6XIQ

Cryo-EM Structure of K63R Ubiquitin Mutant Ribosome under Oxidative Stress


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.20 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

This entry reflects an alternative modeling of the original data in: 6XIR


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: 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 ...

    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 Biology, Duke University, Durham, NC 27708; panagiotis.kastritis@bct.uni-halle.de alberto.bartesaghi@duke.edu gustavo.silva@duke.edu.



Macromolecules

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L2-AA254Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 2
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RPL3 isoform 1B387Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: PACBIOSEQ_LOCUS5453PACBIOSEQ_LOCUS5466PACBIOSEQ_LOCUS5486PACBIOSEQ_LOCUS5554SCNYR20_0002020000SCP684_0003019400
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Entity ID: 3
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RPL4A isoform 1C362Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: PACBIOSEQ_LOCUS939PACBIOSEQ_LOCUS943PACBIOSEQ_LOCUS945PACBIOSEQ_LOCUS955PACBIOSEQ_LOCUS957
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Entity ID: 4
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RPL5 isoform 1D297Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: PACBIOSEQ_LOCUS5940PACBIOSEQ_LOCUS6041SCNYR20_0005013100SCP684_0005013400
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60S ribosomal protein L6-AE176Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L7-AF244Saccharomyces cerevisiaeMutation(s): 0 
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RPL8A isoform 1G256Saccharomyces cerevisiaeMutation(s): 0 
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RPL9A isoform 1H191Saccharomyces cerevisiaeMutation(s): 0 
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RPL10 isoform 1I221Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: PACBIOSEQ_LOCUS3897PACBIOSEQ_LOCUS3913PACBIOSEQ_LOCUS3932PACBIOSEQ_LOCUS3933PACBIOSEQ_LOCUS3954PACBIOSEQ_LOCUS3996SCNYR20_0004012300SCP684_0004012000
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RPL11B isoform 1J174Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: PACBIOSEQ_LOCUS2481PACBIOSEQ_LOCUS2510PACBIOSEQ_LOCUS2511PACBIOSEQ_LOCUS2535PACBIOSEQ_LOCUS2550PACBIOSEQ_LOCUS2552SCNYR20_0003029600
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60S ribosomal protein L13-AK [auth L]199Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L14-AL [auth M]138Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L15-AM [auth N]204Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L16-AN [auth O]199Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L17-AO [auth P]184Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L18-AP [auth Q]186Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L19-AQ [auth R]189Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L20-AR [auth S]172Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L21-AS [auth T]160Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L22-AT [auth U]121Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L23-AU [auth V]137Saccharomyces cerevisiaeMutation(s): 0 
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RPL24A isoform 1V [auth W]155Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: PACBIOSEQ_LOCUS2370PACBIOSEQ_LOCUS2397PACBIOSEQ_LOCUS2399PACBIOSEQ_LOCUS2436PACBIOSEQ_LOCUS2444SCNYR20_0003019300SCP684_0002019100
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60S ribosomal protein L25W [auth X]142Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L26-AX [auth Y]127Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L27-AY [auth Z]136Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S10-AZ [auth AA]105Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S11-AAA [auth AB]156Saccharomyces cerevisiaeMutation(s): 0 
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RPP0 isoform 1EA [auth P0]312Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: SCNYR20_0004034200SCP684_0004033800
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RPL12A isoform 1FA [auth P2]165Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: PACBIOSEQ_LOCUS1719PACBIOSEQ_LOCUS1723PACBIOSEQ_LOCUS1738PACBIOSEQ_LOCUS1740PACBIOSEQ_LOCUS1760SCNYR20_0001058800SCNYR20_0011002300SCP684_0001058300SCP684_0011001900
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60S ribosomal protein L28GA [auth a]149Saccharomyces cerevisiaeMutation(s): 0 
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RPL29 isoform 1HA [auth b]59Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: PACBIOSEQ_LOCUS2109PACBIOSEQ_LOCUS2125PACBIOSEQ_LOCUS2138PACBIOSEQ_LOCUS2146PACBIOSEQ_LOCUS2153PACBIOSEQ_LOCUS2185
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60S ribosomal protein L30IA [auth c]105Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L31-AJA [auth d]113Saccharomyces cerevisiaeMutation(s): 0 
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RPL32 isoform 1KA [auth e]130Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: PACBIOSEQ_LOCUS123PACBIOSEQ_LOCUS127PACBIOSEQ_LOCUS128PACBIOSEQ_LOCUS132SCNYR20_0007001300SCP684_0007001200
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60S ribosomal protein L33-ALA [auth f]107Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L34-AMA [auth g]121Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L35-ANA [auth h]120Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L36-AOA [auth i]100Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L37-APA [auth j]88Saccharomyces cerevisiaeMutation(s): 0 
