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


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 ...

    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: RPL3GI526_G0005401PACBIOSEQ_LOCUS5981PACBIOSEQ_LOCUS5990PACBIOSEQ_LOCUS6038PACBIOSEQ_LOCUS6082PACBIOSEQ_LOCUS6083PACBIOSEQ_LOCUS6136
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Entity ID: 3
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RPL4A isoform 1C362Saccharomyces 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 1D297Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: RPL5GI526_G0005877PACBIOSEQ_LOCUS6524PACBIOSEQ_LOCUS6619
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Entity ID: 5
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60S ribosomal protein L6-AE176Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 6
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60S ribosomal protein L7-AF244Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 7
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RPL8A isoform 1G256Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: RPL8AGI526_G0002725
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Entity ID: 8
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RPL9A isoform 1H191Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: RPL9AGI526_G0002250
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Entity ID: 9
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RPL10 isoform 1I221Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: RPL10GI526_G0003868PACBIOSEQ_LOCUS4030PACBIOSEQ_LOCUS4248PACBIOSEQ_LOCUS4289PACBIOSEQ_LOCUS4296PACBIOSEQ_LOCUS4333PACBIOSEQ_LOCUS4341PACBIOSEQ_LOCUS4373PACBIOSEQ_LOCUS4381
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Entity ID: 10
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RPL11B isoform 1J174Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: RPL11BGI526_G0002491PACBIOSEQ_LOCUS2720PACBIOSEQ_LOCUS2726PACBIOSEQ_LOCUS2776PACBIOSEQ_LOCUS2812PACBIOSEQ_LOCUS2830PACBIOSEQ_LOCUS2834PACBIOSEQ_LOCUS2843PACBIOSEQ_LOCUS2974
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Entity ID: 11
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60S ribosomal protein L13-AL199Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 12
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60S ribosomal protein L14-AM138Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 13
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60S ribosomal protein L15-AN204Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L16-AO199Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 15
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60S ribosomal protein L17-AP184Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 16
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60S ribosomal protein L18-AQ186Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 17
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60S ribosomal protein L19-AR189Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 18
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60S ribosomal protein L20-AS172Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 19
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60S ribosomal protein L21-AT160Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 20
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60S ribosomal protein L22-AU121Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 21
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60S ribosomal protein L23-AV137Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 22
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RPL24A isoform 1W155Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: RPL24AGI526_G0002369PACBIOSEQ_LOCUS2600PACBIOSEQ_LOCUS2604PACBIOSEQ_LOCUS2654PACBIOSEQ_LOCUS2711PACBIOSEQ_LOCUS2713PACBIOSEQ_LOCUS2851
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Entity ID: 23
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60S ribosomal protein L25X142Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 24
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60S ribosomal protein L26-AY127Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 25
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60S ribosomal protein L27-AZ136Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 26
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40S ribosomal protein S10-AAA105Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 27
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40S ribosomal protein S11-AAB156Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 31
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60S ribosomal protein L28a149Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 32
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RPL29 isoform 1b59Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: RPL29GI526_G0002104PACBIOSEQ_LOCUS2319PACBIOSEQ_LOCUS2367PACBIOSEQ_LOCUS2371PACBIOSEQ_LOCUS2382PACBIOSEQ_LOCUS2407PACBIOSEQ_LOCUS2410PACBIOSEQ_LOCUS2419PACBIOSEQ_LOCUS2544
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Entity ID: 33
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60S ribosomal protein L30c105Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 34
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60S ribosomal protein L31-Ad113Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 35
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RPL32 isoform 1e130Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: RPL32GI526_G0000105PACBIOSEQ_LOCUS139PACBIOSEQ_LOCUS146PACBIOSEQ_LOCUS150PACBIOSEQ_LOCUS153PACBIOSEQ_LOCUS154PACBIOSEQ_LOCUS156
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Entity ID: 36
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60S ribosomal protein L33-Af107Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 37
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60S ribosomal protein L34-Ag121Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 38
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60S ribosomal protein L35-Ah120Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 39
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60S ribosomal protein L36-Ai100Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 40
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60S ribosomal protein L37-Aj88Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 41
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RPL38 isoform 1k78Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: RPL38GI526_G0004106PACBIOSEQ_LOCUS4316PACBIOSEQ_LOCUS4524PACBIOSEQ_LOCUS4570PACBIOSEQ_LOCUS4589PACBIOSEQ_LOCUS4617PACBIOSEQ_LOCUS4630PACBIOSEQ_LOCUS4656PACBIOSEQ_LOCUS4671
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Entity ID: 42
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60S ribosomal protein L39l51Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 43
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RPL41A isoform 1n25Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: RPL41BRPL41AGI526_G0000739GI526_G0000786
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Entity ID: 44
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60S ribosomal protein L42-Ao106Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 45
