6SKF

Cryo-EM Structure of T. kodakarensis 70S ribosome

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.95 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history. 


Literature

Dynamic RNA acetylation revealed by quantitative cross-evolutionary mapping.

Sas-Chen, A., Thomas, J.M., Matzov, D., Taoka, M., Nance, K.D., Nir, R., Bryson, K.M., Shachar, R., Liman, G.L.S., Burkhart, B.W., Gamage, S.T., Nobe, Y., Briney, C.A., Levy, M.J., Fuchs, R.T., Robb, G.B., Hartmann, J., Sharma, S., Lin, Q., Florens, L., Washburn, M.P., Isobe, T., Santangelo, T.J., Shalev-Benami, M., Meier, J.L., Schwartz, S.

(2020) Nature 583: 638-643

  • DOI: https://doi.org/10.1038/s41586-020-2418-2
  • Primary Citation of Related Structures:  
    6SKF, 6SKG, 6TH6

  • PubMed Abstract: 

    • N 4 -acetylcytidine (ac 4 C) is an ancient and highly conserved RNA modification that is present on tRNA and rRNA and has recently been investigated in eukaryotic mRNA 1-3 . However, the distribution, dynamics and functions of cytidine acetylation have yet to be fully elucidated ...

    N 4 -acetylcytidine (ac 4 C) is an ancient and highly conserved RNA modification that is present on tRNA and rRNA and has recently been investigated in eukaryotic mRNA 1-3 . However, the distribution, dynamics and functions of cytidine acetylation have yet to be fully elucidated. Here we report ac 4 C-seq, a chemical genomic method for the transcriptome-wide quantitative mapping of ac 4 C at single-nucleotide resolution. In human and yeast mRNAs, ac 4 C sites are not detected but can be induced-at a conserved sequence motif-via the ectopic overexpression of eukaryotic acetyltransferase complexes. By contrast, cross-evolutionary profiling revealed unprecedented levels of ac 4 C across hundreds of residues in rRNA, tRNA, non-coding RNA and mRNA from hyperthermophilic archaea. Ac 4 C is markedly induced in response to increases in temperature, and acetyltransferase-deficient archaeal strains exhibit temperature-dependent growth defects. Visualization of wild-type and acetyltransferase-deficient archaeal ribosomes by cryo-electron microscopy provided structural insights into the temperature-dependent distribution of ac 4 C and its potential thermoadaptive role. Our studies quantitatively define the ac 4 C landscape, providing a technical and conceptual foundation for elucidating the role of this modification in biology and disease 4-6 .

    Organizational Affiliation: 

    Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel. schwartz@weizmann.ac.il.



