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:  
    6XIR, 6XIQ

  • 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-A A254Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 2
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RPL3 isoform 1 B387Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: RPL3GI526_G0005401PACBIOSEQ_LOCUS5981PACBIOSEQ_LOCUS5990PACBIOSEQ_LOCUS6038PACBIOSEQ_LOCUS6082PACBIOSEQ_LOCUS6083PACBIOSEQ_LOCUS6136SCNYR20_0002020000SCP684_0003019400
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Entity ID: 3
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RPL4A isoform 1 C362Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: RPL4AGI526_G0000230PACBIOSEQ_LOCUS1017PACBIOSEQ_LOCUS1034PACBIOSEQ_LOCUS1048PACBIOSEQ_LOCUS1050PACBIOSEQ_LOCUS1051PACBIOSEQ_LOCUS1055PACBIOSEQ_LOCUS1068PACBIOSEQ_LOCUS1070
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Entity ID: 4
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RPL5 isoform 1 D297Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: RPL5GI526_G0005877PACBIOSEQ_LOCUS6524PACBIOSEQ_LOCUS6619SCNYR20_0005013100SCP684_0005013400
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Entity ID: 5
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60S ribosomal protein L6-A E176Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 6
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60S ribosomal protein L7-A F244Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 7
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RPL8A isoform 1 G256Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: RPL8AGI526_G0002725
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Entity ID: 8
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RPL9A isoform 1 H191Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: RPL9AGI526_G0002250
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Entity ID: 9
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RPL10 isoform 1 I221Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 10
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RPL11B isoform 1 J174Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 11
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60S ribosomal protein L13-A L199Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 12
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60S ribosomal protein L14-A M138Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 13
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60S ribosomal protein L15-A N204Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 14
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60S ribosomal protein L16-A O199Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 15
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60S ribosomal protein L17-A P184Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 16
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60S ribosomal protein L18-A Q186Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L19-A R189Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L20-A S172Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 19
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60S ribosomal protein L21-A T160Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L22-A U121Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 21
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60S ribosomal protein L23-A V137Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 22
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RPL24A isoform 1 W155Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: RPL24AGI526_G0002369PACBIOSEQ_LOCUS2600PACBIOSEQ_LOCUS2604PACBIOSEQ_LOCUS2654PACBIOSEQ_LOCUS2711PACBIOSEQ_LOCUS2713PACBIOSEQ_LOCUS2851SCNYR20_0003019300SCP684_0002019100
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Entity ID: 23
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60S ribosomal protein L25 X142Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 24
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60S ribosomal protein L26-A Y127Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 25
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60S ribosomal protein L27-A Z136Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 26
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40S ribosomal protein S10-A AA105Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 27
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40S ribosomal protein S11-A AB156Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 31
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RPP0 isoform 1 P0312Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: RPP0GI526_G0004124SCNYR20_0004034200SCP684_0004033800
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Entity ID: 32
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RPL12A isoform 1 P2165Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: 
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Entity ID: 33
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60S ribosomal protein L28 a149Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 34
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RPL29 isoform 1 b59Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: RPL29GI526_G0002104PACBIOSEQ_LOCUS2319PACBIOSEQ_LOCUS2367PACBIOSEQ_LOCUS2371PACBIOSEQ_LOCUS2382PACBIOSEQ_LOCUS2407PACBIOSEQ_LOCUS2410PACBIOSEQ_LOCUS2419PACBIOSEQ_LOCUS2544
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Entity ID: 35
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60S ribosomal protein L30 c105Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 36
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60S ribosomal protein L31-A d113Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 37
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RPL32 isoform 1 e130Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: RPL32GI526_G0000105PACBIOSEQ_LOCUS139PACBIOSEQ_LOCUS146PACBIOSEQ_LOCUS150PACBIOSEQ_LOCUS153PACBIOSEQ_LOCUS154PACBIOSEQ_LOCUS156SCNYR20_0007001300SCP684_0007001200
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Entity ID: 38
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60S ribosomal protein L33-A f107Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 39
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60S ribosomal protein L34-A g121Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 40
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60S ribosomal protein L35-A h120Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L36-A i100Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 42
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60S ribosomal protein L37-A j88Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 43
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RPL38 isoform 1 k78Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 44
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60S ribosomal protein L39 l51Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 45
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60S ribosomal protein L40 m128Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 46
