8BN3

Yeast 80S, ES7s delta, eIF5A, Stm1 containing


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.40 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Evolving precision: rRNA expansion segment 7S modulates translation velocity and accuracy in eukaryal ribosomes.

Rauscher, R.Eggers, C.Dimitrova-Paternoga, L.Shankar, V.Rosina, A.Cristodero, M.Paternoga, H.Wilson, D.N.Leidel, S.A.Polacek, N.

(2024) Nucleic Acids Res 52: 4021-4036

  • DOI: https://doi.org/10.1093/nar/gkae067
  • Primary Citation of Related Structures:  
    8BN3

  • PubMed Abstract: 

    Ribosome-enhanced translational miscoding of the genetic code causes protein dysfunction and loss of cellular fitness. During evolution, open reading frame length increased, necessitating mechanisms for enhanced translation fidelity. Indeed, eukaryal ribosomes are more accurate than bacterial counterparts, despite their virtually identical, conserved active centers. During the evolution of eukaryotic organisms ribosome expansions at the rRNA and protein level occurred, which potentially increases the options for translation regulation and cotranslational events. Here we tested the hypothesis that ribosomal RNA expansions can modulate the core function of the ribosome, faithful protein synthesis. We demonstrate that a short expansion segment present in all eukaryotes' small subunit, ES7S, is crucial for accurate protein synthesis as its presence adjusts codon-specific velocities and guarantees high levels of cognate tRNA selection. Deletion of ES7S in yeast enhances mistranslation and causes protein destabilization and aggregation, dramatically reducing cellular fitness. Removal of ES7S did not alter ribosome architecture but altered the structural dynamics of inter-subunit bridges thus affecting A-tRNA selection. Exchanging the yeast ES7S sequence with the human ES7S increases accuracy whereas shortening causes the opposite effect. Our study demonstrates that ES7S provided eukaryal ribosomes with higher accuracy without perturbing the structurally conserved decoding center.


  • Organizational Affiliation

    Department for Chemistry, Biochemistry and Pharmaceutical Sciences, University of Bern, Freiestrasse 3, 3012 Bern, Switzerland.


Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L1-AA [auth B]217Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Rps5pB [auth S5]206Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein eS10AC [auth C0]96Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S14-BD [auth C4]127Saccharomyces cerevisiaeMutation(s): 0 
UniProt
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
RPS15 isoform 1E [auth C5]124Saccharomyces cerevisiaeMutation(s): 0 
UniProt
Find proteins for A0A6A5Q6F2 (Saccharomyces cerevisiae)
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S18-AF [auth C8]145Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
RPS20 isoform 1G [auth D0]107Saccharomyces cerevisiaeMutation(s): 0 
UniProt
Find proteins for A0A6A5PVE9 (Saccharomyces cerevisiae)
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S25H [auth D5]70Saccharomyces cerevisiaeMutation(s): 0 
UniProt
Find proteins for A0A6A5PZ18 (Saccharomyces cerevisiae)
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
RPS28A isoform 1I [auth D8]63Saccharomyces cerevisiaeMutation(s): 0 
UniProt
Find proteins for A0A6A5Q700 (Saccharomyces cerevisiae)
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L41-AJ [auth P]15Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein uS2AO [auth S0]251Saccharomyces cerevisiaeMutation(s): 0 
UniProt
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein eS1P [auth S1]214Saccharomyces cerevisiaeMutation(s): 0 
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Find proteins for A0A6A5PRY4 (Saccharomyces cerevisiae)
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
RPS2 isoform 1Q [auth S2]217Saccharomyces cerevisiaeMutation(s): 0 
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Find proteins for A0A6A5PWF7 (Saccharomyces cerevisiae)
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S3R [auth S3]223Saccharomyces cerevisiaeMutation(s): 0 
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Find proteins for A0A6A5Q3Q1 (Saccharomyces cerevisiae)
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein eS6AS [auth S6]226Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S7-AT [auth S7]184Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S8U [auth S8]188Saccharomyces cerevisiaeMutation(s): 0 
UniProt
Find proteins for A0A0J9X221 (Lachancea kluyveri)
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Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein uS4AV [auth S9]185Saccharomyces cerevisiaeMutation(s): 0 
UniProt
Find proteins for O13516 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein uS17AW [auth C1]155Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S13X [auth C3]150Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S16-AY [auth C6]141Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 26
MoleculeChains Sequence LengthOrganismDetailsImage
ES17Z [auth C7]120Saccharomyces cerevisiaeMutation(s): 0 
UniProt
Find proteins for A0A0J9X224 (Lachancea kluyveri)
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Entity ID: 27
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S19-AAA [auth C9]143Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 28
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein eS21ABA [auth D1]87Saccharomyces cerevisiaeMutation(s): 0 
UniProt
Find proteins for P0C0V8 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 29
MoleculeChains Sequence LengthOrganismDetailsImage
RPS22A isoform 1CA [auth D2]129Saccharomyces cerevisiaeMutation(s): 0 
UniProt
Find proteins for A0A6A5PSE9 (Saccharomyces cerevisiae)
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Entity ID: 30
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S23-ADA [auth D3]144Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 31
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S24-AEA [auth D4]134Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 32
MoleculeChains Sequence LengthOrganismDetailsImage
RPS26B isoform 1FA [auth D6]97Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 33
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S27-AGA [auth D7]81Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 34
MoleculeChains Sequence LengthOrganismDetailsImage
RPS29A isoform 1HA [auth D9]53Saccharomyces cerevisiaeMutation(s): 0 
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Find proteins for A0A6A5PV92 (Saccharomyces cerevisiae)
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Entity ID: 35
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S30-AIA [auth E0]60Saccharomyces cerevisiaeMutation(s): 0 
UniProt
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Entity ID: 36
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein RACK1JA [auth SR]318Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 37
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L2-AKA [auth L2]252Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 38
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L3LA [auth L3]386Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 39
MoleculeChains Sequence LengthOrganismDetailsImage
RPL4A isoform 1MA [auth L4]361Saccharomyces cerevisiaeMutation(s): 0 
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Find proteins for A0A6A5Q3W0 (Saccharomyces cerevisiae)
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Entity ID: 40
MoleculeChains Sequence LengthOrganismDetailsImage
RPL5 isoform 1NA [auth L5]295Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 41
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L6-AOA [auth L6]156Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 42
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L7-APA [auth L7]222Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 43
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L8-AQA [auth L8]233Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 44
MoleculeChains Sequence LengthOrganismDetailsImage
RPL9A isoform 1RA [auth L9]189Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 45
MoleculeChains Sequence LengthOrganismDetailsImage
RPL10 isoform 1SA [auth M0]209Saccharomyces cerevisiaeMutation(s): 0 
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Find proteins for A0A6A5PUZ5 (Saccharomyces cerevisiae)
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Entity ID: 46
MoleculeChains Sequence LengthOrganismDetailsImage
RPL11B isoform 1TA [auth M1]168Saccharomyces cerevisiaeMutation(s): 0 
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Find proteins for A0A6A5PYM2 (Saccharomyces cerevisiae)
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Entity ID: 47
