein L41 / Ribosomal protein L13e, conserved site / Ribosomal protein L13e signature. / Ribosomal protein S21e, conserved site / Ribosomal protein S21e signature. / : ...: / : / Ribosomal protein S26e signature. / Ribosomal protein L41 / Ribosomal protein L41 / Ribosomal protein L13e, conserved site / Ribosomal protein L13e signature. / Ribosomal protein S21e, conserved site / Ribosomal protein S21e signature. / : / 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 L22e / Ribosomal protein L22e superfamily / Ribosomal L22e protein family / Ribosomal protein L27e, conserved site / Ribosomal protein L27e signature. / Ribosomal protein L13e / Ribosomal protein L13e / Ribosomal protein S21e / Ribosomal protein L38e / Ribosomal protein L38e superfamily / Ribosomal protein S21e superfamily / Ribosomal protein S21e / Ribosomal L38e protein family / Ribosomal protein S5, eukaryotic/archaeal / Ribosomal protein S19e, conserved site / Ribosomal protein S19e signature. / : / Ribosomal protein S2, eukaryotic / Ribosomal protein L19, eukaryotic / Ribosomal protein L6e signature. / 60S ribosomal protein L18a/ L20, eukaryotes / 40S Ribosomal protein S10 / Ribosomal protein L10e, conserved site / Ribosomal protein L10e signature. / S27a-like superfamily / Plectin/S10, N-terminal / Ribosomal protein L18/L18-A/B/e, conserved site / Ribosomal protein L19/L19e conserved site / Plectin/S10 domain / Ribosomal protein L19e signature. / Ribosomal protein L18e signature. / Ribosomal protein L44e signature. / Ribosomal protein L24e, conserved site / Ribosomal protein L24e signature. / Ribosomal protein L10e / Ribosomal protein S30 / Ribosomal protein S30 / Ribosomal protein L23/L25, N-terminal / Ribosomal protein L5 eukaryotic, C-terminal / Ribosomal protein L23, N-terminal domain / Ribosomal L18 C-terminal region / Ribosomal protein L34e, conserved site / Ribosomal protein L34e signature. / Ribosomal protein S10, eukaryotic/archaeal / Ribosomal L40e family / Ribosomal protein S25 / Ribosomal protein S8e subdomain, eukaryotes / S25 ribosomal protein / Ribosomal protein L36e signature. / 50S ribosomal protein L18Ae/60S ribosomal protein L20 and L18a / Ribosomal protein L30e signature 1. / Ribosomal protein 50S-L18Ae/60S-L20/60S-L18A / Ribosomal proteins 50S-L18Ae/60S-L20/60S-L18A / Eukaryotic Ribosomal Protein L27, KOW domain / Ribosomal protein L27e / Ribosomal protein L27e superfamily / : / Ribosomal L27e protein family / Ribosomal Protein L6, KOW domain / : / Ribosomal protein S7e signature. / Ribosomal protein L35Ae, conserved site / Ribosomal protein L35Ae signature. / Ribosomal protein 60S L18 and 50S L18e / Ribosomal_L40e / Ribosomal protein L40e / Ribosomal protein L40e superfamily / Ribosomal protein L44e / Ribosomal protein S17e, conserved site / Ribosomal protein L44 / Ribosomal protein S17e signature. / : / Ribosomal protein S2, eukaryotic/archaeal / Ribosomal protein S27a / Ribosomal protein S27a / Ribosomal protein S27a / Ribosomal protein L7A/L8 / 60S ribosomal protein L35 / Ribosomal protein L6e / 40S ribosomal protein S29/30S ribosomal protein S14 type Z / Ribosomal protein L30e signature 2. / Ribosomal protein S3, eukaryotic/archaeal
Similarity search - Domain/homology
Chem-3HE / : / : / : / : / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) ...Chem-3HE / : / : / : / : / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Small ribosomal subunit protein uS4A / Large ribosomal subunit protein uL15 / Large ribosomal subunit protein eL24A / Large ribosomal subunit protein uL23 / Large ribosomal subunit protein eL39 / Large ribosomal subunit protein uL30A / Large ribosomal subunit protein uL6A / Large ribosomal subunit protein eL6B / Large ribosomal subunit protein uL22A / Large ribosomal subunit protein uL24A / Large ribosomal subunit protein eL33A / Large ribosomal subunit protein eL36A / Large ribosomal subunit protein eL29 / Large ribosomal subunit protein eL15A / Large ribosomal subunit protein eL22A / Small ribosomal subunit protein uS3 / Small ribosomal subunit protein uS15 / Ubiquitin-ribosomal protein eS31 fusion protein / Small ribosomal subunit protein eS19A / Small ribosomal subunit protein eS21A / Small ribosomal subunit protein uS8A / Large ribosomal subunit protein eL27A / Large ribosomal subunit protein eL31A / Ubiquitin-ribosomal protein eL40A fusion protein / Large ribosomal subunit protein eL20A / Large ribosomal subunit protein eL43A / Large ribosomal subunit protein eL42A / Small ribosomal subunit protein uS12A / Small ribosomal subunit protein eS24A / Small ribosomal subunit protein eS30A / Small ribosomal subunit protein eS4A / Small ribosomal subunit protein eS6A / Small ribosomal subunit protein eS8A / Large ribosomal subunit protein uL14A / Large ribosomal subunit protein uL2A / Small ribosomal subunit protein uS17A / Large ribosomal subunit protein eL18A / Small