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- PDB-8yld: State 4a (S4a) of yeast 80S ribosome bound to 2 tRNAs and open eE... -

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Basic information

Entry
Database: PDB / ID: 8yld
TitleState 4a (S4a) of yeast 80S ribosome bound to 2 tRNAs and open eEF3 and eEF2 during translocation
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


Peptide chain elongation / Synthesis of diphthamide-EEF2 / positive regulation of translational elongation / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, LSU-rRNA,5S) / Negative regulators of DDX58/IFIH1 signaling / negative regulation of glucose mediated signaling pathway / negative regulation of translational frameshifting / positive regulation of translational fidelity / RMTs methylate histone arginines / Protein methylation ...Peptide chain elongation / Synthesis of diphthamide-EEF2 / positive regulation of translational elongation / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, LSU-rRNA,5S) / Negative regulators of DDX58/IFIH1 signaling / negative regulation of glucose mediated signaling pathway / negative regulation of translational frameshifting / positive regulation of translational fidelity / RMTs methylate histone arginines / Protein methylation / mTORC1-mediated signalling / Protein hydroxylation / ribosome-associated ubiquitin-dependent protein catabolic process / GDP-dissociation inhibitor activity / positive regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / pre-mRNA 5'-splice site binding / preribosome, small subunit precursor / Formation of the ternary complex, and subsequently, the 43S complex / nonfunctional rRNA decay / Translation initiation complex formation / 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) / response to cycloheximide / Major pathway of rRNA processing in the nucleolus and cytosol / mRNA destabilization / SRP-dependent cotranslational protein targeting to membrane / GTP hydrolysis and joining of the 60S ribosomal subunit / 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 / negative regulation of mRNA splicing, via spliceosome / preribosome, large subunit precursor / regulation of amino acid metabolic process / L13a-mediated translational silencing of Ceruloplasmin expression / translational elongation / ribosomal large subunit export from nucleus / G-protein alpha-subunit binding / Ub-specific processing proteases / positive regulation of protein kinase activity / 90S preribosome / endonucleolytic cleavage to generate mature 3'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / regulation of translational fidelity / protein-RNA complex assembly / translation elongation factor activity / ribosomal subunit export from nucleus / ribosomal small subunit export from nucleus / translational termination / translation regulator activity / negative regulation of protein phosphorylation / cytosolic ribosome / 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) / DNA-(apurinic or apyrimidinic site) endonuclease activity / Neutrophil degranulation / maturation of LSU-rRNA / cellular response to amino acid starvation / ribosome assembly / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / rescue of stalled ribosome / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of SSU-rRNA / ribosomal large subunit biogenesis / translational initiation / small-subunit processome / negative regulation of protein kinase activity / macroautophagy / protein kinase C binding / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / maintenance of translational fidelity / modification-dependent protein catabolic process / cytoplasmic stress granule / protein tag activity / rRNA processing / ribosome biogenesis / ribosome binding / protein-folding chaperone binding / ribosomal small subunit biogenesis / ribosomal small subunit assembly / small ribosomal subunit / small ribosomal subunit rRNA binding / 5S rRNA binding / large ribosomal subunit rRNA binding / ribosomal large subunit assembly / cytosolic small ribosomal subunit / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / cytosolic large ribosomal subunit / cytoplasmic translation / negative regulation of translation / rRNA binding / ribosome / structural constituent of ribosome / protein ubiquitination / translation / ribonucleoprotein complex / G protein-coupled receptor signaling pathway / 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 / : / : / HEAT repeat profile. / HEAT, type 2 / Elongation Factor G, domain II / Elongation Factor G, domain III ...Four helical bundle domain / : / Four helical bundle domain / Elongation Factor 3 / : / : / 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 S5, eukaryotic/archaeal / Ribosomal protein L29e / Ribosomal L29e protein family / Ribosomal protein S19e, conserved site / Ribosomal protein S19e signature. / Ribosomal protein L13e, conserved site / Ribosomal protein L13e signature. / Ribosomal protein S21e / Ribosomal protein S21e superfamily / Ribosomal protein S21e / Ribosomal protein S2, eukaryotic / Small (40S) ribosomal subunit Asc1/RACK1 / Ribosomal protein L22e / Ribosomal protein L22e superfamily / Ribosomal L22e protein family / S27a-like superfamily / Ribosomal protein L38e / Ribosomal protein L38e superfamily / Ribosomal L38e protein family / 40S Ribosomal protein S10 / Ribosomal protein S10, eukaryotic/archaeal / Ribosomal protein L27e, conserved site / Ribosomal protein L27e signature. / Ribosomal protein L10e, conserved site / Ribosomal protein L44e signature. / Ribosomal protein L10e signature. / Ribosomal protein L10e / Plectin/S10, N-terminal / Plectin/S10 domain / Ribosomal protein L19, eukaryotic / Ribosomal protein S25 / S25 ribosomal protein / Ribosomal protein L13e / Ribosomal protein L13e / Ribosomal protein S27a / Ribosomal protein S27a / Ribosomal protein S27a / Ribosomal protein S8e subdomain, eukaryotes / Ribosomal protein S2, eukaryotic/archaeal / Ribosomal protein S17e, conserved site / Ribosomal protein S17e signature. / 60S ribosomal protein L18a/ L20, eukaryotes / : / Ribosomal protein L19/L19e conserved site / : / Ribosomal protein L19e signature. / Ribosomal protein S7e signature. / Ribosomal protein S30 / Ribosomal protein S30 / Ribosomal protein L24e, conserved site / 40S ribosomal protein S29/30S ribosomal protein S14 type Z / Ribosomal protein L24e signature. / Translation elongation factor EFTu-like, domain 2 / Ribosomal protein L44e / Ribosomal protein L44 / : / Ribosomal protein L34e, conserved site / Ribosomal protein L5 eukaryotic, C-terminal / Ribosomal L18 C-terminal region / Ribosomal protein L34e signature. / Ribosomal protein S3, eukaryotic/archaeal / Ribosomal protein L6e signature. / Ribosomal protein L30e signature 1. / Ribosomal protein S3Ae, conserved site / Ribosomal protein S3Ae signature. / 50S ribosomal protein L18Ae/60S ribosomal protein L20 and L18a / Ribosomal protein S27e signature. / Ribosomal protein S19e
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: To Be Published
Title: Snapshots of ribosome dynamics near atomic resolution in situ: a full insight into eukaryotic elongation cycle
Authors: Cheng, J. / Wu, C.L. / Li, J.X. / Yang, Q. / Zhao, M.J. / Zhang, X.Z.
History
DepositionMar 6, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Dec 11, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
S: Large ribosomal subunit protein eL18A
2: 18S rRNA
A: 25S rRNA
B: 5S rRNA
C: 5.8S rRNA
D: Large ribosomal subunit protein uL2A
E: Large ribosomal subunit protein uL3
F: Large ribosomal subunit protein uL4A
G: Large ribosomal subunit protein uL18
H: Large ribosomal subunit protein eL6B
I: Large ribosomal subunit protein uL30A
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
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
s: tRNA
t: tRNA
v: Elongation factor 3A
x: Elongation factor 2
SC: Small ribosomal subunit protein eS10A
SE: Small ribosomal subunit protein uS19
SA: Small ribosomal subunit protein uS3
SI: Small ribosomal subunit protein eS19A
SL: Small ribosomal subunit protein eS28A
SM: Small ribosomal subunit protein uS14A
SG: Small ribosomal subunit protein eS17A
SB: Small ribosomal subunit protein uS7
SF: Small ribosomal subunit protein uS9A
SH: Small ribosomal subunit protein uS13A
SK: Small ribosomal subunit protein eS25A
SN: Small ribosomal subunit protein eS31
SD: Small ribosomal subunit protein eS12
SZ: Small ribosomal subunit protein uS11B
Se: Small ribosomal subunit protein eS26A
SP: Small ribosomal subunit protein uS2A
SQ: Small ribosomal subunit protein eS1A
SR: Small ribosomal subunit protein uS5
SS: Small ribosomal subunit protein eS4A
ST: Small ribosomal subunit protein eS6A
SU: Small ribosomal subunit protein eS7A
SV: Small ribosomal subunit protein eS8A
SW: Small ribosomal subunit protein uS4A
SX: Small ribosomal subunit protein uS17A
SY: Small ribosomal subunit protein uS15
Sa: Small ribosomal subunit protein eS21A
Sb: Small ribosomal subunit protein uS8A
Sc: Small ribosomal subunit protein uS12A
Sd: Small ribosomal subunit protein eS24A
Sf: Small ribosomal subunit protein eS27A
Sg: Small ribosomal subunit protein eS30A
SJ: Small ribosomal subunit protein uS10
J: Large ribosomal subunit protein eL8A
SO: Small ribosomal subunit protein RACK1


