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: 10.1038/s41586-020-2418-2
  • Primary Citation of Related Structures:  
    6SKG, 6SKF, 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 fun ...

    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 S2Ab201Thermococcus kodakarensisMutation(s): 0 
Find proteins for Q5JJD2 (Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1))
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S3Ac209Thermococcus kodakarensisMutation(s): 0 
Find proteins for Q5JDH5 (Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1))
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S3AeAd200Thermococcus kodakarensisMutation(s): 0 
Find proteins for Q5JGM4 (Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1))
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S4Ae180Thermococcus kodakarensisMutation(s): 0 
Find proteins for Q5JJF2 (Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1))
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S4eAf243Thermococcus kodakarensisMutation(s): 0 
Find proteins for Q5JJG0 (Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1))
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S5Ag235Thermococcus kodakarensisMutation(s): 0 
Find proteins for Q5JJG8 (Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1))
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S6eAh125Thermococcus kodakarensisMutation(s): 0 
Find proteins for Q5JDK8 (Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1))
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S7Ai215Thermococcus kodakarensisMutation(s): 0 
Find proteins for Q5JE04 (Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1))
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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S8Aj130Thermococcus kodakarensisMutation(s): 0 
Find proteins for Q5JJG3 (Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1))
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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S8eAk130Thermococcus kodakarensisMutation(s): 0 
Find proteins for Q5JGF3 (Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1))
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Entity ID: 12
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S9Al135Thermococcus kodakarensisMutation(s): 0 
Find proteins for Q5JJE2 (Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1))
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Entity ID: 13
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S10Am102Thermococcus kodakarensisMutation(s): 0 
Find proteins for Q5JFZ5 (Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1))
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Entity ID: 14
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S11An140Thermococcus kodakarensisMutation(s): 0 
Find proteins for Q5JJF3 (Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1))
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Entity ID: 15
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S12Ao147Thermococcus kodakarensisMutation(s): 0 
Find proteins for Q5JE20 (Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1))
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Entity ID: 16
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S13Ap149Thermococcus kodakarensisMutation(s): 0 
Find proteins for Q5JJF1 (Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1))
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Entity ID: 17
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30S ribosomal protein S15Aq151Thermococcus kodakarensisMutation(s): 0 
Find proteins for Q5JGJ4 (Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1))
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Entity ID: 18
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30S ribosomal protein S14 type ZAr56Thermococcus kodakarensisMutation(s): 0 
Find proteins for Q5JJG2 (Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1))
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Entity ID: 19
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S17As114Thermococcus kodakarensisMutation(s): 0 
Find proteins for Q5JDH9 (Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1))
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Entity ID: 20
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S17eAt67Thermococcus kodakarensisMutation(s): 0 
Find proteins for Q5JDC7 (Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1))
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Entity ID: 21
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S19Au133Thermococcus kodakarensisMutation(s): 0 
Find proteins for Q5JDH3 (Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1))
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Entity ID: 22
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S19eAv150Thermococcus kodakarensisMutation(s): 0 
Find proteins for Q5JGN5 (Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1))
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Entity ID: 23
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S24eAw98Thermococcus kodakarensisMutation(s): 0 
Find proteins for Q5JIY8 (Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1))
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Entity ID: 24
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S27eAx65Thermococcus kodakarensisMutation(s): 0 
Find proteins for Q5JE50 (Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1))
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Entity ID: 25
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S28eAy70Thermococcus kodakarensisMutation(s): 0 
Find proteins for Q5JGR4 (Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1))
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Entity ID: 26
MoleculeChainsSequence LengthOrganismDetailsImage
Predicted zinc-ribbon RNA-binding protein involved in translationAz62Thermococcus kodakarensisMutation(s): 0 
Find proteins for Q5JFE2 (Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1))
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Entity ID: 29
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L2BC239Thermococcus kodakarensisMutation(s): 0 
Find proteins for Q5JDH2 (Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1))
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Entity ID: 30
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L3BD346Thermococcus kodakarensisMutation(s): 0 
Find proteins for Q5JDJ0 (Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1))
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Entity ID: 31
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L4BE255Thermococcus kodakarensisMutation(s): 0 
Find proteins for Q5JDI0 (Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1))
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Entity ID: 32
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L5BF183Thermococcus kodakarensisMutation(s): 0 
Find proteins for Q5JJG1 (Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1))
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Entity ID: 33
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L6BG184Thermococcus kodakarensisMutation(s): 0 
Find proteins for Q5JJG4 (Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1))
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Entity ID: 34
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50S ribosomal protein L7AeBHBI123Thermococcus kodakarensisMutation(s): 0 
Find proteins for Q5JGR3 (Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1))
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Entity ID: 35
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50S ribosomal protein L10eBJ182Thermococcus kodakarensisMutation(s): 0 
Find proteins for Q5JDI6 (Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1))