ribosomal subunit protein uS9A / Small ribosomal subunit protein uS13A / Large ribosomal subunit protein eL19A / Large ribosomal subunit protein uL29A / Small ribosomal subunit protein eS32A / Large ribosomal subunit protein uL4A / Large ribosomal subunit protein eL30 / Large ribosomal subunit protein uL3 / Small ribosomal subunit protein eS17B / Large ribosomal subunit protein eL8A / Small ribosomal subunit protein uS5 / Large ribosomal subunit protein uL18 / Small ribosomal subunit protein uS7 / Large ribosomal subunit protein uL13A / Small ribosomal subunit protein eS7A / Small ribosomal subunit protein uS2A / Small ribosomal subunit protein eS1A / Small ribosomal subunit protein eS27A / Large ribosomal subunit protein eL14A / Small ribosomal subunit protein RACK1 / Large ribosomal subunit protein eL32 / Small ribosomal subunit protein uS10 / Small ribosomal subunit protein uS11B / Small ribosomal subunit protein eS26B / Small ribosomal subunit protein uS14A / Large ribosomal subunit protein uL16 / Small ribosomal subunit protein eS12 / Large ribosomal subunit protein eL37A / Large ribosomal subunit protein eL38 / Large ribosomal subunit protein eL34A / Small ribosomal subunit protein uS19 / Large ribosomal subunit protein eL21A / Small ribosomal subunit protein eS10A / Large ribosomal subunit protein eL13A / Large ribosomal subunit protein uL5B / Small ribosomal subunit protein eS25A / Small ribosomal subunit protein eS28A
Similarity search - Component
Biological speciesSaccharomyces cerevisiae S288C (yeast)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.66 Å
AuthorsGuan, K. / Taylor, D.W.
Funding support United States, 1items
OrganizationGrant numberCountry
Welch FoundationF-1938 United States
CitationJournal: To Be Published
Title: Cryo-EM structure of 80S ribosomal subunit with Rpl10 loop deletion produced in bypass mutant. P/E, A/P tRNA
Authors: Guan, K. / Taylor, D.W.
History
DepositionSep 22, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 30, 2026Provider: repository / Type: Initial release
Revision 1.0Sep 30, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 25S RNA
B: 5S RNA
C: 8S RNA
D: messenger RNA
E: 18S rRNA
LD: 60S ribosomal protein L2-A
LE: 60S ribosomal protein L3
LF: 60S ribosomal protein L4-A
LG: 60S ribosomal protein L5
LH: Large ribosomal subunit protein eL6B
LI: 60S ribosomal protein L7-A
LJ: 60S ribosomal protein L8-A
LK: 60S ribosomal protein L9-A
LL: Large ribosomal subunit protein uL16
LM: Large ribosomal subunit protein uL5B
LN: 60S ribosomal protein L13-A
LO: 60S ribosomal protein L14-A
LP: 60S ribosomal protein L15-A
LQ: 60S ribosomal protein L16-A
LR: 60S ribosomal protein L17-A
LS: 60S ribosomal protein L18-A
LT: 60S ribosomal protein L19-A
LU: 60S ribosomal protein L20-A
LV: 60S ribosomal protein L21-A
LW: 60S ribosomal protein L22-A
LX: 60S ribosomal protein L23-A
LY: 60S ribosomal protein L24-A
LZ: 60S ribosomal protein L25
La: 60S ribosomal protein L26-A
Lb: 60S ribosomal protein L27-A
Lc: 60S ribosomal protein L28
Ld: 60S ribosomal protein L29
Le: 60S ribosomal protein L30
Lf: 60S ribosomal protein L31-A
Lg: 60S ribosomal protein L32
Lh: 60S ribosomal protein L33-A
Li: 60S ribosomal protein L34-A
Lj: 60S ribosomal protein L35-A
Lk: 60S ribosomal protein L36-A
Ll: 60S ribosomal protein L37-A
Lm: 60S ribosomal protein L38
Ln: 60S ribosomal protein L39
Lo: Ubiquitin-60S ribosomal protein L40
Lp: 60S ribosomal protein L41-A
Lq: 60S ribosomal protein L42-A
Lr: 60S ribosomal protein L43-A
SA: 40S ribosomal protein S3
SB: 40S ribosomal protein S5
SC: 40S ribosomal protein S10-A
SD: 40S ribosomal protein S12
SE: 40S ribosomal protein S15
SF: 40S ribosomal protein S16-A
SG: 40S ribosomal protein S17-B
SH: 40S ribosomal protein S18-A
SI: 40S ribosomal protein S19-A
SJ: 40S ribosomal protein S20
SK: 40S ribosomal protein S25-A
SL: 40S ribosomal protein S28-A
SM: 40S ribosomal protein S29-A
SN: Ubiquitin-40S ribosomal protein S31
SO: Guanine nucleotide-binding protein subunit beta-like protein
SP: 40S ribosomal protein S0-A
SQ: Small ribosomal subunit protein eS1A
SR: 40S ribosomal protein S2
SS: 40S ribosomal protein S4-A
ST: 40S ribosomal protein S6-A
SU: 40S ribosomal protein S7-A
SV: 40S ribosomal protein S8-A
SW: 40S ribosomal protein S9-A
SX: 40S ribosomal protein S11-A
SY: 40S ribosomal protein S13
SZ: 40S ribosomal protein S14-B
Sa: 40S ribosomal protein S21-A
Sb: 40S ribosomal protein S22-A
Sc: 40S ribosomal protein S23-A
Sd: 40S ribosomal protein S24-A
Se: Small ribosomal subunit protein eS26B
Sf: 40S ribosomal protein S27-A
Sg: 40S ribosomal protein S30-A
m: A site tRNA
n: P site tRNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)3,156,88382
Polymers3,156,60181
Non-polymers2811
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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RNA chain , 7 types, 7 molecules ABCDEmn

