6SKG

Cryo-EM Structure of T. kodakarensis 70S ribosome in TkNat10 deleted strain


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.65 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: 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
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S3AeD [auth Ad]200Thermococcus kodakarensisMutation(s): 0 
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
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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Entity ID: 8
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30S ribosomal protein S6eH [auth Ah]125Thermococcus kodakarensisMutation(s): 0 
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Entity ID: 9
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30S ribosomal protein S7I [auth Ai]215Thermococcus kodakarensisMutation(s): 0 
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Entity ID: 10
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30S ribosomal protein S8J [auth Aj]130Thermococcus kodakarensisMutation(s): 0 
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Entity ID: 11
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30S ribosomal protein S8eK [auth Ak]130Thermococcus kodakarensisMutation(s): 0 
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Entity ID: 12
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30S ribosomal protein S9L [auth Al]135Thermococcus kodakarensisMutation(s): 0 
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Entity ID: 13
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30S ribosomal protein S10M [auth Am]102Thermococcus kodakarensisMutation(s): 0 
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Entity ID: 14
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30S ribosomal protein S11N [auth An]140Thermococcus kodakarensisMutation(s): 0 
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Entity ID: 15
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30S ribosomal protein S12O [auth Ao]147Thermococcus kodakarensisMutation(s): 0 
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Entity ID: 16
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30S ribosomal protein S13P [auth Ap]149Thermococcus kodakarensisMutation(s): 0 
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Entity ID: 17
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30S ribosomal protein S15Q [auth Aq]151Thermococcus kodakarensisMutation(s): 0 
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Entity ID: 18
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30S ribosomal protein S14 type ZR [auth Ar]56Thermococcus kodakarensisMutation(s): 0 
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Entity ID: 19
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30S ribosomal protein S17S [auth As]114Thermococcus kodakarensisMutation(s): 0 
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Entity ID: 20
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30S ribosomal protein S17eT [auth At],
MB [auth Bm]
67Thermococcus kodakarensisMutation(s): 0 
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Entity ID: 21
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30S ribosomal protein S19U [auth Au]133Thermococcus kodakarensisMutation(s): 0 
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Entity ID: 22
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30S ribosomal protein S19eV [auth Av]150Thermococcus kodakarensisMutation(s): 0 
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Entity ID: 23
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S24eW [auth Aw],
NB [auth Bn]
98Thermococcus kodakarensisMutation(s): 0 
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Entity ID: 24
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30S ribosomal protein S27eX [auth Ax]65Thermococcus kodakarensisMutation(s): 0 
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Entity ID: 25
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30S ribosomal protein S28eY [auth Ay]70Thermococcus kodakarensisMutation(s): 0 
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Entity ID: 26
MoleculeChainsSequence LengthOrganismDetailsImage
Predicted zinc-ribbon RNA-binding protein involved in translationZ [auth Az]62Thermococcus kodakarensisMutation(s): 0 
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Entity ID: 29
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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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Entity ID: 31
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50S ribosomal protein L4EA [auth BE]255Thermococcus kodakarensisMutation(s): 0 
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Entity ID: 32
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50S ribosomal protein L5FA [auth BF]183Thermococcus kodakarensisMutation(s): 0 
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Entity ID: 33
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50S ribosomal protein L6GA [auth BG]184Thermococcus kodakarensisMutation(s): 0 
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Entity ID: 34
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50S ribosomal protein L7AeHA [auth BH],
IA [auth BI]
123Thermococcus kodakarensisMutation(s): 0 
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Entity ID: 35
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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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Entity ID: 37
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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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Entity ID: 39
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50S ribosomal protein L15OA [auth BO]148Thermococcus kodakarensisMutation(s): 0 
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Entity ID: 40
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50S ribosomal protein L15ePA [auth BP]194Thermococcus kodakarensisMutation(s): 0 
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Entity ID: 41
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50S ribosomal protein L18QA [auth BQ]201Thermococcus kodakarensisMutation(s): 0 
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Entity ID: 42
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50S ribosomal protein L18eRA [auth BR]121Thermococcus kodakarensisMutation(s): 0 
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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
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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 
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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
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50S ribosomal protein L34eEB [auth Be]90Thermococcus kodakarensisMutation(s): 0 
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Entity ID: 56
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Ribosomal protein eL35AFB [auth Bf]101Thermococcus kodakarensisMutation(s): 0 
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Entity ID: 57
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50S ribosomal protein L37AeGB [auth Bg]86Thermococcus kodakarensisMutation(s): 0 
UniProt
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Entity ID: 58
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50S ribosomal protein L37eHB [auth Bh]63Thermococcus kodakarensisMutation(s): 0 
UniProt
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Entity ID: 59
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50S ribosomal protein L39eIB [auth Bi]51Thermococcus kodakarensisMutation(s): 0 
UniProt
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Entity ID: 60
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50S ribosomal protein L40eJB [auth Bj]51Thermococcus kodakarensisMutation(s): 0 
UniProt
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Entity ID: 61
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LSU ribosomal protein L41EKB [auth Bk]37Thermococcus kodakarensisMutation(s): 0 
UniProt
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Entity ID: 62
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50S ribosomal protein L44eLB [auth Bl]94Thermococcus kodakarensisMutation(s): 0 
UniProt
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Entity ID: 63
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Nucleic acid-binding protein, containing C2H2 zinc-fingerOB [auth Bo]47Thermococcus kodakarensisMutation(s): 0 
UniProt
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Entity ID: 64
MoleculeChainsSequence LengthOrganismDetailsImage
Predicted exosome subunit, UPF0023 familyPB [auth Bp]236Thermococcus kodakarensisMutation(s): 0 
UniProt
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Entity ID: 65
MoleculeChainsSequence LengthOrganismDetailsImage
Unknown ribosomal proteinQB [auth Bq]34Thermococcus kodakarensisMutation(s): 0 
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Entity ID: 1
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16S ribosomal RNAA [auth Aa]1,498Thermococcus kodakarensis
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Entity ID: 27
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23S ribosomal RNAAA [auth BA]3,037Thermococcus kodakarensis
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Entity ID: 28
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5S ribosomal RNABA [auth BB]126Thermococcus kodakarensis
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Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.65 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



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