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- PDB-8ylr: State 6 (S6) of yeast 80S ribosome bound to 2 tRNAs and eEF2 and ... -

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Basic information

Entry
Database: PDB / ID: 8ylr
TitleState 6 (S6) of yeast 80S ribosome bound to 2 tRNAs and eEF2 and eEF3 during tranlocation
Components
  • (Elongation factor ...) x 2
  • (Large ribosomal subunit protein ...) x 41
  • (Small ribosomal subunit protein ...) x 33
  • 18S rRNA
  • 25S rRNA
  • 5.8S rRNA
  • 5S rRNA
  • tRNA
KeywordsRIBOSOME / 80S / eEF3 / eEF2
Function / homology
Function and homology information


cytoplasmic translational elongation / Peptide chain elongation / Synthesis of diphthamide-EEF2 / cytoplasmic translational termination / positive regulation of translational elongation / 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 / Negative regulators of DDX58/IFIH1 signaling ...cytoplasmic translational elongation / Peptide chain elongation / Synthesis of diphthamide-EEF2 / cytoplasmic translational termination / positive regulation of translational elongation / 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 / Negative regulators of DDX58/IFIH1 signaling / RMTs methylate histone arginines / Protein methylation / mTORC1-mediated signalling / Protein hydroxylation / ribosome-associated ubiquitin-dependent protein catabolic process / GDP-dissociation inhibitor activity / pre-mRNA 5'-splice site binding / positive regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / nonfunctional rRNA decay / Formation of the ternary complex, and subsequently, the 43S complex / Translation initiation complex formation / response to cycloheximide / Ribosomal scanning and start codon recognition / cleavage in ITS2 between 5.8S rRNA and LSU-rRNA of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / preribosome, small subunit precursor / mRNA destabilization / Major pathway of rRNA processing in the nucleolus and cytosol / negative regulation of translational frameshifting / SRP-dependent cotranslational protein targeting to membrane / GTP hydrolysis and joining of the 60S ribosomal subunit / negative regulation of mRNA splicing, via spliceosome / preribosome, large subunit precursor / positive regulation of protein kinase activity / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / Formation of a pool of free 40S subunits / L13a-mediated translational silencing of Ceruloplasmin expression / endonucleolytic cleavage to generate mature 3'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / translational elongation / ribosomal large subunit export from nucleus / G-protein alpha-subunit binding / 90S preribosome / Ub-specific processing proteases / translation elongation factor activity / regulation of translational fidelity / protein-RNA complex assembly / translational termination / ribosomal subunit export from nucleus / 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) / ribosomal small subunit export from nucleus / translation regulator activity / DNA-(apurinic or apyrimidinic site) endonuclease activity / Neutrophil degranulation / cytosolic ribosome / rescue of stalled ribosome / protein kinase C binding / cellular response to amino acid starvation / ribosomal large subunit biogenesis / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / ribosome assembly / maturation of SSU-rRNA / macroautophagy / small-subunit processome / translational initiation / maintenance of translational fidelity / modification-dependent protein catabolic process / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / protein tag activity / cytoplasmic stress granule / rRNA processing / ribosome biogenesis / protein-folding chaperone binding / ribosome binding / ribosomal small subunit biogenesis / ribosomal small subunit assembly / small ribosomal subunit / 5S rRNA binding / ribosomal large subunit assembly / small ribosomal subunit rRNA binding / large ribosomal subunit rRNA binding / cytosolic small ribosomal subunit / cytosolic large ribosomal subunit / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / cytoplasmic translation / negative regulation of translation / rRNA binding / protein ubiquitination / structural constituent of ribosome / ribosome / translation / G protein-coupled receptor signaling pathway / ribonucleoprotein complex / negative regulation of gene expression / response to antibiotic / GTPase activity / mRNA binding / ubiquitin protein ligase binding / GTP binding