Macromolecules

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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S2B [auth Ab]201Thermococcus kodakarensisMutation(s): 0 
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Entity ID: 3
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30S ribosomal protein S3C [auth Ac]209Thermococcus kodakarensisMutation(s): 0 
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Entity ID: 4
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30S ribosomal protein S3AeD [auth Ad]200Thermococcus kodakarensisMutation(s): 0 
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Entity ID: 5
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30S ribosomal protein S4E [auth Ae]180Thermococcus kodakarensisMutation(s): 0 
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Entity ID: 6
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30S ribosomal protein S4eF [auth Af]243Thermococcus kodakarensisMutation(s): 0 
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Entity ID: 7
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30S ribosomal protein S5G [auth Ag]235Thermococcus kodakarensisMutation(s): 0 
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30S ribosomal protein S6eH [auth Ah]125Thermococcus kodakarensisMutation(s): 0 
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30S ribosomal protein S7I [auth Ai]215Thermococcus kodakarensisMutation(s): 0 
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30S ribosomal protein S8J [auth Aj]130Thermococcus kodakarensisMutation(s): 0 
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30S ribosomal protein S8eK [auth Ak]130Thermococcus kodakarensisMutation(s): 0 
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30S ribosomal protein S9L [auth Al]135Thermococcus kodakarensisMutation(s): 0 
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30S ribosomal protein S10M [auth Am]102Thermococcus kodakarensisMutation(s): 0 
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30S ribosomal protein S11N [auth An]140Thermococcus kodakarensisMutation(s): 0 
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30S ribosomal protein S12O [auth Ao]147Thermococcus kodakarensisMutation(s): 0 
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30S ribosomal protein S13P [auth Ap]149Thermococcus kodakarensisMutation(s): 0 
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30S ribosomal protein S15Q [auth Aq]151Thermococcus kodakarensisMutation(s): 0 
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30S ribosomal protein S14 type ZR [auth Ar]56Thermococcus kodakarensisMutation(s): 0 
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30S ribosomal protein S17S [auth As]114Thermococcus kodakarensisMutation(s): 0 
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30S ribosomal protein S17eT [auth At]67Thermococcus kodakarensisMutation(s): 0 
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30S ribosomal protein S19U [auth Au]133Thermococcus kodakarensisMutation(s): 0 
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30S ribosomal protein S19eV [auth Av]150Thermococcus kodakarensisMutation(s): 0 
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30S ribosomal protein S24eW [auth Aw]98Thermococcus kodakarensisMutation(s): 0 
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30S ribosomal protein S27eX [auth Ax]65Thermococcus kodakarensisMutation(s): 0 
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30S ribosomal protein S28eY [auth Ay]70Thermococcus kodakarensisMutation(s): 0 
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Predicted zinc-ribbon RNA-binding protein involved in translationZ [auth Az]62Thermococcus kodakarensisMutation(s): 0 
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50S ribosomal protein L2CA [auth BC]239Thermococcus kodakarensisMutation(s): 0 
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50S ribosomal protein L3DA [auth BD]346Thermococcus kodakarensisMutation(s): 0 
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50S ribosomal protein L4EA [auth BE]255Thermococcus kodakarensisMutation(s): 0 
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50S ribosomal protein L5FA [auth BF]183Thermococcus kodakarensisMutation(s): 0 
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50S ribosomal protein L6GA [auth BG]184Thermococcus kodakarensisMutation(s): 0 
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50S ribosomal protein L7AeHA [auth BH],
IA [auth BI]		123Thermococcus kodakarensisMutation(s): 0 
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50S ribosomal protein L10eJA [auth BJ]182Thermococcus kodakarensisMutation(s): 0 
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50S ribosomal protein L13KA [auth BK]142Thermococcus kodakarensisMutation(s): 0 
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50S ribosomal protein L14LA [auth BL]141Thermococcus kodakarensisMutation(s): 0 
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50S ribosomal protein L14eMA [auth BM],
NA [auth BN]		83Thermococcus kodakarensisMutation(s): 0 
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50S ribosomal protein L15OA [auth BO]148Thermococcus kodakarensisMutation(s): 0 
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50S ribosomal protein L15ePA [auth BP]194Thermococcus kodakarensisMutation(s): 0 
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50S ribosomal protein L18QA [auth BQ]201Thermococcus kodakarensisMutation(s): 0 
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50S ribosomal protein L18eRA [auth BR]121Thermococcus kodakarensisMutation(s): 0 
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UniProt GroupQ5JJF5
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Entity ID: 43
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L19eSA [auth BS]150Thermococcus kodakarensisMutation(s): 0 
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Entity ID: 44
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50S ribosomal protein L18AeTA [auth BT]77Thermococcus kodakarensisMutation(s): 0 
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Entity ID: 45
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50S ribosomal protein L21eUA [auth BU]98Thermococcus kodakarensisMutation(s): 0 
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Entity ID: 46
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50S ribosomal protein L22VA [auth BV]156Thermococcus kodakarensisMutation(s): 0 
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Entity ID: 47
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50S ribosomal protein L23WA [auth BW]86Thermococcus kodakarensisMutation(s): 0 
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Entity ID: 48
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L24XA [auth BX]121Thermococcus kodakarensisMutation(s): 0 
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Entity ID: 49
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50S ribosomal protein L24eYA [auth BY]67Thermococcus kodakarensisMutation(s): 0 
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Entity ID: 50
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50S ribosomal protein L29ZA [auth BZ]66Thermococcus kodakarensisMutation(s): 0 
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Entity ID: 51
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50S ribosomal protein L30AB [auth Ba]155Thermococcus kodakarensisMutation(s): 0 
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Entity ID: 52
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50S ribosomal protein L30eBB [auth Bb]102Thermococcus kodakarensisMutation(s): 0 
UniProt
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Entity ID: 53
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50S ribosomal protein L31eCB [auth Bc]90Thermococcus kodakarensisMutation(s): 0 
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Entity ID: 54
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50S ribosomal protein L32eDB [auth Bd]125Thermococcus kodakarensisMutation(s): 0 
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Entity ID: 55
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L34eEB [auth Be]90Thermococcus kodakarensisMutation(s): 0 
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Entity ID: 56
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L37AeFB [auth Bg]86Thermococcus kodakarensisMutation(s): 0 
UniProt
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Entity ID: 57
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L37eGB [auth Bh]63Thermococcus kodakarensisMutation(s): 0 
UniProt
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Entity ID: 58
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L39eHB [auth Bi]51Thermococcus kodakarensisMutation(s): 0 
UniProt
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Entity ID: 59
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50S ribosomal protein L40eIB [auth Bj]51Thermococcus kodakarensisMutation(s): 0 
UniProt
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Entity ID: 60
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LSU ribosomal protein L41EJB [auth Bk]37Thermococcus kodakarensisMutation(s): 0 
UniProt
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Entity ID: 61
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L44eKB [auth Bl]94Thermococcus kodakarensisMutation(s): 0 
UniProt
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Entity ID: 1
MoleculeChainsLengthOrganismImage
16S rRNAA [auth Aa]1,498Thermococcus kodakarensis
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Entity ID: 27
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23S rRNAAA [auth BA]3,037Thermococcus kodakarensis
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Entity ID: 28
MoleculeChainsLengthOrganismImage
5S rRNABA [auth BB]126Thermococcus kodakarensis
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Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.95 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION3
MODEL REFINEMENTPHENIX

Structure Validation

View Full Validation Report



View more in-depth experimental data
Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2020-07-29
    Type: Initial release
  • Version 1.1: 2020-08-05
    Changes: Database references