#1: RNA chain 25S RNA


Mass: 1097454.750 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / References: GenBank: 831416132
#2: RNA chain 5S RNA


Mass: 38951.105 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / References: GenBank: 1329886537
#3: RNA chain 8S RNA


Mass: 50682.922 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / References: GenBank: 1489318609
#4: RNA chain messenger RNA


Mass: 3217.021 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast)
#5: RNA chain 18S rRNA


Mass: 579761.938 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / References: GenBank: 831416138
#80: RNA chain A site tRNA


Mass: 24378.408 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast)
#81: RNA chain P site tRNA


Mass: 24222.500 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / References: GenBank: 176433

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60S ribosomal protein ... , 37 types, 37 molecules LDLELFLGLILJLKLNLOLPLQLRLSLTLULVLWLXLYLZLaLbLcLdLeLfLgLhLiLj...

#6: Protein 60S ribosomal protein L2-A / L5 / Large ribosomal subunit protein uL2-A / RP8 / YL6


Mass: 27463.574 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / References: UniProt: P0CX45
#7: Protein 60S ribosomal protein L3 / Large ribosomal subunit protein uL3 / Maintenance of killer protein 8 / RP1 / Trichodermin ...Large ribosomal subunit protein uL3 / Maintenance of killer protein 8 / RP1 / Trichodermin resistance protein / YL1


Mass: 43850.793 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / References: UniProt: P14126
#8: Protein 60S ribosomal protein L4-A / L2 / Large ribosomal subunit protein uL4-A / RP2 / YL2


Mass: 39159.125 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / References: UniProt: P10664
#9: Protein 60S ribosomal protein L5 / L1 / L1a / Large ribosomal subunit protein uL18 / Ribosomal 5S RNA-binding protein / YL3


Mass: 33764.828 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / References: UniProt: P26321
#11: Protein 60S ribosomal protein L7-A / L6 / Large ribosomal subunit protein uL30-A / RP11 / YL8


Mass: 27686.281 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / References: UniProt: P05737
#12: Protein 60S ribosomal protein L8-A / L4 / L4-2 / L7a-1 / Large ribosomal subunit protein eL8-A / Maintenance of killer protein 7 / RP6 / YL5