Similarity search - Function
Four helical bundle domain / : / Four helical bundle domain / Elongation Factor 3 / : / : / Elongation factor 3/GNC1 HEAT repeat / EF3 N-terminal HEAT repeat / HEAT repeat profile. / HEAT, type 2 ...Four helical bundle domain / : / Four helical bundle domain / Elongation Factor 3 / : / : / Elongation factor 3/GNC1 HEAT repeat / EF3 N-terminal HEAT repeat / HEAT repeat profile. / HEAT, type 2 / Elongation Factor G, domain II / Elongation Factor G, domain III / Translation elongation factor EFG/EF2, domain IV / Elongation factor G, domain IV / Elongation factor G, domain IV / Elongation factor G C-terminus / Elongation factor EFG, domain V-like / Elongation factor G C-terminus / EF-G domain III/V-like / : / Tr-type G domain, conserved site / Translational (tr)-type guanine nucleotide-binding (G) domain signature. / : / Ribosomal protein S26e signature. / Ribosomal protein L41 / Ribosomal protein L41 / Ribosomal protein S21e, conserved site / Ribosomal protein S21e signature. / Ribosomal protein S26e / Ribosomal protein S26e superfamily / Ribosomal protein S26e / : / Ribosomal protein S12e signature. / Ribosomal protein S12e / Ribosomal protein L13e, conserved site / Ribosomal protein L13e signature. / Ribosomal protein L29e / Ribosomal L29e protein family / Small (40S) ribosomal subunit Asc1/RACK1 / Ribosomal protein S5, eukaryotic/archaeal / 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 L27e, conserved site / Ribosomal protein L27e signature. / Ribosomal protein L22e / Ribosomal protein L22e superfamily / Ribosomal L22e protein family / Ribosomal protein L38e / Translation elongation factor EFTu-like, domain 2 / Ribosomal protein L38e superfamily / S27a-like superfamily / Ribosomal L38e protein family / 40S Ribosomal protein S10 / Ribosomal protein L10e, conserved site / Ribosomal protein L10e signature. / Ribosomal protein L19, eukaryotic / : / Ribosomal protein L10e / Ribosomal protein L6e signature. / Plectin/S10, N-terminal / Ribosomal protein L24e, conserved site / Plectin/S10 domain / Ribosomal protein L24e signature. / Ribosomal protein L13e / Ribosomal protein L13e / Ribosomal protein L44e signature. / Ribosomal protein L19/L19e conserved site / : / Ribosomal protein L19e signature. / 60S ribosomal protein L18a/ L20, eukaryotes / Ribosomal protein S7e signature. / Ribosomal protein S10, eukaryotic/archaeal / Ribosomal protein S30 / Ribosomal protein S30 / Ribosomal protein S17e, conserved site / Ribosomal protein S17e signature. / Ribosomal protein S25 / S25 ribosomal protein / Ribosomal protein L34e, conserved site / Ribosomal protein S8e subdomain, eukaryotes / Ribosomal protein L34e signature. / Ribosomal protein S27a / Ribosomal protein S27a / Ribosomal protein S27a / : / Ribosomal protein S2, eukaryotic/archaeal / Ribosomal protein L5 eukaryotic, C-terminal / Ribosomal L18 C-terminal region / Ribosomal protein L23/L25, N-terminal / Ribosomal protein L23, N-terminal domain / Ribosomal protein L44e / Ribosomal protein L44 / Ribosomal L40e family / Ribosomal protein L18/L18-A/B/e, conserved site / Ribosomal protein L18e signature. / 50S ribosomal protein L18Ae/60S ribosomal protein L20 and L18a
Similarity search - Domain/homology
: / : / : / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Small ribosomal subunit protein uS4A / Large ribosomal subunit protein uL15 ...: / : / : / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Small ribosomal subunit protein uS4A / Large ribosomal subunit protein uL15 / Small ribosomal subunit protein eS17A / 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 / Elongation factor 3A / 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 / Elongation factor 2 / 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 eS26A / 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: 3.9 Å
AuthorsCheng, J. / Wu, C.L. / Li, J.X. / Zhang, X.Z.
Funding support China, 3items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31930069 China
National Natural Science Foundation of China (NSFC)32150010 China
Chinese Academy of SciencesXDB37040101 China
CitationJournal: Nat Struct Mol Biol / Year: 2025
Title: Capturing eukaryotic ribosome dynamics in situ at high resolution.
Authors: Jing Cheng / Chunling Wu / Junxi Li / Qi Yang / Mingjie Zhao / Xinzheng Zhang /
