6XIR

Cryo-EM Structure of K63 Ubiquitinated Yeast Translocating Ribosome under Oxidative Stress


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.20 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

Re-refinement Note

A newer entry is available that reflects an alternative modeling of the original data: 6XIQ


Literature

Structural impact of K63 ubiquitin on yeast translocating ribosomes under oxidative stress.

Zhou, Y.Kastritis, P.L.Dougherty, S.E.Bouvette, J.Hsu, A.L.Burbaum, L.Mosalaganti, S.Pfeffer, S.Hagen, W.J.H.Forster, F.Borgnia, M.J.Vogel, C.Beck, M.Bartesaghi, A.Silva, G.M.

(2020) Proc Natl Acad Sci U S A 117: 22157-22166

  • DOI: https://doi.org/10.1073/pnas.2005301117
  • Primary Citation of Related Structures:  
    6XIQ, 6XIR

  • PubMed Abstract: 

    Subpopulations of ribosomes are responsible for fine tuning the control of protein synthesis in dynamic environments. K63 ubiquitination of ribosomes has emerged as a new posttranslational modification that regulates protein synthesis during cellular response to oxidative stress. K63 ubiquitin, a type of ubiquitin chain that functions independently of the proteasome, modifies several sites at the surface of the ribosome, however, we lack a molecular understanding on how this modification affects ribosome structure and function. Using cryoelectron microscopy (cryo-EM), we resolved the first three-dimensional (3D) structures of K63 ubiquitinated ribosomes from oxidatively stressed yeast cells at 3.5-3.2 Å resolution. We found that K63 ubiquitinated ribosomes are also present in a polysome arrangement, similar to that observed in yeast polysomes, which we determined using cryoelectron tomography (cryo-ET). We further showed that K63 ubiquitinated ribosomes are captured uniquely at the rotated pretranslocation stage of translation elongation. In contrast, cryo-EM structures of ribosomes from mutant cells lacking K63 ubiquitin resolved at 4.4-2.7 Å showed 80S ribosomes represented in multiple states of translation, suggesting that K63 ubiquitin regulates protein synthesis at a selective stage of elongation. Among the observed structural changes, ubiquitin mediates the destabilization of proteins in the 60S P-stalk and in the 40S beak, two binding regions of the eukaryotic elongation factor eEF2. These changes would impact eEF2 function, thus, inhibiting translocation. Our findings help uncover the molecular effects of K63 ubiquitination on ribosomes, providing a model of translation control during oxidative stress, which supports elongation halt at pretranslocation.


  • Organizational Affiliation

    Department of Computer Science, Duke University, Durham, NC 27708.


Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L2-A254Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
RPL3 isoform 1387Saccharomyces cerevisiaeMutation(s): 0 
UniProt
Find proteins for A0A6A5Q627 (Saccharomyces cerevisiae)
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
RPL4A isoform 1362Saccharomyces cerevisiaeMutation(s): 0 
UniProt
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
RPL5 isoform 1297Saccharomyces cerevisiaeMutation(s): 0 
UniProt
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L6-A176Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L7-A244Saccharomyces cerevisiaeMutation(s): 0 
UniProt
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
RPL8A isoform 1256Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
RPL9A isoform 1191Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
RPL10 isoform 1221Saccharomyces cerevisiaeMutation(s): 0 
UniProt
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
RPL11B isoform 1174Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L13-AK [auth L]199Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L14-AL [auth M]138Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L15-AM [auth N]204Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L16-AN [auth O]199Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L17-AO [auth P]184Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L18-AP [auth Q]186Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L19-AQ [auth R]189Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L20-AR [auth S]172Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L21-AS [auth T]160Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L22-AT [auth U]121Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L23-AU [auth V]137Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
RPL24A isoform 1V [auth W]155Saccharomyces cerevisiaeMutation(s): 0 
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Find proteins for A0A6A5PY83 (Saccharomyces cerevisiae)
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Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L25W [auth X]142Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L26-AX [auth Y]127Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L27-AY [auth Z]136Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 26
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S10-AZ [auth AA]105Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 27
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S11-AAA [auth AB]156Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 31
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L28EA [auth a]149Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 32
MoleculeChains Sequence LengthOrganismDetailsImage
RPL29 isoform 1FA [auth b]59Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 33
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L30GA [auth c]105Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 34
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L31-AHA [auth d]113Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 35
MoleculeChains Sequence LengthOrganismDetailsImage
RPL32 isoform 1IA [auth e]130Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 36
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L33-AJA [auth f]107Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 37
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L34-AKA [auth g]121Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 38
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L35-ALA [auth h]120Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 39
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L36-AMA [auth i]100Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 40
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L37-ANA [auth j]88Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 41
MoleculeChains Sequence LengthOrganismDetailsImage
RPL38 isoform 1OA [auth k]78Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 42
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L39PA [auth l]51Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 43
MoleculeChains Sequence LengthOrganismDetailsImage
RPL41A isoform 1QA [auth n]25Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 44
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L42-ARA [auth o]106Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 45
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L43-ASA [auth p]92Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 47
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S0-AUA [auth q]252Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 48
MoleculeChains Sequence LengthOrganismDetailsImage
RPS1A isoform 1VA [auth r]255Saccharomyces cerevisiaeMutation(s): 0 
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Find proteins for A0A6A5PRY4 (Saccharomyces cerevisiae)
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Entity ID: 49
MoleculeChains Sequence LengthOrganismDetailsImage
RPS2 isoform 1WA [auth s]254Saccharomyces cerevisiaeMutation(s): 0 
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UniProt GroupA0A6A5PWF7
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Entity ID: 50
MoleculeChains Sequence LengthOrganismDetailsImage
RPS3 isoform 1XA [auth t]240Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 51
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S4-AYA [auth u]261Saccharomyces cerevisiaeMutation(s): 0 
UniProt
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Entity ID: 52
MoleculeChains Sequence LengthOrganismDetailsImage
Rps5pZA [auth v]225Saccharomyces cerevisiaeMutation(s): 0 
UniProt
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Entity ID: 53
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S6-AAB [auth w]236Saccharomyces cerevisiaeMutation(s): 0 
UniProt
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Entity ID: 54
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S7-ABB [auth x]190Saccharomyces cerevisiaeMutation(s): 0 
UniProt
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Entity ID: 55
MoleculeChains Sequence LengthOrganismDetailsImage
RPS8A isoform 1CB [auth y]200Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 56
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S9-ADB [auth z]197Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 57
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S13EB [auth AD]151Saccharomyces cerevisiaeMutation(s): 0 
UniProt
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Entity ID: 58
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S14-BFB [auth AE]138Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 59
MoleculeChains Sequence LengthOrganismDetailsImage
RPS15 isoform 1GB [auth AF]142Saccharomyces cerevisiaeMutation(s): 0 
UniProt
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UniProt GroupA0A6A5Q6F2
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Entity ID: 60
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S16-AHB [auth AG]143Saccharomyces cerevisiaeMutation(s): 0 
UniProt
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Entity ID: 61
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S17-BIB [auth AH]136Saccharomyces cerevisiaeMutation(s): 0 
UniProt
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Entity ID: 62
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S18-AJB [auth AI]146Saccharomyces cerevisiaeMutation(s): 0 
UniProt
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Entity ID: 63
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S19-AKB [auth AJ]144Saccharomyces cerevisiaeMutation(s): 0 
UniProt
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Entity ID: 64
MoleculeChains Sequence LengthOrganismDetailsImage
RPS20 isoform 1LB [auth AK]121Saccharomyces cerevisiaeMutation(s): 0 
UniProt
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UniProt GroupA0A6A5PVE9
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Entity ID: 65
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S21-AMB [auth AL]87Saccharomyces cerevisiaeMutation(s): 0 
UniProt
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Entity ID: 66
MoleculeChains Sequence LengthOrganismDetailsImage
RPS22A isoform 1NB [auth AM]130Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 67
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S23-AOB [auth AN]145Saccharomyces cerevisiaeMutation(s): 0 
UniProt
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Entity ID: 68
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S24-APB [auth AO]135Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 69
MoleculeChains Sequence LengthOrganismDetailsImage
RPS25A isoform 1QB [auth AP]108Saccharomyces cerevisiaeMutation(s): 0 
UniProt
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UniProt GroupA0A6A5PZ18
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Entity ID: 70
MoleculeChains Sequence LengthOrganismDetailsImage
RPS26B isoform 1RB [auth AQ]119Saccharomyces cerevisiaeMutation(s): 0 
UniProt
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UniProt GroupA0A6A5Q0E8
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Entity ID: 71
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S27-ASB [auth AR]82Saccharomyces cerevisiaeMutation(s): 0 
UniProt
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Entity ID: 72
MoleculeChains Sequence LengthOrganismDetailsImage
RPS28A isoform 1TB [auth AS]67Saccharomyces cerevisiaeMutation(s): 0 
UniProt
Find proteins for A0A6A5Q700 (Saccharomyces cerevisiae)
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UniProt GroupA0A6A5Q700
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Entity ID: 73
MoleculeChains Sequence LengthOrganismDetailsImage
RPS29A isoform 1UB [auth AT]56Saccharomyces cerevisiaeMutation(s): 0 
UniProt
Find proteins for A0A6A5PV92 (Saccharomyces cerevisiae)
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UniProt GroupA0A6A5PV92
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Entity ID: 74
MoleculeChains Sequence LengthOrganismDetailsImage
Guanine nucleotide-binding protein subunit beta-like proteinVB [auth AV]319Saccharomyces cerevisiaeMutation(s): 0 
UniProt
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UniProt GroupP38011
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Entity ID: 28
MoleculeChains LengthOrganismImage
35S ribosomal RNABA [auth 1]3,395Saccharomyces cerevisiae
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Entity ID: 29
MoleculeChains LengthOrganismImage
5S ribosomal RNACA [auth 3]121Saccharomyces cerevisiae
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Entity ID: 30
MoleculeChains LengthOrganismImage
5.8S ribosomal RNADA [auth 4]158Saccharomyces cerevisiae
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