Mass: 28175.820 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / References: UniProt: P17076
#13: Protein 60S ribosomal protein L9-A / L8 / Large ribosomal subunit protein uL6-A / RP24 / YL11


Mass: 21605.061 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / References: UniProt: P05738
#16: Protein 60S ribosomal protein L13-A / Large ribosomal subunit protein eL13-A


Mass: 22604.164 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / References: UniProt: Q12690
#17: Protein 60S ribosomal protein L14-A / Large ribosomal subunit protein eL14-A


Mass: 15195.066 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / References: UniProt: P36105
#18: Protein 60S ribosomal protein L15-A / L13 / Large ribosomal subunit protein eL15-A / RP15R / YL10 / YP18


Mass: 24482.357 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / References: UniProt: P05748
#19: Protein 60S ribosomal protein L16-A / L13a / L21 / Large ribosomal subunit protein uL13-A / RP22 / YL15


Mass: 22247.227 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / References: UniProt: P26784
#20: Protein 60S ribosomal protein L17-A / L20A / Large ribosomal subunit protein uL22-A / YL17


Mass: 20589.518 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / References: UniProt: P05740
#21: Protein 60S ribosomal protein L18-A / Large ribosomal subunit protein eL18-A / RP28


Mass: 20609.252 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / References: UniProt: P0CX49
#22: Protein 60S ribosomal protein L19-A / L23 / Large ribosomal subunit protein eL19-A / RP15L / RP33 / YL14


Mass: 21762.316 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / References: UniProt: P0CX82
#23: Protein 60S ribosomal protein L20-A / L18a / Large ribosomal subunit protein eL20-A


Mass: 20478.852 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / References: UniProt: P0CX23
#24: Protein 60S ribosomal protein L21-A / Large ribosomal subunit protein eL21-A


Mass: 18279.266 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / References: UniProt: Q02753
#25: Protein 60S ribosomal protein L22-A / L1c / Large ribosomal subunit protein eL22-A / RP4 / YL31


Mass: 13711.359 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / References: UniProt: P05749
#26: Protein 60S ribosomal protein L23-A / L17a / Large ribosomal subunit protein uL14-A / YL32


Mass: 14493.950 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / References: UniProt: P0CX41
#27: Protein 60S ribosomal protein L24-A / L30 / Large ribosomal subunit protein eL24-A / RP29 / YL21


Mass: 17661.717 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / References: UniProt: P04449
#28: Protein 60S ribosomal protein L25 / Large ribosomal subunit protein uL23 / RP16L / YL25 / YP42'


Mass: 15787.612 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / References: UniProt: P04456
#29: Protein 60S ribosomal protein L26-A / L33 / Large ribosomal subunit protein uL24-A / YL33


Mass: 14265.784 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / References: UniProt: P05743
#30: Protein 60S ribosomal protein L27-A / Large ribosomal subunit protein eL27-A


Mass: 15568.360 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / References: UniProt: P0C2H6
#31: Protein 60S ribosomal protein L28 / L27a / L29 / Large ribosomal subunit protein uL15 / RP44 / RP62 / YL24


Mass: 16761.666 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / References: UniProt: P02406
#32: Protein 60S ribosomal protein L29 / Large ribosomal subunit protein eL29 / YL43


Mass: 6691.884 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / References: UniProt: P05747
#33: Protein 60S ribosomal protein L30 / L32 / Large ribosomal subunit protein eL30 / RP73 / YL38


Mass: 11430.364 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / References: UniProt: P14120
#34: Protein 60S ribosomal protein L31-A / L34 / Large ribosomal subunit protein eL31-A / YL28


Mass: 12980.158 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / References: UniProt: P0C2H8
#35: Protein 60S ribosomal protein L32 / Large ribosomal subunit protein eL32


Mass: 14809.441 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / References: UniProt: P38061
#36: Protein 60S ribosomal protein L33-A / L37 / Large ribosomal subunit protein eL33-A / RP47 / YL37


Mass: 12177.130 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / References: UniProt: P05744
#37: Protein 60S ribosomal protein L34-A / Large ribosomal subunit protein eL34-A


Mass: 13673.196 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / References: UniProt: P87262
#38: Protein 60S ribosomal protein L35-A / Large ribosomal subunit protein uL29-A


Mass: 13942.640 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / References: UniProt: P0CX84
#39: Protein 60S ribosomal protein L36-A / L39 / Large ribosomal subunit protein eL36-A / YL39