Abstract: Many protein complexes are highly dynamic in cells; thus, characterizing their conformational changes in cells is crucial for unraveling their functions. Here, using cryo-electron microscopy, 451,700 ...Many protein complexes are highly dynamic in cells; thus, characterizing their conformational changes in cells is crucial for unraveling their functions. Here, using cryo-electron microscopy, 451,700 ribosome particles from Saccharomyces cerevisiae cell lamellae were obtained to solve the 60S region to 2.9-Å resolution by in situ single-particle analysis. Over 20 distinct conformations were identified by three-dimensional classification with resolutions typically higher than 4 Å. These conformations were used to reconstruct a complete elongation cycle of eukaryotic translation with elongation factors (eEFs). We found that compact eEF2 anchors to the partially rotated ribosome after subunit rolling and hypothesize that it stabilizes the local conformation for peptidyl transfer. Moreover, open-eEF3 binding to a fully rotated ribosome was observed, whose conformational change was coupled with head swiveling and body back-rotation of the 40S subunit.
History
DepositionMar 6, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Dec 11, 2024Provider: repository / Type: Initial release
Revision 1.1Jul 2, 2025Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
2: 18S rRNA
A: 25S rRNA
B: 5S rRNA
C: 5.8S rRNA
D: Large ribosomal subunit protein uL2A
F: Large ribosomal subunit protein uL4A
G: Large ribosomal subunit protein uL18
H: Large ribosomal subunit protein eL6B
I: Large ribosomal subunit protein uL30A
J: Large ribosomal subunit protein eL8A
K: Large ribosomal subunit protein uL6A
L: Large ribosomal subunit protein uL16
M: Large ribosomal subunit protein uL5B
N: Large ribosomal subunit protein eL13A
O: Large ribosomal subunit protein eL14A
P: Large ribosomal subunit protein eL15A
Q: Large ribosomal subunit protein uL13A
R: Large ribosomal subunit protein uL22A
S: Large ribosomal subunit protein eL18A
T: Large ribosomal subunit protein eL19A
U: Large ribosomal subunit protein eL20A
V: Large ribosomal subunit protein eL21A
W: Large ribosomal subunit protein eL22A
X: Large ribosomal subunit protein uL14A
Y: Large ribosomal subunit protein eL24A
Z: Large ribosomal subunit protein uL23
a: Large ribosomal subunit protein uL24A
b: Large ribosomal subunit protein eL27A
c: Large ribosomal subunit protein uL15
d: Large ribosomal subunit protein eL29
e: Large ribosomal subunit protein eL30
f: Large ribosomal subunit protein eL31A
g: Large ribosomal subunit protein eL32
h: Large ribosomal subunit protein eL33A
i: Large ribosomal subunit protein eL34A
j: Large ribosomal subunit protein uL29A
k: Large ribosomal subunit protein eL36A
l: Large ribosomal subunit protein eL37A
m: Large ribosomal subunit protein eL38
n: Large ribosomal subunit protein eL39
o: Large ribosomal subunit protein eL40A
p: Large ribosomal subunit protein eL41A
q: Large ribosomal subunit protein eL42A
r: Large ribosomal subunit protein eL43A
t: tRNA
u: tRNA
v: Elongation factor 3A
x: Elongation factor 2
SA: Small ribosomal subunit protein uS3
SC: Small ribosomal subunit protein eS10A
SD: Small ribosomal subunit protein eS12
SE: Small ribosomal subunit protein uS19
SF: Small ribosomal subunit protein uS9A
SH: Small ribosomal subunit protein uS13A
SI: Small ribosomal subunit protein eS19A
SJ: Small ribosomal subunit protein uS10
SK: Small ribosomal subunit protein eS25A
SM: Small ribosomal subunit protein uS14A
SN: Small ribosomal subunit protein eS31
SO: Small ribosomal subunit protein RACK1
SQ: Small ribosomal subunit protein eS1A
SS: Small ribosomal subunit protein eS4A
ST: Small ribosomal subunit protein eS6A
SR: Small ribosomal subunit protein uS5
SV: Small ribosomal subunit protein eS8A
SW: Small ribosomal subunit protein uS4A
SX: Small ribosomal subunit protein uS17A
SY: Small ribosomal subunit protein uS15
SZ: Small ribosomal subunit protein uS11B
Sa: Small ribosomal subunit protein eS21A
Sb: Small ribosomal subunit protein uS8A
Sc: Small ribosomal subunit protein uS12A
Sd: Small ribosomal subunit protein eS24A
Se: Small ribosomal subunit protein eS26A
Sf: Small ribosomal subunit protein eS27A
Sg: Small ribosomal subunit protein eS30A
SG: Small ribosomal subunit protein eS17A
SP: Small ribosomal subunit protein uS2A
SU: Small ribosomal subunit protein eS7A
SL: Small ribosomal subunit protein eS28A
SB: Small ribosomal subunit protein uS7
E: Large ribosomal subunit protein uL3


