6TH6

Cryo-EM Structure of T. kodakarensis 70S ribosome


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.55 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
  • Structures With Same Primary Citation

  • 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 LengthOrganismDetails
30S ribosomal protein S2Ab201Thermococcus kodakarensis KOD1Mutation(s): 0 
Gene Names: rps2TK1496
Find proteins for Q5JJD2 (Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1))
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S3Ac209Thermococcus kodakarensis KOD1Mutation(s): 0 
Gene Names: rps3TK1536
Find proteins for Q5JDH5 (Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1))
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S3AeAd200Thermococcus kodakarensis KOD1Mutation(s): 0 
Gene Names: rps3aeTK1254
Find proteins for Q5JGM4 (Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1))
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S4Ae180Thermococcus kodakarensis KOD1Mutation(s): 0 
Gene Names: rps4TK1505
Find proteins for Q5JJF2 (Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1))
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S4eAf243Thermococcus kodakarensis KOD1Mutation(s): 0 
Gene Names: rps4eTK1529
Find proteins for Q5JJG0 (Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1))
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S5Ag235Thermococcus kodakarensis KOD1Mutation(s): 0 
Gene Names: rps5TK1521
Find proteins for Q5JJG8 (Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1))
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S6eAh125Thermococcus kodakarensis KOD1Mutation(s): 0 
Gene Names: rps6eTK1951
Find proteins for Q5JDK8 (Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1))
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S7Ai215Thermococcus kodakarensis KOD1Mutation(s): 0 
Gene Names: rps7TK1077
Find proteins for Q5JE04 (Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1))
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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S8Aj130Thermococcus kodakarensis KOD1Mutation(s): 0 
Gene Names: rps8TK1526
Find proteins for Q5JJG3 (Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1))
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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S8eAk130Thermococcus kodakarensis KOD1Mutation(s): 0 
Gene Names: rps8eTK1191
Find proteins for Q5JGF3 (Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1))
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Entity ID: 12
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S9Al135Thermococcus kodakarensis KOD1Mutation(s): 0 
Gene Names: rps9TK1500
Find proteins for Q5JJE2 (Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1))
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Entity ID: 13
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S10Am102Thermococcus kodakarensis KOD1Mutation(s): 0 
Gene Names: rps10TK0307
Find proteins for Q5JFZ5 (Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1))
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Entity ID: 14
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S11An140Thermococcus kodakarensis KOD1Mutation(s): 0 
Gene Names: rps11TK1504
Find proteins for Q5JJF3 (Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1))
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Entity ID: 15
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S12Ao147Thermococcus kodakarensis KOD1Mutation(s): 0 
Gene Names: rps12TK1078
Find proteins for Q5JE20 (Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1))
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Entity ID: 16
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S13Ap149Thermococcus kodakarensis KOD1Mutation(s): 0 
Gene Names: rps13TK1506
Find proteins for Q5JJF1 (Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1))
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Entity ID: 18
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S14 type ZAr56Thermococcus kodakarensis KOD1Mutation(s): 0 
Gene Names: rps14TK1527
Find proteins for Q5JJG2 (Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1))
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Entity ID: 19
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S17As114Thermococcus kodakarensis KOD1Mutation(s): 0 
Gene Names: rps17TK1532
Find proteins for Q5JDH9 (Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1))
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Entity ID: 20
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S17eAt67Thermococcus kodakarensis KOD1Mutation(s): 0 
Gene Names: rps17eTK2292
Find proteins for Q5JDC7 (Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1))
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Entity ID: 21
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S19Au133Thermococcus kodakarensis KOD1Mutation(s): 0 
Gene Names: rps19TK1538
Find proteins for Q5JDH3 (Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1))
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Entity ID: 22
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S19eAv150Thermococcus kodakarensis KOD1Mutation(s): 0 
Gene Names: rps19eTK1276
Find proteins for Q5JGN5 (Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1))
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Entity ID: 23
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S24eAw98Thermococcus kodakarensis KOD1Mutation(s): 0 
Gene Names: rps24eTK1696
