6XA1

Structure of a drug-like compound stalled human translation termination complex

  • Classification: RIBOSOME
  • Organism(s): Homo sapiens
  • Expression System: Homo sapiens
  • Mutation(s): Yes 

  • Deposited: 2020-06-03 Released: 2020-10-07 
  • Deposition Author(s): Li, W., Cate, J.
  • Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.80 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

Selective inhibition of human translation termination by a drug-like compound.

Li, W.Chang, S.T.Ward, F.R.Cate, J.H.D.

(2020) Nat Commun 11: 4941-4941

  • DOI: 10.1038/s41467-020-18765-2
  • Primary Citation of Related Structures:  
    6XA1

  • PubMed Abstract: 
  • Methods to directly inhibit gene expression using small molecules hold promise for the development of new therapeutics targeting proteins that have evaded previous attempts at drug discovery. Among these, small molecules including the drug-like compound PF-06446846 (PF846) selectively inhibit the synthesis of specific proteins, by stalling translation elongation ...

    Methods to directly inhibit gene expression using small molecules hold promise for the development of new therapeutics targeting proteins that have evaded previous attempts at drug discovery. Among these, small molecules including the drug-like compound PF-06446846 (PF846) selectively inhibit the synthesis of specific proteins, by stalling translation elongation. These molecules also inhibit translation termination by an unknown mechanism. Using cryo-electron microscopy (cryo-EM) and biochemical approaches, we show that PF846 inhibits translation termination by arresting the nascent chain (NC) in the ribosome exit tunnel. The arrested NC adopts a compact α-helical conformation that induces 28 S rRNA nucleotide rearrangements that suppress the peptidyl transferase center (PTC) catalytic activity stimulated by eukaryotic release factor 1 (eRF1). These data support a mechanism of action for a small molecule targeting translation that suppresses peptidyl-tRNA hydrolysis promoted by eRF1, revealing principles of eukaryotic translation termination and laying the foundation for new therapeutic strategies.


    Organizational Affiliation

    Department of Chemistry, University of California, Berkeley, CA, USA. j-h-doudna-cate@berkeley.edu.