Theoretical massNumber of molelcules
Total (without water)3,284,77182
Polymers3,284,77182
Non-polymers00
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 , 5 types, 6 molecules 2ABCtu

#1: RNA chain 18S rRNA


Mass: 579432.750 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / References: GenBank: 831416138
#2: RNA chain 25S rRNA


Mass: 1096842.375 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast)
#3: RNA chain 5S rRNA


Mass: 38951.105 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / References: GenBank: 834774822
#4: RNA chain 5.8S rRNA


Mass: 50682.922 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / References: GenBank: 1531397035
#45: RNA chain tRNA


Mass: 24222.500 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / References: GenBank: 176433

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Large ribosomal subunit protein ... , 41 types, 41 molecules DFGHIJKLMNOPQRSTUVWXYZabcdefgh...

#5: Protein Large ribosomal subunit protein uL2A / 60S ribosomal protein L2-A / L5 / RP8 / YL6


Mass: 27089.158 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / References: UniProt: P0CX45
#6: Protein Large ribosomal subunit protein uL4A / 60S ribosomal protein L4-A / L2 / RP2 / YL2


Mass: 39027.926 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / References: UniProt: P10664
#7: Protein Large ribosomal subunit protein uL18 / 60S ribosomal protein L5 / L1 / L1a / Ribosomal 5S RNA-binding protein / YL3


Mass: 33415.387 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / References: UniProt: P26321
#8: Protein Large ribosomal subunit protein eL6B / 60S ribosomal protein L6-B / L17 / RP18 / YL16


Mass: 19893.346 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / References: UniProt: P05739
#9: Protein Large ribosomal subunit protein uL30A / 60S ribosomal protein L7-A / L6 / RP11 / YL8


Mass: 25353.535 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / References: UniProt: P05737
#10: Protein Large ribosomal subunit protein eL8A / 60S ribosomal protein L8-A / L4 / L4-2 / L7a-1 / Maintenance of killer protein 7 / RP6 / YL5


Mass: 25814.998 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / References: UniProt: P17076
#11: Protein Large ribosomal subunit protein uL6A / 60S ribosomal protein L9-A / L8 / 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
#12: Protein Large ribosomal subunit protein uL16 / 60S ribosomal protein L10 / L9 / Ubiquinol-cytochrome C reductase complex subunit VI-requiring protein


Mass: 25080.062 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / References: UniProt: P41805
#13: Protein Large ribosomal subunit protein uL5B / 60S ribosomal protein L11-B / L16 / RP39 / YL22


Mass: 19266.082 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / References: UniProt: Q3E757
#14: Protein Large ribosomal subunit protein eL13A / 60S ribosomal protein L13-A


Mass: 21885.234 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / References: UniProt: Q12690
#15: Protein Large ribosomal subunit protein eL14A / 60S ribosomal protein L14-A


Mass: 14976.794 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / References: UniProt: P36105
#16: Protein Large ribosomal subunit protein eL15A / 60S ribosomal protein L15-A / L13 / RP15R / YL10 / YP18


Mass: 24351.162 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / References: UniProt: P05748
#17: Protein Large ribosomal subunit protein uL13A / 60S ribosomal protein L16-A / L13a / L21 / RP22 / YL15


