7MPI

Stm1 bound vacant 80S structure isolated from cbf5-D95A

  • Classification: RIBOSOME
  • Organism(s): Saccharomyces cerevisiae
  • Mutation(s): No 

  • Deposited: 2021-05-04 Released: 2022-05-11 
  • Deposition Author(s): Rai, J., Zhao, Y., Li, H.
  • Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.05 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

CryoEM structures of pseudouridine-free ribosome suggest impacts of chemical modifications on ribosome conformations.

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

(2022) Structure 

  • DOI: 10.1016/j.str.2022.04.002
  • Primary Citation of Related Structures:  
    7MPI, 7MPJ, 7N8B

  • PubMed Abstract: 
  • Pseudouridine, the most abundant form of RNA modification, is known to play important roles in ribosome function. Mutations in human DKC1, the pseudouridine synthase responsible for catalyzing the ribosome RNA modification, cause translation deficiencies and are associated with a complex cancer predisposition ...

    Pseudouridine, the most abundant form of RNA modification, is known to play important roles in ribosome function. Mutations in human DKC1, the pseudouridine synthase responsible for catalyzing the ribosome RNA modification, cause translation deficiencies and are associated with a complex cancer predisposition. The structural basis for how pseudouridine impacts ribosome function remains uncharacterized. Here, we characterized structures and conformations of a fully modified and a pseudouridine-free ribosome from Saccharomyces cerevisiae in the absence of ligands or when bound with translocation inhibitor cycloheximide by electron cryomicroscopy. In the modified ribosome, the rearranged N1 atom of pseudouridine is observed to stabilize key functional motifs by establishing predominately water-mediated close contacts with the phosphate backbone. The pseudouridine-free ribosome, however, is devoid of such interactions and displays conformations reflective of abnormal inter-subunit movements. The erroneous motions of the pseudouridine-free ribosome may explain its observed deficiencies in translation.


    Organizational Affiliation

    Institute of Molecular Biophysics, Florida State University, Tallahassee, FL 32306, USA; Department of Chemistry and Biochemistry, Florida State University, Tallahassee, FL 32306, USA. Electronic address: hong.li@fsu.edu.



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Entity ID: 1
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40S ribosomal protein S0-AA [auth BA]206Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S1-AB [auth BB]214Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S2C [auth BC]217Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S3D [auth BD]223Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S4-AE [auth BE]260Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S5F [auth BF]206Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S6-AG [auth BG]226Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S7-AH [auth BH]184Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S8-AI [auth BI]188Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S9-AJ [auth BJ]185Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S10-AK [auth BK]96Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S11-AL [auth BL]155Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S12M [auth BM]121Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S13N [auth BN]150Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S14-AO [auth BO]127Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S15P [auth BP]124Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S16-AQ [auth BQ]141Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S17-AR [auth BR]121Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S18-AS [auth BS]145Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S19-AT [auth BT]141Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S20U [auth BU]107Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S21-AV [auth BV]87Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S22-AW [auth BW]129Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S23-AX [auth BX]144Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S24-AY [auth BY]134Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S25-AZ [auth BZ]69Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S26-BAA [auth Ba]97Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S27-ABA [auth Bb]81Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S28-ACA [auth Bc]63Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S29-ADA [auth Bd]53Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S30-AEA [auth Be]60Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S31FA [auth Bf]57Saccharomyces cerevisiaeMutation(s): 0 
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Guanine nucleotide-binding protein subunit beta-like proteinGA [auth Bg]312Saccharomyces cerevisiaeMutation(s): 0 
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Suppressor protein STM1HA [auth Bh]89Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L2-AMA [auth AA]247Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L3NA [auth AB]386Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L4-AOA [auth AC]361Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L5PA [auth AD]292Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L6-AQA [auth AE]156Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L7-ARA [auth AF]222Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L8-ASA [auth AG]230Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L9-ATA [auth AH]190Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L10UA [auth AI]205Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L11-AVA [auth AJ]169Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L13-AWA [auth AL]193Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 50
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60S ribosomal protein L14-AXA [auth AM]136Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 51
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60S ribosomal protein L15-AYA [auth AN]203Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 52
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60S ribosomal protein L16-AZA [auth AO]197Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 53
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60S ribosomal protein L17-AAB [auth AP]175Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 54
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60S ribosomal protein L18-ABB [auth AQ]185Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 55
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60S ribosomal protein L19-ACB [auth AR]188Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 56
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60S ribosomal protein L20-ADB [auth AS]172Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 57
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60S ribosomal protein L21-AEB [auth AT]159Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 58
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60S ribosomal protein L22-AFB [auth AU]100Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 59
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60S ribosomal protein L23-AGB [auth AV]136Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 60
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60S ribosomal protein L24-AHB [auth AW]63Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 61
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60S ribosomal protein L25IB [auth AX]121Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 62
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60S ribosomal protein L26-AJB [auth AY]126Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 63
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60S ribosomal protein L27-AKB [auth AZ]135Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 64
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60S ribosomal protein L28LB [auth Aa]148Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 65
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60S ribosomal protein L29MB [auth Ab]58Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 66
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60S ribosomal protein L30NB [auth Ac]97Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 67
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60S ribosomal protein L31-AOB [auth Ad]109Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 68
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60S ribosomal protein L32PB [auth Ae]127Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 69
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60S ribosomal protein L33-AQB [auth Af]106Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 70
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60S ribosomal protein L34-ARB [auth Ag]112Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 71
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60S ribosomal protein L35-ASB [auth Ah]119Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 72
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60S ribosomal protein L36-ATB [auth Ai]99Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 73
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60S ribosomal protein L37-AUB [auth Aj]87Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 74
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60S ribosomal protein L38VB [auth Ak]77Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 75
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60S ribosomal protein L39WB [auth Al]50Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 76
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60S ribosomal protein L40-AXB [auth Am]52Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 77
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60S ribosomal protein L41-AYB [auth An]25Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 78
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60S ribosomal protein L42-AZB [auth Ao]105Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 79
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60S ribosomal protein L43-AAC [auth Ap]91Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 35
MoleculeChainsLengthOrganismImage
18S rRNAIA [auth B5]1781Saccharomyces cerevisiae
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Entity ID: 36
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25S rRNAJA [auth A1]3137Saccharomyces cerevisiae
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Entity ID: 37
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5s rRNAKA [auth A3]121Saccharomyces cerevisiae
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Entity ID: 38
MoleculeChainsLengthOrganismImage
5.8 S rRNALA [auth A4]158Saccharomyces cerevisiae
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Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

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EC [auth Bb],
EQ [auth Ao]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

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