Find proteins for Q5JIY8 (Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1))
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Entity ID: 24
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S27eAx65Thermococcus kodakarensis KOD1Mutation(s): 0 
Gene Names: rps27eTK1099
Find proteins for Q5JE50 (Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1))
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Entity ID: 25
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S28eAy70Thermococcus kodakarensis KOD1Mutation(s): 0 
Gene Names: rps28eTK1310
Find proteins for Q5JGR4 (Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1))
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Entity ID: 26
MoleculeChainsSequence LengthOrganismDetails
Predicted zinc-ribbon RNA-binding protein involved in translationAz62Thermococcus kodakarensis KOD1Mutation(s): 0 
Gene Names: TK0111
Find proteins for Q5JFE2 (Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1))
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Entity ID: 29
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L2BC239Thermococcus kodakarensis KOD1Mutation(s): 0 
Gene Names: rpl2TK1539
Find proteins for Q5JDH2 (Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1))
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Entity ID: 30
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L3BD346Thermococcus kodakarensis KOD1Mutation(s): 0 
Gene Names: rpl3TK1542
Find proteins for Q5JDJ0 (Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1))
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Entity ID: 31
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L4BE255Thermococcus kodakarensis KOD1Mutation(s): 0 
Gene Names: rpl4TK1541
Find proteins for Q5JDI0 (Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1))
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Entity ID: 32
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L5BF183Thermococcus kodakarensis KOD1Mutation(s): 0 
Gene Names: rpl5TK1528
Find proteins for Q5JJG1 (Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1))
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Entity ID: 33
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L6BG184Thermococcus kodakarensis KOD1Mutation(s): 0 
Gene Names: rpl6TK1525
Find proteins for Q5JJG4 (Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1))
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Entity ID: 34
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L7AeBH, BI123Thermococcus kodakarensis KOD1Mutation(s): 0 
Gene Names: rpl7aeTK1311
Find proteins for Q5JGR3 (Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1))
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Entity ID: 35
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L10eBJ182Thermococcus kodakarensis KOD1Mutation(s): 0 
Gene Names: rpl10eTK1546
Find proteins for Q5JDI6 (Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1))
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Entity ID: 36
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L13BK142Thermococcus kodakarensis KOD1Mutation(s): 0 
Gene Names: rpl13TK1501
Find proteins for Q5JJF6 (Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1))
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Entity ID: 37
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L14BL141Thermococcus kodakarensis KOD1Mutation(s): 0 
Gene Names: rpl14TK1531
Find proteins for Q5JJF8 (Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1))
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Entity ID: 38
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L14eBM, BN83Thermococcus kodakarensis KOD1Mutation(s): 0 
Gene Names: rpl14eTK1513
Find proteins for Q5JJE4 (Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1))
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Entity ID: 39
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L15BO148Thermococcus kodakarensis KOD1Mutation(s): 0 
Gene Names: rpl15TK1519
Find proteins for Q5JJH0 (Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1))
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Entity ID: 40
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L15eBP194Thermococcus kodakarensis KOD1Mutation(s): 0 
Gene Names: rpl15eTK1454
Find proteins for Q5JH43 (Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1))
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Entity ID: 41
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L18BQ201Thermococcus kodakarensis KOD1Mutation(s): 0 
Gene Names: rpl18TK1522
Find proteins for Q5JJG7 (Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1))
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Entity ID: 42
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L18eBR121Thermococcus kodakarensis KOD1Mutation(s): 0 
Gene Names: rpl18eTK1502
Find proteins for Q5JJF5 (Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1))
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Entity ID: 43
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L19eBS150Thermococcus kodakarensis KOD1Mutation(s): 0 
Gene Names: rpl19eTK1523
Find proteins for Q5JJG6 (Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1))
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Entity ID: 44
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L18AeBT77Thermococcus kodakarensis KOD1Mutation(s): 0 
Gene Names: rpl18arpl20erplXTK1322
Find proteins for Q5JGT3 (Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1))
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Entity ID: 45