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60S ribosomal protein L43-Ap92Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S0-Aq252Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 48
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RPS1A isoform 1r255Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: RPS1AGI526_G0004228PACBIOSEQ_LOCUS4451PACBIOSEQ_LOCUS4654PACBIOSEQ_LOCUS4699PACBIOSEQ_LOCUS4731PACBIOSEQ_LOCUS4749PACBIOSEQ_LOCUS4761PACBIOSEQ_LOCUS4795PACBIOSEQ_LOCUS4811
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Entity ID: 49
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RPS2 isoform 1s254Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: RPS2GI526_G0002273PACBIOSEQ_LOCUS2491PACBIOSEQ_LOCUS2499PACBIOSEQ_LOCUS2608PACBIOSEQ_LOCUS2736
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Entity ID: 50
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RPS3 isoform 1t240Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: RPS3GI526_G0004897PACBIOSEQ_LOCUS5476PACBIOSEQ_LOCUS5531
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Entity ID: 51
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40S ribosomal protein S4-Au261Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 52
MoleculeChainsSequence LengthOrganismDetailsImage
Rps5pv225Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: RPS5GI526_G0003357PACBIOSEQ_LOCUS2208PACBIOSEQ_LOCUS3487PACBIOSEQ_LOCUS3669PACBIOSEQ_LOCUS3731PACBIOSEQ_LOCUS3784PACBIOSEQ_LOCUS3808PACBIOSEQ_LOCUS3826
Find proteins for A0A1L4AA68 (Saccharomyces cerevisiae)
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Entity ID: 53
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S6-Aw236Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 54
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S7-Ax190Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 55
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RPS8A isoform 1y200Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: 
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Entity ID: 56
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S9-Az197Saccharomyces cerevisiaeMutation(s): 0 
Find proteins for O13516 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 57
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S13AD151Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 58
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S14-BAE138Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 59
MoleculeChainsSequence LengthOrganismDetailsImage
RPS15 isoform 1AF142Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: RPS15GI526_G0005288PACBIOSEQ_LOCUS5778PACBIOSEQ_LOCUS5861PACBIOSEQ_LOCUS5869PACBIOSEQ_LOCUS5914PACBIOSEQ_LOCUS5919PACBIOSEQ_LOCUS5959PACBIOSEQ_LOCUS5965PACBIOSEQ_LOCUS6011
Find proteins for A0A6A5Q6F2 (Saccharomyces cerevisiae)
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Entity ID: 60
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S16-AAG143Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 61
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S17-BAH136Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 62
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40S ribosomal protein S18-AAI146Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 63
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40S ribosomal protein S19-AAJ144Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 64
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RPS20 isoform 1AK121Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: RPS20GI526_G0002745PACBIOSEQ_LOCUS3008PACBIOSEQ_LOCUS3020PACBIOSEQ_LOCUS3079PACBIOSEQ_LOCUS3122PACBIOSEQ_LOCUS3138PACBIOSEQ_LOCUS3275PACBIOSEQ_LOCUS5098
Find proteins for A0A6A5PVE9 (Saccharomyces cerevisiae)
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Entity ID: 65
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40S ribosomal protein S21-AAL87Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 66
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RPS22A isoform 1AM130Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: RPS22AGI526_G0003042PACBIOSEQ_LOCUS2003PACBIOSEQ_LOCUS3148PACBIOSEQ_LOCUS3328PACBIOSEQ_LOCUS3345PACBIOSEQ_LOCUS3378PACBIOSEQ_LOCUS3455PACBIOSEQ_LOCUS3456PACBIOSEQ_LOCUS3480
Find proteins for A0A6A5PSE9 (Saccharomyces cerevisiae)
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Entity ID: 67
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40S ribosomal protein S23-AAN145Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 68
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S24-AAO135Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 69
MoleculeChainsSequence LengthOrganismDetailsImage
RPS25A isoform 1AP108Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: RPS25AGI526_G0002427PACBIOSEQ_LOCUS2660PACBIOSEQ_LOCUS2662PACBIOSEQ_LOCUS2709PACBIOSEQ_LOCUS2749PACBIOSEQ_LOCUS2770PACBIOSEQ_LOCUS2781PACBIOSEQ_LOCUS2910
Find proteins for A0A6A5PZ18 (Saccharomyces cerevisiae)
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Entity ID: 70
MoleculeChainsSequence LengthOrganismDetailsImage
RPS26B isoform 1AQ119Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: RPS26BGI526_G0001921PACBIOSEQ_LOCUS2106PACBIOSEQ_LOCUS2126PACBIOSEQ_LOCUS2145PACBIOSEQ_LOCUS2158PACBIOSEQ_LOCUS2172PACBIOSEQ_LOCUS2175PACBIOSEQ_LOCUS2188PACBIOSEQ_LOCUS2325
Find proteins for A0A6A5Q0E8 (Saccharomyces cerevisiae)
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Entity ID: 71
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S27-AAR82Saccharomyces cerevisiaeMutation(s): 0 
Find proteins for P35997 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 72
MoleculeChainsSequence LengthOrganismDetailsImage
RPS28A isoform 1AS67Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: RPS28AGI526_G0005503
Find proteins for A0A6A5Q700 (Saccharomyces cerevisiae)
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Entity ID: 73
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RPS29A isoform 1AT56Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: RPS29AGI526_G0004174PACBIOSEQ_LOCUS4394PACBIOSEQ_LOCUS4597PACBIOSEQ_LOCUS4643PACBIOSEQ_LOCUS4693PACBIOSEQ_LOCUS4707PACBIOSEQ_LOCUS4733
Find proteins for A0A6A5PV92 (Saccharomyces cerevisiae)
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Entity ID: 74
MoleculeChainsSequence LengthOrganismDetailsImage
Guanine nucleotide-binding protein subunit beta-like proteinAV319Saccharomyces cerevisiaeMutation(s): 0 
Find proteins for P38011 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 28
MoleculeChainsLengthOrganismImage
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
MoleculeChainsLengthOrganismImage
5.8S ribosomal RNA4158Saccharomyces cerevisiae
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Entity ID: 46
MoleculeChainsLengthOrganismImage
18S ribosomal RNA21800Saccharomyces cerevisiae
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Entity ID: 75
MoleculeChainsLengthOrganismImage
Transfer RNAAX, AZ76Saccharomyces cerevisiae
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download CCD File 
AQ, AR, AT, j, o, p
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.20 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 

  • 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