Macromolecules

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L8A [auth LA]248Homo sapiensMutation(s): 0 
Gene Names: RPL8
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GTEx:  ENSG00000161016 
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Entity ID: 2
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60S ribosomal protein L3B [auth LB]396Homo sapiensMutation(s): 0 
Gene Names: RPL3OK/SW-cl.32
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GTEx:  ENSG00000100316 
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L4F [auth LC]358Homo sapiensMutation(s): 0 
Gene Names: RPL4RPL1
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GTEx:  ENSG00000174444 
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Entity ID: 7
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60S ribosomal protein L5G [auth LD]290Homo sapiensMutation(s): 0 
Gene Names: RPL5MSTP030
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GTEx:  ENSG00000122406 
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Entity ID: 8
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60S ribosomal protein L6H [auth LE]247Homo sapiensMutation(s): 0 
Gene Names: RPL6TXREB1
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GTEx:  ENSG00000089009 
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Entity ID: 9
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60S ribosomal protein L7I [auth LF]225Homo sapiensMutation(s): 0 
Gene Names: RPL7
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GTEx:  ENSG00000147604 
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Entity ID: 10
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60S ribosomal protein L7aJ [auth LG]241Homo sapiensMutation(s): 0 
Gene Names: RPL7ASURF-3SURF3
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GTEx:  ENSG00000148303 
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Entity ID: 11
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60S ribosomal protein L9K [auth LH]190Homo sapiensMutation(s): 0 
Gene Names: RPL9OK/SW-cl.103RPL9P7RPL9P8RPL9P9
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GTEx:  ENSG00000163682 
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Entity ID: 12
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60S ribosomal protein L10-likeL [auth LI]213Homo sapiensMutation(s): 0 
Gene Names: RPL10L
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GTEx:  ENSG00000165496 
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Entity ID: 13
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60S ribosomal protein L11M [auth LJ]176Homo sapiensMutation(s): 0 
Gene Names: RPL11
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GTEx:  ENSG00000142676 
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Entity ID: 14
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60S ribosomal protein L13N [auth LL]204Homo sapiensMutation(s): 0 
Gene Names: RPL13BBC1OK/SW-cl.46
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GTEx:  ENSG00000167526 
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Entity ID: 15
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60S ribosomal protein L14O [auth LM]139Homo sapiensMutation(s): 0 
Gene Names: RPL14
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Entity ID: 16
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60S ribosomal protein L15P [auth LN]203Homo sapiensMutation(s): 0 
Gene Names: RPL15EC45TCBAP0781
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GTEx:  ENSG00000174748 
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Entity ID: 17
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60S ribosomal protein L13aQ [auth LO]201Homo sapiensMutation(s): 0 
Gene Names: RPL13A
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GTEx:  ENSG00000142541 
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Entity ID: 18
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60S ribosomal protein L17R [auth LP]153Homo sapiensMutation(s): 0 
Gene Names: RPL17
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GTEx:  ENSG00000265681 
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Entity ID: 19
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60S ribosomal protein L18S [auth LQ]187Homo sapiensMutation(s): 0 
Gene Names: RPL18
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GTEx:  ENSG00000063177 
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Entity ID: 20
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60S ribosomal protein L19T [auth LR]187Homo sapiensMutation(s): 0 
Gene Names: RPL19
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GTEx:  ENSG00000108298 
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Entity ID: 21
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60S ribosomal protein L18aU [auth LS]175Homo sapiensMutation(s): 0 
Gene Names: RPL18A
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GTEx:  ENSG00000105640 
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Entity ID: 22
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60S ribosomal protein L21V [auth LT]159Homo sapiensMutation(s): 0 
Gene Names: RPL21
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GTEx:  ENSG00000122026 
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Entity ID: 23
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Heparin-binding protein HBp15W [auth LU]101Homo sapiensMutation(s): 0 
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Entity ID: 24
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60S ribosomal protein L23X [auth LV]131Homo sapiensMutation(s): 0 
Gene Names: RPL23
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GTEx:  ENSG00000125691 
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Entity ID: 25
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60S ribosomal protein L24Y [auth LW]124Homo sapiensMutation(s): 0 
Gene Names: RPL24
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GTEx:  ENSG00000114391 
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Entity ID: 26
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60S ribosomal protein L23aZ [auth LX]120Homo sapiensMutation(s): 0 
Gene Names: RPL23A
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GTEx:  ENSG00000198242 
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Entity ID: 27
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60S ribosomal protein L26AA [auth LY]134Homo sapiensMutation(s): 0 
Gene Names: RPL26
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GTEx:  ENSG00000161970 
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Entity ID: 28
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60S ribosomal protein L27BA [auth LZ]135Homo sapiensMutation(s): 0 
Gene Names: RPL27
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GTEx:  ENSG00000131469 
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60S ribosomal protein L27aCA [auth La]147Homo sapiensMutation(s): 0 
Gene Names: RPL27A
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GTEx:  ENSG00000166441 
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Entity ID: 30
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60S ribosomal protein L29DA [auth Lb]121Homo sapiensMutation(s): 0 
Gene Names: RPL29