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RPL41A isoform 1 n25Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: RPL41BRPL41AGI526_G0000739GI526_G0000786
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Entity ID: 47
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60S ribosomal protein L42-A o106Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 48
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60S ribosomal protein L43-A p92Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 50
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40S ribosomal protein S0-A q252Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 51
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RPS1A isoform 1 r255Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: RPS1AGI526_G0004228PACBIOSEQ_LOCUS4451PACBIOSEQ_LOCUS4654PACBIOSEQ_LOCUS4699PACBIOSEQ_LOCUS4731PACBIOSEQ_LOCUS4749PACBIOSEQ_LOCUS4761PACBIOSEQ_LOCUS4795PACBIOSEQ_LOCUS4811
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Entity ID: 52
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RPS2 isoform 1 s254Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: RPS2GI526_G0002273PACBIOSEQ_LOCUS2491PACBIOSEQ_LOCUS2499PACBIOSEQ_LOCUS2608PACBIOSEQ_LOCUS2736SCNYR20_0003011900SCP684_0002011800
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Entity ID: 53
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RPS3 isoform 1 t240Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: RPS3GI526_G0004897PACBIOSEQ_LOCUS5476PACBIOSEQ_LOCUS5531SCNYR20_0008013800SCP684_0008013400
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Entity ID: 54
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40S ribosomal protein S4-A u261Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 55
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Rps5p v225Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 56
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40S ribosomal protein S6-A w236Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 57
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40S ribosomal protein S7-A x190Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 58
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RPS8A isoform 1 y200Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: 
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Entity ID: 59
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40S ribosomal protein S9-A z197Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 60
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40S ribosomal protein S13 AD151Saccharomyces cerevisiaeMutation(s): 0 
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-B AE138Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 62
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RPS15 isoform 1 AF142Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: 
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Entity ID: 63
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40S ribosomal protein S16-A AG143Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 64
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40S ribosomal protein S17-B AH136Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 65
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40S ribosomal protein S18-A AI146Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 66
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40S ribosomal protein S19-A AJ144Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 67
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RPS20 isoform 1 AK121Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: 
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Entity ID: 68
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40S ribosomal protein S21-A AL87Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 69
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RPS22A isoform 1 AM130Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: 
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Entity ID: 70
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40S ribosomal protein S23-A AN145Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 71
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40S ribosomal protein S24-A AO135Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 72
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RPS25A isoform 1 AP108Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: 
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Entity ID: 73
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RPS26B isoform 1 AQ119Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: RPS26BGI526_G0001921PACBIOSEQ_LOCUS2106PACBIOSEQ_LOCUS2126PACBIOSEQ_LOCUS2145PACBIOSEQ_LOCUS2158PACBIOSEQ_LOCUS2172PACBIOSEQ_LOCUS2175PACBIOSEQ_LOCUS2188PACBIOSEQ_LOCUS2325
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Entity ID: 74
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40S ribosomal protein S27-A AR82Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 75
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RPS28A isoform 1 AS67Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: RPS28AGI526_G0005503SCNYR20_0002029200SCP684_0003028600
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Entity ID: 76
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RPS29A isoform 1 AT56Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: RPS29AGI526_G0004174PACBIOSEQ_LOCUS4394PACBIOSEQ_LOCUS4597PACBIOSEQ_LOCUS4643PACBIOSEQ_LOCUS4693PACBIOSEQ_LOCUS4707PACBIOSEQ_LOCUS4733
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Entity ID: 77
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40S ribosomal protein S30-A AU63Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 78
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Guanine nucleotide-binding protein subunit beta-like protein AV319Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 81
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RPL1A isoform 1 L1217Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: 
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Entity ID: 28
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35S ribosomal RNA13395Saccharomyces cerevisiae
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Entity ID: 29
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5S ribosomal RNA3121Saccharomyces cerevisiae
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Entity ID: 30
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5.8S ribosomal RNA4158Saccharomyces cerevisiae
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Entity ID: 49
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18S ribosomal RNA21800Saccharomyces cerevisiae
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Entity ID: 79
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Transfer RNAAX, AZ76Saccharomyces cerevisiae
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  • Entity ID: 80
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    mRNAAY8Saccharomyces cerevisiae
    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