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L21eBU98Thermococcus kodakarensis KOD1Mutation(s): 0 
Gene Names: rpl21eTK0902
Find proteins for Q5JI51 (Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1))
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Entity ID: 46
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L22BV156Thermococcus kodakarensis KOD1Mutation(s): 0 
Gene Names: rpl22TK1537
Find proteins for Q5JDH4 (Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1))
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Entity ID: 47
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L23BW86Thermococcus kodakarensis KOD1Mutation(s): 0 
Gene Names: rpl23TK1540
Find proteins for Q5JDH1 (Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1))
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Entity ID: 48
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L24BX121Thermococcus kodakarensis KOD1Mutation(s): 0 
Gene Names: rpl24TK1530
Find proteins for Q5JJF9 (Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1))
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Entity ID: 49
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L24eBY67Thermococcus kodakarensis KOD1Mutation(s): 0 
Gene Names: rpl24eTK1309
Find proteins for Q5JGR5 (Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1))
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Entity ID: 50
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L29BZ66Thermococcus kodakarensis KOD1Mutation(s): 0 
Gene Names: rpl29TK1535
Find proteins for Q5JDH6 (Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1))
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Entity ID: 51
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L30Ba155Thermococcus kodakarensis KOD1Mutation(s): 0 
Gene Names: rpl30TK1520
Find proteins for Q5JJG9 (Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1))
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Entity ID: 52
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L30eBb102Thermococcus kodakarensis KOD1Mutation(s): 0 
Gene Names: rpl30eTK1080
Find proteins for Q5JE35 (Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1))
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Entity ID: 53
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L31eBc90Thermococcus kodakarensis KOD1Mutation(s): 0 
Gene Names: rpl31eTK1320
Find proteins for Q5JGT5 (Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1))
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Entity ID: 54
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L32eBd125Thermococcus kodakarensis KOD1Mutation(s): 0 
Gene Names: rpl32eTK1524
Find proteins for Q5JJG5 (Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1))
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Entity ID: 55
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L34eBe90Thermococcus kodakarensis KOD1Mutation(s): 0 
Gene Names: rpl34eTK1515
Find proteins for Q5JJF7 (Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1))
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Entity ID: 56
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L37AeBg86Thermococcus kodakarensis KOD1Mutation(s): 0 
Gene Names: rpl37aeTK0615
Find proteins for Q5JDM6 (Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1))
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Entity ID: 57
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L37eBh63Thermococcus kodakarensis KOD1Mutation(s): 0 
Gene Names: rpl37eTK0975
Find proteins for Q5JIE1 (Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1))
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Entity ID: 58
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L39eBi51Thermococcus kodakarensis KOD1Mutation(s): 0 
Gene Names: rpl39eTK1319
Find proteins for Q5JGT6 (Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1))
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Entity ID: 59
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L40eBj51Thermococcus kodakarensis KOD1Mutation(s): 0 
Gene Names: rpl40eTK1495
Find proteins for Q5JJD3 (Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1))
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Entity ID: 60
MoleculeChainsSequence LengthOrganismDetails
LSU ribosomal protein L41EBk37Thermococcus kodakarensis KOD1Mutation(s): 0 
Gene Names: TK1915
Find proteins for Q5JEV0 (Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1))
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Entity ID: 61
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L44eBl94Thermococcus kodakarensis KOD1Mutation(s): 0 
Gene Names: rpl44eTK1098
Find proteins for Q5JE51 (Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1))
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Entity ID: 17
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S15Aq151Thermococcus kodakarensis KOD1Mutation(s): 0 
Gene Names: rps15TK1251
Find proteins for Q5JGJ4 (Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1))
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Entity ID: 1
MoleculeChainsLengthOrganism
16S ribosomal RNAAa1498Thermococcus kodakarensis KOD1

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Entity ID: 27
MoleculeChainsLengthOrganism
23S ribosomal RNABA3037Thermococcus kodakarensis KOD1

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Entity ID: 28
MoleculeChainsLengthOrganism
5S ribosomal RNABB126Thermococcus kodakarensis KOD1
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: 2.55 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