8EUB

Hypopseudouridylated yeast 80S bound with Taura syndrome virus (TSV) internal ribosome entry site (IRES), eEF2 and GDP, Structure I


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.52 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


Literature

Regulation of translation by ribosomal RNA pseudouridylation.

Zhao, Y.Rai, J.Li, H.

(2023) Sci Adv 9: eadg8190-eadg8190

  • DOI: https://doi.org/10.1126/sciadv.adg8190
  • Primary Citation of Related Structures:  
    8EUB, 8EVP, 8EVQ, 8EVR, 8EVS, 8EVT, 8EWB, 8EWC

  • PubMed Abstract: 

    Pseudouridine is enriched in ribosomal, spliceosomal, transfer, and messenger RNA and thus integral to the central dogma. The chemical basis for how pseudouridine affects the molecular apparatus such as ribosome, however, remains elusive owing to the lack of structures without this natural modification. Here, we studied the translation of a hypopseudouridylated ribosome initiated by the internal ribosome entry site (IRES) elements. We analyzed eight cryo-electron microscopy structures of the ribosome bound with the Taura syndrome virus IRES in multiple functional states. We found widespread loss of pseudouridine-mediated interactions through water and long-range base pairings. In the presence of the translocase, eukaryotic elongation factor 2, and guanosine 5'-triphosphate hydrolysis, the hypopseudouridylated ribosome favors a rare unconducive conformation for decoding that is partially recouped in the ribosome population that remains modified at the P-site uridine. The structural principles learned establish the link between functional defects and modification loss and are likely applicable to other pseudouridine-associated processes.


  • Organizational Affiliation

    Institute of Molecular Biophysics, Florida State University, Tallahassee, FL 32306, USA.


Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S0-AA [auth BA]252Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
RPS1A isoform 1B [auth BB]255Saccharomyces cerevisiaeMutation(s): 0 
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Find proteins for A0A6A5PRY4 (Saccharomyces cerevisiae)
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
RPS2 isoform 1C [auth BC]254Saccharomyces cerevisiaeMutation(s): 0 
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Find proteins for A0A6A5PWF7 (Saccharomyces cerevisiae)
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S4-AD [auth BE]261Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S6-AE [auth BG]236Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S7-AF [auth BH]190Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S8-AG [auth BI]200Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S9-AH [auth BJ]197Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S11-AI [auth BL]156Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S13J [auth BN]151Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S14-AK [auth BO]137Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S21-AL [auth BV]87Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
RPS22A isoform 1M [auth BW]130Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S23-AN [auth BX]145Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S24-AO [auth BY]135Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
RPS26B isoform 1P [auth Ba]119Saccharomyces cerevisiaeMutation(s): 0 
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Find proteins for A0A6A5Q0E8 (Saccharomyces cerevisiae)
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S27-AQ [auth Bb]82Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S30-AR [auth Be]63Saccharomyces cerevisiaeMutation(s): 0 
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Find proteins for P0CX33 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
RPS3 isoform 1S [auth BD]240Saccharomyces cerevisiaeMutation(s): 0 
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Find proteins for A0A6A5Q3Q1 (Saccharomyces cerevisiae)
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
Rps5pT [auth BF]225Saccharomyces cerevisiaeMutation(s): 0 
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Find proteins for A0A1L4AA68 (Saccharomyces cerevisiae)
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S10-AU [auth BK]105Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
RPS15 isoform 1V [auth BP]142Saccharomyces cerevisiaeMutation(s): 0 
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Find proteins for A0A6A5Q6F2 (Saccharomyces cerevisiae)
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Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S16-AW [auth BQ]143Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S17-AX [auth BR]136Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S18-AY [auth BS]146Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 26
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S19-AZ [auth BT]144Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 27
MoleculeChains Sequence LengthOrganismDetailsImage
RPS20 isoform 1AA [auth BU]121Saccharomyces cerevisiaeMutation(s): 0 
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Find proteins for A0A6A5PVE9 (Saccharomyces cerevisiae)
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Entity ID: 28
MoleculeChains Sequence LengthOrganismDetailsImage
RPS25A isoform 1BA [auth BZ]108Saccharomyces cerevisiaeMutation(s): 0 
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Find proteins for A0A6A5PZ18 (Saccharomyces cerevisiae)
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Entity ID: 29
MoleculeChains Sequence LengthOrganismDetailsImage
RPS28A isoform 1CA [auth Bc]67Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 30
MoleculeChains Sequence LengthOrganismDetailsImage
RPS29A isoform 1DA [auth Bd]56Saccharomyces cerevisiaeMutation(s): 0 
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Find proteins for A0A6A5PV92 (Saccharomyces cerevisiae)
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Entity ID: 31
MoleculeChains Sequence LengthOrganismDetailsImage
Guanine nucleotide-binding protein subunit beta-like proteinEA [auth Bg]319Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 33
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L2-AGA [auth AA]254Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 34
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L3HA [auth AB]387Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 35
MoleculeChains Sequence LengthOrganismDetailsImage
RPL4A isoform 1IA [auth AC]362Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 39
MoleculeChains Sequence LengthOrganismDetailsImage
RPL5 isoform 1MA [auth AD]297Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 40
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L6-ANA [auth AE]176Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 41
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L7-AOA [auth AF]244Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 42
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L8-APA [auth AG]256Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 43
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L9-AQA [auth AH]191Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 44
MoleculeChains Sequence LengthOrganismDetailsImage
RPL10 isoform 1RA [auth AI]221Saccharomyces cerevisiaeMutation(s): 0 
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Find proteins for A0A6A5PUZ5 (Saccharomyces cerevisiae)
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Entity ID: 45
MoleculeChains Sequence LengthOrganismDetailsImage
RPL11A isoform 1SA [auth AJ]174Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 46
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L13-ATA [auth AL]199Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 47
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L14-AUA [auth AM]138Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 48
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L15-AVA [auth AN]204Saccharomyces cerevisiaeMutation(s): 0 
UniProt
Find proteins for P05748 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 49
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L16-AWA [auth AO]199Saccharomyces cerevisiaeMutation(s): 0 
UniProt
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Entity ID: 50
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L17-AXA [auth AP]184Saccharomyces cerevisiaeMutation(s): 0 
UniProt
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Entity ID: 51
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L18-AYA [auth AQ]186Saccharomyces cerevisiaeMutation(s): 0 
UniProt
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Entity ID: 52
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L19-AZA [auth AR]189Saccharomyces cerevisiaeMutation(s): 0 
UniProt
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Entity ID: 53
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L20AB [auth AS]178Saccharomyces cerevisiaeMutation(s): 0 
UniProt
Find proteins for B3LMD0 (Saccharomyces cerevisiae (strain RM11-1a))
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Entity ID: 54
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L21-ABB [auth AT]160Saccharomyces cerevisiaeMutation(s): 0 
UniProt
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Entity ID: 55
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L22-ACB [auth AU]121Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 56
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L23-ADB [auth AV]137Saccharomyces cerevisiaeMutation(s): 0 
UniProt
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Entity ID: 57
MoleculeChains Sequence LengthOrganismDetailsImage
RPL24A isoform 1EB [auth AW]155Saccharomyces cerevisiaeMutation(s): 0 
UniProt
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Entity ID: 58
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L25FB [auth AX]142Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 59
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L26-AGB [auth AY]127Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 60
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L27-AHB [auth AZ]136Saccharomyces cerevisiaeMutation(s): 0 
UniProt
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Entity ID: 61
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L28IB [auth Aa]149Saccharomyces cerevisiaeMutation(s): 0 
UniProt
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Entity ID: 62
MoleculeChains Sequence LengthOrganismDetailsImage
RPL29 isoform 1JB [auth Ab]59Saccharomyces cerevisiaeMutation(s): 0 
UniProt
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Entity ID: 63
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L30KB [auth Ac]105Saccharomyces cerevisiaeMutation(s): 0 
UniProt
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Entity ID: 64
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L31-ALB [auth Ad]113Saccharomyces cerevisiaeMutation(s): 0 
UniProt
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Entity ID: 65
MoleculeChains Sequence LengthOrganismDetailsImage
RPL32 isoform 1MB [auth Ae]130Saccharomyces cerevisiaeMutation(s): 0 
UniProt
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Entity ID: 66
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L33-ANB [auth Af]107Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 67
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L34-AOB [auth Ag]121Saccharomyces cerevisiaeMutation(s): 0 
UniProt
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Entity ID: 68
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L35-APB [auth Ah]120Saccharomyces cerevisiaeMutation(s): 0 
UniProt
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Entity ID: 69
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L36-AQB [auth Ai]100Saccharomyces cerevisiaeMutation(s): 0 
UniProt
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Entity ID: 70
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L37-ARB [auth Aj]88Saccharomyces cerevisiaeMutation(s): 0 
UniProt
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Entity ID: 71
MoleculeChains Sequence LengthOrganismDetailsImage
RPL38 isoform 1SB [auth Ak]78Saccharomyces cerevisiaeMutation(s): 0 
UniProt
Find proteins for A0A6A5PUL8 (Saccharomyces cerevisiae)
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Entity ID: 72
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L39TB [auth Al]51Saccharomyces cerevisiaeMutation(s): 0 
UniProt
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Entity ID: 73
MoleculeChains Sequence LengthOrganismDetailsImage
Ubiquitin-60S ribosomal protein L40UB [auth Am]128Saccharomyces cerevisiaeMutation(s): 0 
UniProt
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Entity ID: 74
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L41-AVB [auth An]25Saccharomyces cerevisiaeMutation(s): 0 
UniProt
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Entity ID: 75
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L42-AWB [auth Ao]106Saccharomyces cerevisiaeMutation(s): 0 
UniProt
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Entity ID: 76
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L43-AXB [auth Ap]92Saccharomyces cerevisiaeMutation(s): 0 
UniProt
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Entity ID: 77
MoleculeChains Sequence LengthOrganismDetailsImage
RPL1A isoform 1YB [auth E]217Saccharomyces cerevisiaeMutation(s): 0 
UniProt
Find proteins for A0A6A5Q2N7 (Saccharomyces cerevisiae)
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Entity ID: 79
MoleculeChains Sequence LengthOrganismDetailsImage
Elongation factor 2AC [auth DC]842Saccharomyces cerevisiaeMutation(s): 0 
UniProt
Find proteins for P32324 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 80
MoleculeChains </