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Entity ID: 36
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50S ribosomal protein L13BK142Thermococcus kodakarensisMutation(s): 0 
Find proteins for Q5JJF6 (Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1))
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Entity ID: 37
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L14BL141Thermococcus kodakarensisMutation(s): 0 
Find proteins for Q5JJF8 (Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1))
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Entity ID: 38
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L14eBMBN83Thermococcus kodakarensisMutation(s): 0 
Find proteins for Q5JJE4 (Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1))
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Entity ID: 39
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50S ribosomal protein L15BO148Thermococcus kodakarensisMutation(s): 0 
Find proteins for Q5JJH0 (Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1))
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Entity ID: 40
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50S ribosomal protein L15eBP194Thermococcus kodakarensisMutation(s): 0 
Find proteins for Q5JH43 (Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1))
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Entity ID: 41
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50S ribosomal protein L18BQ201Thermococcus kodakarensisMutation(s): 0 
Find proteins for Q5JJG7 (Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1))
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Entity ID: 42
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50S ribosomal protein L18eBR121Thermococcus kodakarensisMutation(s): 0 
Find proteins for Q5JJF5 (Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1))
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Entity ID: 43
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50S ribosomal protein L19eBS150Thermococcus kodakarensisMutation(s): 0 
Find proteins for Q5JJG6 (Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1))
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Entity ID: 44
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50S ribosomal protein L18AeBT77Thermococcus kodakarensisMutation(s): 0 
Find proteins for Q5JGT3 (Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1))
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Entity ID: 45
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50S ribosomal protein L21eBU98Thermococcus kodakarensisMutation(s): 0 
Find proteins for Q5JI51 (Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1))
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Entity ID: 46
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50S ribosomal protein L22BV156Thermococcus kodakarensisMutation(s): 0 
Find proteins for Q5JDH4 (Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1))
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Entity ID: 47
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50S ribosomal protein L23BW86Thermococcus kodakarensisMutation(s): 0 
Find proteins for Q5JDH1 (Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1))
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Entity ID: 48
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50S ribosomal protein L24BX121Thermococcus kodakarensisMutation(s): 0 
Find proteins for Q5JJF9 (Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1))
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Entity ID: 49
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50S ribosomal protein L24eBY67Thermococcus kodakarensisMutation(s): 0 
Find proteins for Q5JGR5 (Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1))
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Entity ID: 50
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50S ribosomal protein L29BZ66Thermococcus kodakarensisMutation(s): 0 
Find proteins for Q5JDH6 (Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1))
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Entity ID: 51
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50S ribosomal protein L30Ba155Thermococcus kodakarensisMutation(s): 0 
Find proteins for Q5JJG9 (Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1))
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Entity ID: 52
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L30eBb102Thermococcus kodakarensisMutation(s): 0 
Find proteins for Q5JE35 (Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1))
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Entity ID: 53
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50S ribosomal protein L31eBc90Thermococcus kodakarensisMutation(s): 0 
Find proteins for Q5JGT5 (Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1))
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Entity ID: 54
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50S ribosomal protein L32eBd125Thermococcus kodakarensisMutation(s): 0 
Find proteins for Q5JJG5 (Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1))
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Entity ID: 55
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50S ribosomal protein L34eBe90Thermococcus kodakarensisMutation(s): 0 
Find proteins for Q5JJF7 (Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1))
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Entity ID: 56
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50S ribosomal protein L37AeBg86Thermococcus kodakarensisMutation(s): 0 
Find proteins for Q5JDM6 (Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1))
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Entity ID: 57
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50S ribosomal protein L37eBh63Thermococcus kodakarensisMutation(s): 0 
Find proteins for Q5JIE1 (Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1))
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Entity ID: 58
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50S ribosomal protein L39eBi51Thermococcus kodakarensisMutation(s): 0 
Find proteins for Q5JGT6 (Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1))
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Entity ID: 59
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50S ribosomal protein L40eBj51Thermococcus kodakarensisMutation(s): 0 
Find proteins for Q5JJD3 (Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1))
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Entity ID: 60
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LSU ribosomal protein L41EBk37Thermococcus kodakarensisMutation(s): 0 
Find proteins for Q5JEV0 (Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1))
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Entity ID: 61
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50S ribosomal protein L44eBl94Thermococcus kodakarensisMutation(s): 0 
Find proteins for Q5JE51 (Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1))
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Entity ID: 1
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16S rRNAAa1498Thermococcus kodakarensis
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Entity ID: 27
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23S rRNABA3037Thermococcus kodakarensis
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Entity ID: 28
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5S rRNABB126Thermococcus kodakarensis
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download CCD File 
Ag, Ar, As, Ax, Az, BY, Be, Bg, Bh, Bj, Bl
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

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

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

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