Mass: 11151.259 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / References: UniProt: P05745
#40: Protein 60S ribosomal protein L37-A / L43 / Large ribosomal subunit protein eL37-A / YL35 / YP55


Mass: 9877.395 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / References: UniProt: P49166
#41: Protein 60S ribosomal protein L38 / Large ribosomal subunit protein eL38


Mass: 8845.561 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / References: UniProt: P49167
#42: Protein 60S ribosomal protein L39 / L46 / Large ribosomal subunit protein eL39 / YL40


Mass: 6358.640 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / References: UniProt: P04650
#44: Protein/peptide 60S ribosomal protein L41-A / L47 / YL41


Mass: 3354.243 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / References: UniProt: P0CX86
#45: Protein 60S ribosomal protein L42-A / L41 / Large ribosomal subunit protein eL42-A / YL27 / YP44


Mass: 12246.658 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / References: UniProt: P0CX27
#46: Protein 60S ribosomal protein L43-A / L37a / Large ribosomal subunit protein eL43-A / YL35


Mass: 10112.952 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / References: UniProt: P0CX25

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Large ribosomal subunit protein ... , 3 types, 3 molecules LHLLLM

#10: Protein Large ribosomal subunit protein eL6B / 60S ribosomal protein L6-B / L17 / RP18 / YL16


Mass: 20024.541 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / References: UniProt: P05739
#14: Protein Large ribosomal subunit protein uL16 / 60S ribosomal protein L10 / L9 / Ubiquinol-cytochrome C reductase complex subunit VI-requiring protein


Mass: 24263.113 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / References: UniProt: P41805
#15: Protein Large ribosomal subunit protein uL5B / 60S ribosomal protein L11-B / L16 / RP39 / YL22


Mass: 19785.719 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / References: UniProt: Q3E757

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Protein , 3 types, 3 molecules LoSNSO

#43: Protein Ubiquitin-60S ribosomal protein L40


Mass: 14583.077 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / References: UniProt: P0CH08
#60: Protein Ubiquitin-40S ribosomal protein S31


Mass: 17254.227 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / References: UniProt: P05759
#61: Protein Guanine nucleotide-binding protein subunit beta-like protein / Receptor for activated C kinase / Receptor of activated protein kinase C 1 / RACK1 / Small ...Receptor for activated C kinase / Receptor of activated protein kinase C 1 / RACK1 / Small ribosomal subunit protein RACK1


Mass: 34841.219 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / References: UniProt: P38011

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40S ribosomal protein ... , 29 types, 29 molecules SASBSCSDSESFSGSHSISJSKSLSMSPSRSSSTSUSVSWSXSYSZSaSbScSdSfSg

#47: Protein 40S ribosomal protein S3 / RP13 / YS3


Mass: 26542.789 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / References: UniProt: P05750
#48: Protein 40S ribosomal protein S5 / RP14 / S2 / YS8


Mass: 25072.600 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / References: UniProt: P26783
#49: Protein 40S ribosomal protein S10-A / Small ribosomal subunit protein eS10-A


Mass: 12757.445 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / References: UniProt: Q08745
#50: Protein 40S ribosomal protein S12


Mass: 15488.631 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / References: UniProt: P48589
#51: Protein 40S ribosomal protein S15 / RIG protein / RP52 / S21 / YS21


Mass: 16031.907 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / References: UniProt: Q01855
#52: Protein 40S ribosomal protein S16-A / RP61R


Mass: 15877.490 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / References: UniProt: P0CX51
#53: Protein 40S ribosomal protein S17-B / RP51B / Small ribosomal subunit protein eS17-B


Mass: 15835.384 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / References: UniProt: P14127
#54: Protein 40S ribosomal protein S18-A / Small ribosomal subunit protein uS13-A


Mass: 17071.641 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / References: UniProt: P0CX55
#55: Protein 40S ribosomal protein S19-A / RP55A / S16a / Small ribosomal subunit protein eS19-A / YP45 / YS16A


Mass: 15942.125 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / References: UniProt: P07280
#56: Protein 40S ribosomal protein S20


Mass: 13929.044 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / References: UniProt: P38701
#57: Protein 40S ribosomal protein S25-A / RP45 / S31 / YS23


Mass: 12067.272 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / References: UniProt: Q3E792
#58: Protein 40S ribosomal protein S28-A / S33 / Small ribosomal subunit protein eS28-A / YS27