Mass: 22028.951 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / References: UniProt: P26784
#18: Protein Large ribosomal subunit protein uL22A / 60S ribosomal protein L17-A / L20A / YL17


Mass: 20458.322 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / References: UniProt: P05740
#19: Protein Large ribosomal subunit protein eL18A / 60S ribosomal protein L18-A / RP28


Mass: 20478.059 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / References: UniProt: P0CX49
#20: Protein Large ribosomal subunit protein eL19A / 60S ribosomal protein L19-A / L23 / RP15L / RP33 / YL14


Mass: 21631.121 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / References: UniProt: P0CX82
#21: Protein Large ribosomal subunit protein eL20A / 60S ribosomal protein L20-A / L18a


Mass: 20347.654 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / References: UniProt: P0CX23
#22: Protein Large ribosomal subunit protein eL21A / 60S ribosomal protein L21-A


Mass: 18148.066 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / References: UniProt: Q02753
#23: Protein Large ribosomal subunit protein eL22A / 60S ribosomal protein L22-A / L1c / RP4 / YL31


Mass: 11263.863 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / References: UniProt: P05749
#24: Protein Large ribosomal subunit protein uL14A / 60S ribosomal protein L23-A / L17a / YL32


Mass: 14362.755 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / References: UniProt: P0CX41
#25: Protein Large ribosomal subunit protein eL24A / 60S ribosomal protein L24-A / L30 / RP29 / YL21


Mass: 14645.270 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / References: UniProt: P04449
#26: Protein Large ribosomal subunit protein uL23 / 60S ribosomal protein L25 / RP16L / YL25 / YP42'


Mass: 13771.176 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / References: UniProt: P04456
#27: Protein Large ribosomal subunit protein uL24A / 60S ribosomal protein L26-A / L33 / YL33


Mass: 14005.475 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / References: UniProt: P05743
#28: Protein Large ribosomal subunit protein eL27A / 60S ribosomal protein L27-A


Mass: 15437.166 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / References: UniProt: P0C2H6
#29: Protein Large ribosomal subunit protein uL15 / 60S ribosomal protein L28 / L27a / L29 / RP44 / RP62 / YL24


Mass: 16630.471 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / References: UniProt: P02406
#30: Protein Large ribosomal subunit protein eL29 / 60S ribosomal protein L29 / YL43


Mass: 6560.688 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / References: UniProt: P05747
#31: Protein Large ribosomal subunit protein eL30 / 60S ribosomal protein L30 / L32 / RP73 / YL38


Mass: 10487.266 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / References: UniProt: P14120
#32: Protein Large ribosomal subunit protein eL31A / 60S ribosomal protein L31-A / L34 / YL28


Mass: 12649.754 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / References: UniProt: P0C2H8
#33: Protein Large ribosomal subunit protein eL32 / 60S ribosomal protein L32


Mass: 14478.054 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / References: UniProt: P38061
#34: Protein Large ribosomal subunit protein eL33A / 60S ribosomal protein L33-A / L37 / RP47 / YL37


Mass: 12045.935 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / References: UniProt: P05744
#35: Protein Large ribosomal subunit protein eL34A / 60S ribosomal protein L34-A


Mass: 12608.831 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / References: UniProt: P87262
#36: Protein Large ribosomal subunit protein uL29A / 60S ribosomal protein L35-A


Mass: 13811.444 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / References: UniProt: P0CX84
#37: Protein Large ribosomal subunit protein eL36A / 60S ribosomal protein L36-A / L39 / YL39


Mass: 11020.063 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / References: UniProt: P05745
#38: Protein Large ribosomal subunit protein eL37A / 60S ribosomal protein L37-A / L43 / YL35 / YP55


Mass: 9229.632 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / References: UniProt: P49166
#39: Protein Large ribosomal subunit protein eL38 / 60S ribosomal protein L38


Mass: 8714.363 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / References: UniProt: P49167
#40: Protein/peptide Large ribosomal subunit protein eL39 / 60S ribosomal protein L39 / L46 / YL40