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RPL38 isoform 1QA [auth k]78Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: PACBIOSEQ_LOCUS4142PACBIOSEQ_LOCUS4161PACBIOSEQ_LOCUS4177PACBIOSEQ_LOCUS4179PACBIOSEQ_LOCUS4201PACBIOSEQ_LOCUS4249SCNYR20_0004033000SCP684_0004032600
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60S ribosomal protein L39RA [auth l]51Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 45
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60S ribosomal protein L40SA [auth m]128Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 46
MoleculeChainsSequence LengthOrganismDetailsImage
RPL41A isoform 1TA [auth n]25Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 47
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60S ribosomal protein L42-AUA [auth o]106Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 48
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60S ribosomal protein L43-AVA [auth p]92Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 50
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40S ribosomal protein S0-AXA [auth q]252Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 51
MoleculeChainsSequence LengthOrganismDetailsImage
RPS1A isoform 1YA [auth r]255Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: RPS1PACBIOSEQ_LOCUS4264PACBIOSEQ_LOCUS4279PACBIOSEQ_LOCUS4293PACBIOSEQ_LOCUS4298PACBIOSEQ_LOCUS4323PACBIOSEQ_LOCUS4374
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Find proteins for A0A6A5PRY4 (Saccharomyces cerevisiae)
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Entity ID: 52
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RPS2 isoform 1ZA [auth s]254Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: PACBIOSEQ_LOCUS2274PACBIOSEQ_LOCUS2304PACBIOSEQ_LOCUS2329PACBIOSEQ_LOCUS2350SCNYR20_0003011900SCP684_0002011800
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Entity ID: 53
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RPS3 isoform 1AB [auth t]240Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: PACBIOSEQ_LOCUS4952PACBIOSEQ_LOCUS5003PACBIOSEQ_LOCUS5055SCNYR20_0008013800SCP684_0008013400
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Find proteins for A0A6A5Q3Q1 (Saccharomyces cerevisiae)
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Entity ID: 54
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40S ribosomal protein S4-ABB [auth u]261Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 55
MoleculeChainsSequence LengthOrganismDetailsImage
Rps5pCB [auth v]225Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: RPS5PACBIOSEQ_LOCUS3372PACBIOSEQ_LOCUS3390PACBIOSEQ_LOCUS3391PACBIOSEQ_LOCUS3422PACBIOSEQ_LOCUS3460SCNYR20_0009028700SCP684_0009028200
UniProt
Find proteins for A0A1L4AA68 (Saccharomyces cerevisiae)
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Entity ID: 56
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40S ribosomal protein S6-ADB [auth w]236Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 57
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40S ribosomal protein S7-AEB [auth x]190Saccharomyces cerevisiaeMutation(s): 0 
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Find proteins for P26786 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 58
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RPS8A isoform 1FB [auth y]200Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: 
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Entity ID: 59
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40S ribosomal protein S9-AGB [auth z]197Saccharomyces cerevisiaeMutation(s): 0 
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Find proteins for O13516 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 60
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40S ribosomal protein S13HB [auth AD]151Saccharomyces cerevisiaeMutation(s): 0 
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Find proteins for P05756 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 61
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40S ribosomal protein S14-BIB [auth AE]138Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 62
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RPS15 isoform 1JB [auth AF]142Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: PACBIOSEQ_LOCUS5346PACBIOSEQ_LOCUS5348PACBIOSEQ_LOCUS5355PACBIOSEQ_LOCUS5374PACBIOSEQ_LOCUS5401PACBIOSEQ_LOCUS5445SCNYR20_0002011200SCP684_0003010500
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Find proteins for A0A6A5Q6F2 (Saccharomyces cerevisiae)
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Entity ID: 63
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40S ribosomal protein S16-AKB [auth AG]143Saccharomyces cerevisiaeMutation(s): 0 
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Find proteins for P0CX51 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 64
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40S ribosomal protein S17-BLB [auth AH]136Saccharomyces cerevisiaeMutation(s): 0 
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Find proteins for P14127 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 65
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40S ribosomal protein S18-AMB [auth AI]146Saccharomyces cerevisiaeMutation(s): 0 
UniProt
Find proteins for P0CX55 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 66