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GTEx:  ENSG00000162244 
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Entity ID: 31
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60S ribosomal protein L30EA [auth Lc]98Homo sapiensMutation(s): 0 
Gene Names: RPL30
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GTEx:  ENSG00000156482 
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Entity ID: 32
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60S ribosomal protein L31FA [auth Ld]107Homo sapiensMutation(s): 0 
Gene Names: RPL31
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GTEx:  ENSG00000071082 
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Entity ID: 33
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60S ribosomal protein L32GA [auth Le]128Homo sapiensMutation(s): 0 
Gene Names: RPL32PP9932
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GTEx:  ENSG00000144713 
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Entity ID: 34
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60S ribosomal protein L35aHA [auth Lf]109Homo sapiensMutation(s): 0 
Gene Names: RPL35AGIG33
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GTEx:  ENSG00000182899 
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Entity ID: 35
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60S ribosomal protein L34IA [auth Lg]114Homo sapiensMutation(s): 0 
Gene Names: RPL34
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GTEx:  ENSG00000109475 
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Entity ID: 36
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60S ribosomal protein L35JA [auth Lh]122Homo sapiensMutation(s): 0 
Gene Names: RPL35
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GTEx:  ENSG00000136942 
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Entity ID: 37
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60S ribosomal protein L36KA [auth Li]102Homo sapiensMutation(s): 0 
Gene Names: RPL36
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GTEx:  ENSG00000130255 
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Entity ID: 38
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60S ribosomal protein L37LA [auth Lj]86Homo sapiensMutation(s): 0 
Gene Names: RPL37
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GTEx:  ENSG00000145592 
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Entity ID: 39
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60S ribosomal protein L38MA [auth Lk]69Homo sapiensMutation(s): 0 
Gene Names: RPL38
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GTEx:  ENSG00000172809 
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Entity ID: 40
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60S ribosomal protein L39NA [auth Ll]50Homo sapiensMutation(s): 0 
Gene Names: RPL39
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GTEx:  ENSG00000198918 
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Entity ID: 41
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60S ribosomal protein L40OA [auth Lm]52Homo sapiensMutation(s): 0 
Gene Names: UBA52UBCEP2
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GTEx:  ENSG00000221983 
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Entity ID: 42
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L41PA [auth Ln]24Homo sapiensMutation(s): 0 
Gene Names: RPL41
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GTEx:  ENSG00000229117 
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Entity ID: 43
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L36aQA [auth Lo]105Homo sapiensMutation(s): 0 
Gene Names: RPL36ARPL44GIG15MIG6
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Entity ID: 44
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L37aRA [auth Lp]91Homo sapiensMutation(s): 0 
Gene Names: RPL37A
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GTEx:  ENSG00000197756 
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Entity ID: 45
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L28SA [auth Lr]125Homo sapiensMutation(s): 0 
Gene Names: RPL28
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GTEx:  ENSG00000108107 
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Entity ID: 47
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein SAUA [auth SA]216Homo sapiensMutation(s): 0 
Gene Names: RPSALAMBRLAMR1
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GTEx:  ENSG00000168028 
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Entity ID: 48
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S3aVA [auth SB]211Homo sapiensMutation(s): 0 
Gene Names: RPS3AFTE1MFTL
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GTEx:  ENSG00000145425 
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Entity ID: 49
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S3WA [auth SD]224Homo sapiensMutation(s): 0 
Gene Names: RPS3OK/SW-cl.26
EC: 4.2.99.18
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GTEx:  ENSG00000149273 
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Entity ID: 50
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S4, X isoformXA [auth SE]258Homo sapiensMutation(s): 0 
Gene Names: RPS4XCCG2RPS4SCAR
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GTEx:  ENSG00000198034 
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Entity ID: 51
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40S ribosomal protein S5YA [auth SF]189Homo sapiensMutation(s): 0 
Gene Names: RPS5
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GTEx:  ENSG00000083845 
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Entity ID: 52
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40S ribosomal protein S7ZA [auth SH]189Homo sapiensMutation(s): 0 
Gene Names: RPS7
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GTEx:  ENSG00000171863 
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Entity ID: 53
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S8AB [auth SI]205Homo sapiensMutation(s): 0 
Gene Names: RPS8OK/SW-cl.83
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GTEx:  ENSG00000142937 
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Entity ID: 54
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40S ribosomal protein S10BB [auth SK]95Homo sapiensMutation(s): 0 
Gene Names: RPS10
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Entity ID: 55
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40S ribosomal protein S11CB [auth SL]150Homo sapiensMutation(s): 0 
Gene Names: RPS11
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GTEx:  ENSG00000142534 
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Entity ID: 56
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S15DB [auth SP]131Homo sapiensMutation(s): 0 
Gene Names: RPS15RIG
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GTEx:  ENSG00000115268 
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Entity ID: 57
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S16EB [auth SQ]140Homo sapiensMutation(s): 0 
Gene Names: RPS16
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GTEx:  ENSG00000105193 
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Entity ID: 58