Mass: 6227.444 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / References: UniProt: P04650
#41: Protein Large ribosomal subunit protein eL40A / 60S ribosomal protein L40-A / CEP52


Mass: 6032.321 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / References: UniProt: P0CH08
#42: Protein/peptide Large ribosomal subunit protein eL41A / 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
#43: Protein Large ribosomal subunit protein eL42A / 60S ribosomal protein L42-A / L41 / YL27 / YP44


Mass: 11840.159 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / References: UniProt: P0CX27
#44: Protein Large ribosomal subunit protein eL43A / 60S ribosomal protein L43-A / L37a / YL35


Mass: 9981.756 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / References: UniProt: P0CX25
#81: Protein Large ribosomal subunit protein uL3 / 60S ribosomal protein L3 / Maintenance of killer protein 8 / RP1 / Trichodermin resistance protein / YL1


Mass: 43719.602 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / References: UniProt: P14126

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Elongation factor ... , 2 types, 2 molecules vx

#46: Protein Elongation factor 3A / EF-3 / EF-3A / Eukaryotic elongation factor 3 / eEF3 / Translation elongation factor 3A / Yeast ...EF-3 / EF-3A / Eukaryotic elongation factor 3 / eEF3 / Translation elongation factor 3A / Yeast elongation factor 3


Mass: 116097.680 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast)
References: UniProt: P16521, Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement
#47: Protein Elongation factor 2 / EF-2 / Eukaryotic elongation factor 2 / eEF2 / Ribosomal translocase / Translation elongation factor 2


Mass: 93407.125 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast)
References: UniProt: P32324, Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement

+
Small ribosomal subunit protein ... , 33 types, 33 molecules SASCSDSESFSHSISJSKSMSNSOSQSSSTSRSVSWSXSYSZSaSbScSdSeSfSgSGSP...

#48: Protein Small ribosomal subunit protein uS3 / 40S ribosomal protein S3 / RP13 / YS3


Mass: 24631.713 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / References: UniProt: P05750
#49: Protein Small ribosomal subunit protein eS10A / 40S ribosomal protein S10-A


Mass: 11042.562 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / References: UniProt: Q08745
#50: Protein Small ribosomal subunit protein eS12 / 40S ribosomal protein S12


Mass: 13028.008 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / References: UniProt: P48589
#51: Protein Small ribosomal subunit protein uS19 / 40S ribosomal protein S15 / RIG protein / RP52 / S21 / YS21


Mass: 13265.591 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / References: UniProt: Q01855
#52: Protein Small ribosomal subunit protein uS9A / 40S ribosomal protein S16-A / RP61R


Mass: 15659.216 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / References: UniProt: P0CX51
#53: Protein Small ribosomal subunit protein uS13A / 40S ribosomal protein S18-A


Mass: 16940.443 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / References: UniProt: P0CX55
#54: Protein Small ribosomal subunit protein eS19A / 40S ribosomal protein S19-A / RP55A / S16a / YP45 / YS16A


Mass: 15810.930 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / References: UniProt: P07280
#55: Protein Small ribosomal subunit protein uS10 / 40S ribosomal protein S20


Mass: 11363.321 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / References: UniProt: P38701
#56: Protein Small ribosomal subunit protein eS25A / 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
#57: Protein Small ribosomal subunit protein uS14A / 40S ribosomal protein S29-A / S36 / YS29


Mass: 6335.303 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / References: UniProt: P41057
#58: Protein Small ribosomal subunit protein eS31 / 40S ribosomal protein S31 / CEP76 / S37 / YS24


Mass: 8388.049 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / References: UniProt: P05759
#59: Protein Small ribosomal subunit protein RACK1 / Guanine nucleotide-binding protein subunit beta-like protein / Receptor for activated C kinase / ...Guanine nucleotide-binding protein subunit beta-like protein / Receptor for activated C kinase / Receptor of activated protein kinase C 1 / RACK1


Mass: 34151.484 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / References: UniProt: P38011
#60: Protein Small ribosomal subunit protein eS1A / 40S ribosomal protein S1-A / RP10A


