6OLG

Human ribosome nascent chain complex stalled by a drug-like small molecule (CDH1_RNC with PP tRNA)

  • Classification: RIBOSOME
  • Organism(s): Homo sapiens
  • Mutation(s): No 

  • Deposited: 2019-04-16 Released: 2019-06-19 
  • Deposition Author(s): Li, W., Cate, J.H.D.
  • Funding Organization(s): National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.40 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

Structural basis for selective stalling of human ribosome nascent chain complexes by a drug-like molecule.

Li, W.Ward, F.R.McClure, K.F.Chang, S.T.Montabana, E.Liras, S.Dullea, R.G.Cate, J.H.D.

(2019) Nat Struct Mol Biol 26: 501-509

  • DOI: https://doi.org/10.1038/s41594-019-0236-8
  • Primary Citation of Related Structures:  
    6OLE, 6OLF, 6OLG, 6OLI, 6OLZ, 6OM0, 6OM7

  • PubMed Abstract: 

    The drug-like molecule PF-06446846 (PF846) binds the human ribosome and selectively blocks the translation of a small number of proteins by an unknown mechanism. In structures of PF846-stalled human ribosome nascent chain complexes, PF846 binds in the ribosome exit tunnel in a eukaryotic-specific pocket formed by 28S ribosomal RNA, and alters the path of the nascent polypeptide chain. PF846 arrests the translating ribosome in the rotated state of translocation, in which the peptidyl-transfer RNA 3'-CCA end is improperly docked in the peptidyl transferase center. Selections of messenger RNAs from mRNA libraries using translation extracts reveal that PF846 can stall translation elongation, arrest termination or even enhance translation, depending on nascent chain sequence context. These results illuminate how a small molecule selectively targets translation by the human ribosome, and provides a foundation for developing small molecules that modulate the production of proteins of therapeutic interest.


  • Organizational Affiliation

    Department of Molecular & Cell Biology, University of California, Berkeley, Berkeley, CA, USA.


Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L8A [auth AA]257Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000161016 
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein SAB [auth BA]215Homo sapiensMutation(s): 0 
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Find proteins for P08865 (Homo sapiens)
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PHAROS:  P08865
GTEx:  ENSG00000168028 
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L3C [auth AB]394Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000100316 
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S3aD [auth BB]212Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000145425 
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L4E [auth AC]363Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000174444 
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S2F [auth BC]222Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000140988 
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L5I [auth AD]294Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000122406 
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L6J [auth AE]194Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000089009 
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L7K [auth AF]234Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000147604 
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L7aL [auth AG]234Homo sapiensMutation(s): 0 
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PHAROS:  P62424
GTEx:  ENSG00000148303 
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L9M [auth AH]191Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000163682 
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L10N [auth AI]211Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000147403 
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L11O [auth AJ]169Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000142676 
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
60S acidic ribosomal protein P0P [auth AK]109Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000089157 
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L13Q [auth AL]205Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000167526 
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L14R [auth AM]139Homo sapiensMutation(s): 0 
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PHAROS:  P50914
GTEx:  ENSG00000188846 
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L15S [auth AN]203Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000174748 
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L13aT [auth AO]195Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000142541 
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L17U [auth AP]153Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000265681 
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Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L18V [auth AQ]187Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000063177 
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Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L19W [auth AR]181Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000108298 
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Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L18aX [auth AS]175Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000105640 
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Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L21Y [auth AT]157Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000122026 
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Entity ID: 26
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L22Z [auth AU]99Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000116251 
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Entity ID: 27
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L23AA [auth AV]129Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000125691 
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Entity ID: 28
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L24BA [auth AW]121Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000114391 
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Entity ID: 29
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L23aCA [auth AX]117Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000198242 
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Entity ID: 30
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L26DA [auth AY]127Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000161970 
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Entity ID: 31
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L27EA [auth AZ]134Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000131469 
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Entity ID: 32
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L27aFA [auth Aa]147Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000166441 
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Entity ID: 33
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L29GA [auth Ab]121Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000162244 
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Entity ID: 34
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L30HA [auth Ac]103Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000156482 
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Entity ID: 35
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L31IA [auth Ad]106Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000071082 
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Entity ID: 36
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L32JA [auth Ae]129Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000144713 
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Entity ID: 37
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L35aKA [auth Af]109Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000182899 
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Entity ID: 38
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L34LA [auth Ag]114Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000109475 
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Entity ID: 39
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L35MA [auth Ah]122Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000136942 
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Entity ID: 40
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L36NA [auth Ai]97Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000130255 
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Entity ID: 41
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L37OA [auth Aj]84Homo sapiensMutation(s): 0 
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Find proteins for P61927 (Homo sapiens)
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GTEx:  ENSG00000145592 
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Entity ID: 42
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L38PA [auth Ak]69Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000172809 
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Entity ID: 43
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L39QA [auth Al]50Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000198918 
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Entity ID: 44
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L40RA [auth Am]50Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000221983 
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Entity ID: 45
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L41SA [auth An]25Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000229117 
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Entity ID: 46
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L36aTA [auth Ao]105Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000241343 
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Entity ID: 47
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L37aUA [auth Ap]91Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000197756 
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Entity ID: 48
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L12VA [auth Aq]138Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000197958 
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Entity ID: 49
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L28WA [auth At]122Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000108107 
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Entity ID: 50
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L10aXA [auth Au]217Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000198755 
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Entity ID: 53
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S3AB [auth BD]220Homo sapiensMutation(s): 0 
EC: 4.2.99.18
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GTEx:  ENSG00000149273 
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Entity ID: 54
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S4, Y isoform 1BB [auth BE]257Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000129824 
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Entity ID: 55
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S5CB [auth BF]190Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000083845 
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Entity ID: 56
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S6DB [auth BG]232Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000137154 
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Entity ID: 57
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S7EB [auth BH]183Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000171863 
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Entity ID: 58
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S8FB [auth BI]207Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000142937 
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Entity ID: 59
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S9GB [auth BJ]179Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000170889 
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Entity ID: 60
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S10HB [auth BK]98Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000124614 
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Entity ID: 61
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S11IB [auth BL]153Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000142534 
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Entity ID: 62
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S12JB [auth BM]120Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000112306 
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Entity ID: 63
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S13KB [auth BN]149Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000110700 
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Entity ID: 64
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S14LB [auth BO]136Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000164587 
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Entity ID: 65
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S15MB [auth BP]120Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000115268 
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Entity ID: 66
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S16NB [auth BQ]139Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000105193 
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Entity ID: 67
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S17OB [auth BR]125Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000182774 
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Entity ID: 68
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S18PB [auth BS]139Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000231500 
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Entity ID: 69
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S19QB [auth BT]143Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000105372 
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Entity ID: 70
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S20RB [auth BU]97Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000008988 
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Entity ID: 71
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S21SB [auth BV]81Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000171858 
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Entity ID: 72
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S15aTB [auth BW]129Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000134419 
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Entity ID: 73
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S23UB [auth BX]139Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000186468 
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Entity ID: 74
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S24VB [auth BY]125Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000138326 
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Entity ID: 75
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S25WB [auth BZ]86Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000118181 
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