Mass: 7605.847 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / References: UniProt: Q3E7X9
#59: Protein 40S ribosomal protein S29-A / S36 / YS29


Mass: 6675.723 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / References: UniProt: P41057
#62: Protein 40S ribosomal protein S0-A / Nucleic acid-binding protein NAB1A / Small ribosomal subunit protein uS2-A


Mass: 28051.330 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / References: UniProt: P32905
#64: Protein 40S ribosomal protein S2 / Omnipotent suppressor protein SUP44 / RP12 / S4 / YS5


Mass: 27490.826 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / References: UniProt: P25443
#65: Protein 40S ribosomal protein S4-A / RP5 / S7 / YS6


Mass: 29469.330 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / References: UniProt: P0CX35
#66: Protein 40S ribosomal protein S6-A / RP9 / S10 / YS4


Mass: 27054.486 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / References: UniProt: P0CX37
#67: Protein 40S ribosomal protein S7-A / RP30 / RP40


Mass: 21658.209 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / References: UniProt: P26786
#68: Protein 40S ribosomal protein S8-A / RP19 / S14 / YS9


Mass: 22537.803 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / References: UniProt: P0CX39
#69: Protein 40S ribosomal protein S9-A / RP21 / S13 / YP28 / YS11


Mass: 22487.893 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / References: UniProt: O13516
#70: Protein 40S ribosomal protein S11-A / RP41 / S18 / YS12


Mass: 17785.934 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / References: UniProt: P0CX47
#71: Protein 40S ribosomal protein S13 / S27a / Small ribosomal subunit protein uS15 / YS15


Mass: 17059.945 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / References: UniProt: P05756
#72: Protein 40S ribosomal protein S14-B / RP59B / Small ribosomal subunit protein uS11-B


Mass: 14675.771 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / References: UniProt: P39516
#73: Protein 40S ribosomal protein S21-A / S26 / Small ribosomal subunit protein eS21-A / YS25


Mass: 9758.829 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / References: UniProt: P0C0V8
#74: Protein 40S ribosomal protein S22-A / RP50 / S24 / YP58 / YS22


Mass: 14650.062 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / References: UniProt: P0C0W1
#75: Protein 40S ribosomal protein S23-A / RP37 / S28 / YS14


Mass: 16073.896 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / References: UniProt: P0CX29
#76: Protein 40S ribosomal protein S24-A / RP50


Mass: 15362.848 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / References: UniProt: P0CX31
#78: Protein 40S ribosomal protein S27-A / RP61 / Small ribosomal subunit protein eS27-A / YS20


Mass: 8893.391 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / References: UniProt: P35997
#79: Protein 40S ribosomal protein S30-A / Small ribosomal subunit protein eS30-A


Mass: 7137.541 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / References: UniProt: P0CX33

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Small ribosomal subunit protein ... , 2 types, 2 molecules SQSe

#63: Protein Small ribosomal subunit protein eS1A / 40S ribosomal protein S1-A / RP10A


Mass: 28798.467 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / References: UniProt: P33442
#77: Protein Small ribosomal subunit protein eS26B / 40S ribosomal protein S26-B


Mass: 13480.886 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / References: UniProt: P39939

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Non-polymers , 1 types, 1 molecules

#82: Chemical ChemComp-3HE / 4-{(2R)-2-[(1S,3S,5S)-3,5-dimethyl-2-oxocyclohexyl]-2-hydroxyethyl}piperidine-2,6-dione


Mass: 281.347 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H23NO4 / Feature type: SUBJECT OF INVESTIGATION

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Details

Has ligand of interestY
Has protein modificationY

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Experimental details

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Experiment

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

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Sample preparation

ComponentName: 60S ribosomal subunit with Rpl10 loop deletion produced in bypass mutant. NMD3, LSG1, TIF6 present
Type: RIBOSOME / Entity ID: #1-#81 / Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: Saccharomyces cerevisiae S288C (yeast)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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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 defocus max: 2000 nm / Nominal defocus min: 1000 nm
Image recordingElectron dose: 80 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM software
IDNameVersionCategory
1cryoSPARCparticle selection
2PHENIX1.21.2_5419:model refinement
13cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.66 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 79307 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.006208700
ELECTRON MICROSCOPYf_angle_d0.948306400
ELECTRON MICROSCOPYf_dihedral_angle_d22.18685175
ELECTRON MICROSCOPYf_chiral_restr0.05138421
ELECTRON MICROSCOPYf_plane_restr0.01520086

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