Mass: 26314.684 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / References: UniProt: P33442
#61: Protein Small ribosomal subunit protein eS4A / 40S ribosomal protein S4-A / RP5 / S7 / YS6


Mass: 29167.926 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / References: UniProt: P0CX35
#62: Protein Small ribosomal subunit protein eS6A / 40S ribosomal protein S6-A / RP9 / S10 / YS4


Mass: 26181.445 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / References: UniProt: P0CX37
#63: Protein Small ribosomal subunit protein uS5 / 40S ribosomal protein S2 / Omnipotent suppressor protein SUP44 / RP12 / S4 / YS5


Mass: 23084.850 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / References: UniProt: P25443
#64: Protein Small ribosomal subunit protein eS8A / 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
#65: Protein Small ribosomal subunit protein uS4A / 40S ribosomal protein S9-A / RP21 / S13 / YP28 / YS11


Mass: 21081.549 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / References: UniProt: O13516
#66: Protein Small ribosomal subunit protein uS17A / 40S ribosomal protein S11-A / RP41 / S18 / YS12


Mass: 16272.149 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / References: UniProt: P0CX47
#67: Protein Small ribosomal subunit protein uS15 / 40S ribosomal protein S13 / S27a / YS15


Mass: 16928.748 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / References: UniProt: P05756
#68: Protein Small ribosomal subunit protein uS11B / 40S ribosomal protein S14-B / RP59B


Mass: 13446.426 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / References: UniProt: P39516
#69: Protein Small ribosomal subunit protein eS21A / 40S ribosomal protein S21-A / S26 / 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
#70: Protein Small ribosomal subunit protein uS8A / 40S ribosomal protein S22-A / RP50 / S24 / YP58 / YS22


Mass: 14518.867 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / References: UniProt: P0C0W1
#71: Protein Small ribosomal subunit protein uS12A / 40S ribosomal protein S23-A / RP37 / S28 / YS14


Mass: 15942.699 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / References: UniProt: P0CX29
#72: Protein Small ribosomal subunit protein eS24A / 40S ribosomal protein S24-A / RP50


Mass: 15231.650 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / References: UniProt: P0CX31
#73: Protein Small ribosomal subunit protein eS26A / 40S ribosomal protein S26-A


Mass: 10757.683 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / References: UniProt: P39938
#74: Protein Small ribosomal subunit protein eS27A / 40S ribosomal protein S27-A / RP61 / YS20


Mass: 8762.195 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / References: UniProt: P35997
#75: Protein Small ribosomal subunit protein eS30A / 40S ribosomal protein S30-A


Mass: 6779.086 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / References: UniProt: P0CX33
#76: Protein Small ribosomal subunit protein eS17A / 40S ribosomal protein S17-A / RP51A


Mass: 13897.153 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / References: UniProt: P02407
#77: Protein Small ribosomal subunit protein uS2A / 40S ribosomal protein S0-A / Nucleic acid-binding protein NAB1A


Mass: 22811.074 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / References: UniProt: P32905
#78: Protein Small ribosomal subunit protein eS7A / 40S ribosomal protein S7-A / RP30 / RP40


Mass: 21000.492 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / References: UniProt: P26786
#79: Protein Small ribosomal subunit protein eS28A / 40S ribosomal protein S28-A / S33 / YS27


Mass: 7116.281 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / References: UniProt: Q3E7X9
#80: Protein Small ribosomal subunit protein uS7 / 40S ribosomal protein S5 / RP14 / S2 / YS8


Mass: 22908.338 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / References: UniProt: P26783

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Details

Has protein modificationY

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Experimental details

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Experiment

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

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Sample preparation

ComponentName: 80S / Type: RIBOSOME / Entity ID: all / Source: NATURAL
Source (natural)Organism: Saccharomyces cerevisiae S288C (yeast)
Buffer solutionpH: 4.5
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: 3000 nm / Nominal defocus min: 800 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K2 QUANTUM (4k x 4k)

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Processing

CTF correctionType: NONE
3D reconstructionResolution: 3.9 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 11880 / Symmetry type: POINT

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