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40S ribosomal protein S19-ANB [auth AJ]144Saccharomyces cerevisiaeMutation(s): 0 
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Find proteins for P07280 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 67
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RPS20 isoform 1OB [auth AK]121Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: PACBIOSEQ_LOCUS2753PACBIOSEQ_LOCUS2784PACBIOSEQ_LOCUS2788PACBIOSEQ_LOCUS2828PACBIOSEQ_LOCUS2831SCNYR20_0012002900SCP684_0012002900
UniProt
Find proteins for A0A6A5PVE9 (Saccharomyces cerevisiae)
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Entity ID: 68
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40S ribosomal protein S21-APB [auth AL]87Saccharomyces cerevisiaeMutation(s): 0 
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Find proteins for P0C0V8 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 69
MoleculeChainsSequence LengthOrganismDetailsImage
RPS22A isoform 1QB [auth AM]130Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: PACBIOSEQ_LOCUS3047PACBIOSEQ_LOCUS3077PACBIOSEQ_LOCUS3079PACBIOSEQ_LOCUS3119PACBIOSEQ_LOCUS3120PACBIOSEQ_LOCUS3139SCNYR20_0009002300SCP684_0009002400
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Entity ID: 70
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S23-ARB [auth AN]145Saccharomyces cerevisiaeMutation(s): 0 
UniProt
Find proteins for P0CX29 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 71
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40S ribosomal protein S24-ASB [auth AO]135Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 72
MoleculeChainsSequence LengthOrganismDetailsImage
RPS25A isoform 1TB [auth AP]108Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: PACBIOSEQ_LOCUS2424PACBIOSEQ_LOCUS2453PACBIOSEQ_LOCUS2477PACBIOSEQ_LOCUS2490PACBIOSEQ_LOCUS2496SCNYR20_0003024600SCP684_0002024400
UniProt
Find proteins for A0A6A5PZ18 (Saccharomyces cerevisiae)
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Entity ID: 73
MoleculeChainsSequence LengthOrganismDetailsImage
RPS26B isoform 1UB [auth AQ]119Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: PACBIOSEQ_LOCUS1930PACBIOSEQ_LOCUS1934PACBIOSEQ_LOCUS1954PACBIOSEQ_LOCUS1955PACBIOSEQ_LOCUS1957PACBIOSEQ_LOCUS1978
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Find proteins for A0A6A5Q0E8 (Saccharomyces cerevisiae)
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Entity ID: 74
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40S ribosomal protein S27-AVB [auth AR]82Saccharomyces cerevisiaeMutation(s): 0 
UniProt
Find proteins for P35997 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 75
MoleculeChainsSequence LengthOrganismDetailsImage
RPS28A isoform 1WB [auth AS]67Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: SCNYR20_0002029200SCP684_0003028600
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Find proteins for A0A6A5Q700 (Saccharomyces cerevisiae)
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Entity ID: 76
MoleculeChainsSequence LengthOrganismDetailsImage
RPS29A isoform 1XB [auth AT]56Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: PACBIOSEQ_LOCUS4227PACBIOSEQ_LOCUS4242PACBIOSEQ_LOCUS4246PACBIOSEQ_LOCUS4271PACBIOSEQ_LOCUS4319
UniProt
Find proteins for A0A6A5PV92 (Saccharomyces cerevisiae)
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Entity ID: 77
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S30-AYB [auth AU]63Saccharomyces cerevisiaeMutation(s): 0 
UniProt
Find proteins for P0CX33 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 78
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Guanine nucleotide-binding protein subunit beta-like proteinZB [auth AV]319Saccharomyces cerevisiaeMutation(s): 0 
UniProt
Find proteins for P38011 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 81
MoleculeChainsSequence LengthOrganismDetailsImage
RPL1A isoform 1CC [auth L1]217Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: 
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Find proteins for A0A6A5Q2N7 (Saccharomyces cerevisiae)
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Entity ID: 28
MoleculeChainsLengthOrganismImage
35S ribosomal RNABA [auth 1]3395Saccharomyces cerevisiae
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Entity ID: 29
MoleculeChainsLengthOrganismImage
5S ribosomal RNACA [auth 3]121Saccharomyces cerevisiae
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Entity ID: 30
MoleculeChainsLengthOrganismImage
5.8S ribosomal RNADA [auth 4]158Saccharomyces cerevisiae
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Entity ID: 49
MoleculeChainsLengthOrganismImage
18S ribosomal RNAWA [auth 2]1800Saccharomyces cerevisiae
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Entity ID: 79
MoleculeChainsLengthOrganismImage
Transfer RNAAC [auth AX],
DC [auth AZ]
76Saccharomyces cerevisiae
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Entity ID: 80
MoleculeChainsLengthOrganismImage
mRNABC [auth AY]8Saccharomyces cerevisiae
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Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.20 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report




Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of Environmental Health Sciences (NIH/NIEHS)United States5R00ES025835-05

Revision History  (Full details and data files)

  • Version 1.0: 2020-08-26
    Type: Initial release
  • Version 1.1: 2020-09-09
    Changes: Database references
  • Version 1.2: 2020-09-23
    Changes: Database references