Theoretical massNumber of molelcules
Total (without water)3,277,78082
Polymers3,277,78082
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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Large ribosomal subunit protein ... , 41 types, 41 molecules SDEFGHIKLMNOPQRTUVWXYZabcdefgh...

#1: 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
#6: 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
#7: 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
#8: 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
#9: 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
#10: 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
#11: 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
#12: 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
#13: 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
#14: 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
#15: 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
#16: 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
#17: 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
#18: 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
#19: 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
#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
#80: 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

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RNA chain , 5 types, 6 molecules 2ABCst

#2: 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
#3: 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)
#4: 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
#5: 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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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: 108547.969 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

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Small ribosomal subunit protein ... , 33 types, 33 molecules SCSESASISLSMSGSBSFSHSKSNSDSZSeSPSQSRSSSTSUSVSWSXSYSaSbScSdSf...

#48: 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
#49: 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
#50: 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
#51: 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
#52: 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
#53: 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
#54: 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
#55: 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
#56: 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
#57: 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
#58: 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
#59: 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
#60: 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
#61: 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
#62: 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
#63: 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
#64: 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
#65: 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
#66: 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
#67: 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
#68: 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
#69: 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
#70: 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
#71: 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
#72: 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
#73: 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
#74: 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
#75: 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
#76: 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
#77: 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
#78: 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
#79: 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
#81: 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: 34710.023 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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Details

Has protein modificationN

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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: 8681 / Symmetry type: POINT

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