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40S ribosomal protein S17FB [auth SR]131Homo sapiensMutation(s): 0 
Gene Names: RPS17RPS17L
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GTEx:  ENSG00000182774 
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Entity ID: 59
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40S ribosomal protein S18GB [auth SS]143Homo sapiensMutation(s): 0 
Gene Names: RPS18D6S218E
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GTEx:  ENSG00000231500 
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Entity ID: 60
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40S ribosomal protein S19HB [auth ST]141Homo sapiensMutation(s): 0 
Gene Names: RPS19
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GTEx:  ENSG00000105372 
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Entity ID: 61
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40S ribosomal protein S20IB [auth SU]100Homo sapiensMutation(s): 0 
Gene Names: RPS20
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GTEx:  ENSG00000008988 
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Entity ID: 62
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40S ribosomal protein S21JB [auth SV]84Homo sapiensMutation(s): 1 
Gene Names: RPS21
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GTEx:  ENSG00000171858 
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Entity ID: 63
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40S ribosomal protein S23KB [auth SX]139Homo sapiensMutation(s): 0 
Gene Names: RPS23
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GTEx:  ENSG00000186468 
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Entity ID: 64
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40S ribosomal protein S26LB [auth Sa]99Homo sapiensMutation(s): 0 
Gene Names: RPS26
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GTEx:  ENSG00000197728 
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Entity ID: 65
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40S ribosomal protein S28MB [auth Sc]61Homo sapiensMutation(s): 0 
Gene Names: RPS28
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GTEx:  ENSG00000233927 
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Entity ID: 66
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40S ribosomal protein S29NB [auth Sd]55Homo sapiensMutation(s): 0 
Gene Names: RPS29
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GTEx:  ENSG00000213741 
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Entity ID: 67
MoleculeChainsSequence LengthOrganismDetailsImage
Receptor of activated protein C kinase 1OB [auth Sg]313Homo sapiensMutation(s): 0 
Gene Names: RACK1GNB2L1HLC7PIG21
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GTEx:  ENSG00000204628 
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Entity ID: 68
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40S ribosomal protein S2PB [auth SC]220Homo sapiensMutation(s): 0 
Gene Names: RPS2RPS4
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GTEx:  ENSG00000140988 
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Entity ID: 69
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40S ribosomal protein S6QB [auth SG]228Homo sapiensMutation(s): 0 
Gene Names: RPS6OK/SW-cl.2
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GTEx:  ENSG00000137154 
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Entity ID: 70
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40S ribosomal protein S9RB [auth SJ]180Homo sapiensMutation(s): 0 
Gene Names: RPS9
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GTEx:  ENSG00000170889 
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Entity ID: 71
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40S ribosomal protein S12SB [auth SM]120Homo sapiensMutation(s): 0 
Gene Names: RPS12
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GTEx:  ENSG00000112306 
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Entity ID: 72
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40S ribosomal protein S13TB [auth SN]150Homo sapiensMutation(s): 0 
Gene Names: RPS13
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GTEx:  ENSG00000110700 
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Entity ID: 73
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40S ribosomal protein S14UB [auth SO]135Homo sapiensMutation(s): 0 
Gene Names: RPS14PRO2640
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Entity ID: 74
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40S ribosomal protein S15aVB [auth SW]129Homo sapiensMutation(s): 0 
Gene Names: RPS15AOK/SW-cl.82
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GTEx:  ENSG00000134419 
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Entity ID: 75
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40S ribosomal protein S24WB [auth SY]122Homo sapiensMutation(s): 0 
Gene Names: RPS24
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Entity ID: 76
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40S ribosomal protein S25XB [auth SZ]70Homo sapiensMutation(s): 0 
Gene Names: RPS25
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GTEx:  ENSG00000118181 
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Entity ID: 77
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40S ribosomal protein S27YB [auth Sb]82Homo sapiensMutation(s): 0 
Gene Names: RPS27MPS1
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GTEx:  ENSG00000177954 
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Entity ID: 78
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40S ribosomal protein S30ZB [auth Se]54Homo sapiensMutation(s): 0 
Gene Names: FAU
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GTEx:  ENSG00000149806 
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Entity ID: 79
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40S ribosomal protein S27aAC [auth Sf]63Homo sapiensMutation(s): 0 
Gene Names: RPS27AUBA80UBCEP1
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GTEx:  ENSG00000143947 
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Entity ID: 81
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Eukaryotic peptide chain release factor subunit 1CC [auth j]411Homo sapiensMutation(s): 0 
Gene Names: ETF1ERF1RF1SUP45L1
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GTEx:  ENSG00000120705 
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Entity ID: 83
MoleculeChainsSequence LengthOrganismDetailsImage
Stalled Nascent chainEC [auth NC]25Homo sapiensMutation(s): 0 
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Entity ID: 3
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28S rRNAC [auth L5]3510Homo sapiens
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Entity ID: 4
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5S rRNAD [auth L7]120Homo sapiens
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Entity ID: 5
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5.8S rRNAE [auth L8]155Homo sapiens
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Entity ID: 46
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18S rRNATA [auth S2]1590Homo sapiens
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