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L13-AUA [auth M3]193Saccharomyces cerevisiaeMutation(s): 0 
UniProt
Find proteins for Q12690 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 48
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L14-AVA [auth M4]136Saccharomyces cerevisiaeMutation(s): 0 
UniProt
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Entity ID: 49
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein L15WA [auth M5]202Saccharomyces cerevisiaeMutation(s): 0 
UniProt
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Entity ID: 50
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L16-AXA [auth M6]197Saccharomyces cerevisiaeMutation(s): 0 
UniProt
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Entity ID: 51
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L17-AYA [auth M7]183Saccharomyces cerevisiaeMutation(s): 0 
UniProt
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Entity ID: 52
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L18-AZA [auth M8]185Saccharomyces cerevisiaeMutation(s): 0 
UniProt
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Entity ID: 53
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L19-AAB [auth M9]188Saccharomyces cerevisiaeMutation(s): 0 
UniProt
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Entity ID: 54
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L20-ABB [auth N0]172Saccharomyces cerevisiaeMutation(s): 0 
UniProt
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Entity ID: 55
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L21-ACB [auth N1]159Saccharomyces cerevisiaeMutation(s): 0 
UniProt
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Entity ID: 56
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L22-ADB [auth N2]100Saccharomyces cerevisiaeMutation(s): 0 
UniProt
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Entity ID: 57
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L23-AEB [auth N3]136Saccharomyces cerevisiaeMutation(s): 0 
UniProt
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Entity ID: 58
MoleculeChains Sequence LengthOrganismDetailsImage
RPL24A isoform 1FB [auth N4]98Saccharomyces cerevisiaeMutation(s): 0 
UniProt
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Entity ID: 59
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L25GB [auth N5]121Saccharomyces cerevisiaeMutation(s): 0 
UniProt
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Entity ID: 60
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL24AHB [auth N6]126Saccharomyces cerevisiaeMutation(s): 0 
UniProt
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Entity ID: 61
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L27-AIB [auth N7]135Saccharomyces cerevisiaeMutation(s): 0 
UniProt
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Entity ID: 62
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L28JB [auth N8]148Saccharomyces cerevisiaeMutation(s): 0 
UniProt
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Entity ID: 63
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L29KB [auth N9]56Saccharomyces cerevisiaeMutation(s): 0 
UniProt
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Entity ID: 64
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L30LB [auth O0]97Saccharomyces cerevisiaeMutation(s): 0 
UniProt
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Entity ID: 65
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L31-AMB [auth O1]109Saccharomyces cerevisiaeMutation(s): 0 
UniProt
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Entity ID: 66
MoleculeChains Sequence LengthOrganismDetailsImage
RPL32 isoform 1NB [auth O2]127Saccharomyces cerevisiaeMutation(s): 0 
UniProt
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Entity ID: 67
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L33-AOB [auth O3]106Saccharomyces cerevisiaeMutation(s): 0 
UniProt
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Entity ID: 68
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein eL34APB [auth O4]111Saccharomyces cerevisiaeMutation(s): 0 
UniProt
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Entity ID: 69
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L35-AQB [auth O5]119Saccharomyces cerevisiaeMutation(s): 0 
UniProt
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Entity ID: 70
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L36-ARB [auth O6]99Saccharomyces cerevisiaeMutation(s): 0 
UniProt
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Entity ID: 71
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein eL37ASB [auth O7]86Saccharomyces cerevisiaeMutation(s): 0 
UniProt
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Entity ID: 72
MoleculeChains Sequence LengthOrganismDetailsImage
RPL38 isoform 1TB [auth O8]77Saccharomyces cerevisiaeMutation(s): 0 
UniProt
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Entity ID: 73
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L39UB [auth O9]50Saccharomyces cerevisiaeMutation(s): 0 
UniProt
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Entity ID: 74
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L40-AVB [auth Q0]52Saccharomyces cerevisiaeMutation(s): 0 
UniProt
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Entity ID: 75
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein eL41BWB [auth Q1]25Saccharomyces cerevisiaeMutation(s): 0 
UniProt
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Entity ID: 76
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L42-AXB [auth Q2]105Saccharomyces cerevisiaeMutation(s): 0 
UniProt
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Entity ID: 77
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L43-AYB [auth Q3]91Saccharomyces cerevisiaeMutation(s): 0 
UniProt
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Entity ID: 78
MoleculeChains Sequence LengthOrganismDetailsImage
STM1 isoform 1ZB [auth SM]118Saccharomyces cerevisiaeMutation(s): 0 
UniProt
Find proteins for A0A8H4FBL9 (Saccharomyces cerevisiae)
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Entity ID: 79
MoleculeChains Sequence LengthOrganismDetailsImage
Eukaryotic translation initiation factor 5AAC [auth eI]145Saccharomyces cerevisiaeMutation(s): 0 
UniProt
Find proteins for A0A8H8ULI0 (Saccharomyces cerevisiae)
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Entity ID: 80
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein eS4ABC [auth S4]260Saccharomyces cerevisiaeMutation(s): 0 
UniProt
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