6OLF

Human ribosome nascent chain complex (CDH1-RNC) stalled by a drug-like molecule with AA and PE tRNAs

  • 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: 3.90 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: 2
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein SAB [auth SA]221Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000168028 
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S3aC [auth SB]214Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000145425 
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S3D [auth SD]226Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000149273 
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S4, X isoformE [auth SE]259Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000198034 
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S5F [auth SF]189Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000083845 
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S7G [auth SH]189Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000171863 
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S8H [auth SI]204Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000142937 
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S10I [auth SK]98Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000124614 
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S11J [auth SL]153Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000142534 
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S15K [auth SP]127Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000115268 
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S16L [auth SQ]146Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000105193 
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S17M [auth SR]134Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000182774 
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S18N [auth SS]145Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000231500 
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S19O [auth ST]143Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000105372 
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S20P [auth SU]104Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000008988 
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S21Q [auth SV]82Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000171858 
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S23R [auth SX]141Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000186468 
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S26S [auth Sa]102Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000197728 
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S28T [auth Sc]64Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000233927 
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S29U [auth Sd]55Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000213741 
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Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
Receptor of activated protein C kinase 1V [auth Sg]312Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000204628 
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Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S2W [auth SC]220Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000140988 
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Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S6X [auth SG]237Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000137154 
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Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S9Y [auth SJ]185Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000170889 
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Entity ID: 26
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S12Z [auth SM]118Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000112306 
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Entity ID: 27
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S13AA [auth SN]150Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000110700 
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Entity ID: 28
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S14BA [auth SO]137Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000164587 
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Entity ID: 29
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S15aCA [auth SW]129Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000134419 
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Entity ID: 30
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S24DA [auth SY]131Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000138326 
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Entity ID: 31
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S25EA [auth SZ]73Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000118181 
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Entity ID: 32
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S27FA [auth Sb]82Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000177954 
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Entity ID: 33
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S30GA [auth Se]57Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000149806 
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Entity ID: 34
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S27aHA [auth Sf]67Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000143947 
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Entity ID: 35
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L8IA [auth A]252Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000161016 
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Entity ID: 36
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L3JA [auth B]397Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000100316 
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Entity ID: 37
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L4KA [auth C]363Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000174444 
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Entity ID: 40
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L5NA [auth F]294Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000122406 
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Entity ID: 41
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L6OA [auth G]247Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000089009 
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Entity ID: 42
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L7PA [auth H]225Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000147604 
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Entity ID: 43
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L7aQA [auth I]234Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000148303 
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Entity ID: 44
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L9RA [auth J]191Homo sapiensMutation(s): 0 
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Find proteins for P32969 (Homo sapiens)
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GTEx:  ENSG00000163682 
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Entity ID: 45
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L10SA [auth K]211Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000147403 
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Entity ID: 46
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L11TA [auth L]169Homo sapiensMutation(s): 0 
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Find proteins for P62913 (Homo sapiens)
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GTEx:  ENSG00000142676 
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Entity ID: 47
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L13UA [auth M]205Homo sapiensMutation(s): 0 
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Find proteins for P26373 (Homo sapiens)
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GTEx:  ENSG00000167526 
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Entity ID: 48
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L14VA [auth N]139Homo sapiensMutation(s): 0 
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Find proteins for P50914 (Homo sapiens)
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GTEx:  ENSG00000188846 
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Entity ID: 49
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L15WA [auth O]203Homo sapiensMutation(s): 0 
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Find proteins for P61313 (Homo sapiens)
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GTEx:  ENSG00000174748 
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Entity ID: 50
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L13aXA [auth P]195Homo sapiensMutation(s): 0 
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Find proteins for P40429 (Homo sapiens)
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GTEx:  ENSG00000142541 
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Entity ID: 51
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L17YA [auth Q]153Homo sapiensMutation(s): 0 
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Find proteins for P18621 (Homo sapiens)
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GTEx:  ENSG00000265681 
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Entity ID: 52
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L18ZA [auth R]187Homo sapiensMutation(s): 0 
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Find proteins for Q07020 (Homo sapiens)
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GTEx:  ENSG00000063177 
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Entity ID: 53
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L19AB [auth S]181Homo sapiensMutation(s): 0 
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Find proteins for P84098 (Homo sapiens)
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GTEx:  ENSG00000108298 
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Entity ID: 54
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L18aBB [auth T]175Homo sapiensMutation(s): 0 
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Find proteins for Q02543 (Homo sapiens)
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GTEx:  ENSG00000105640 
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Entity ID: 55
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L21CB [auth U]157Homo sapiensMutation(s): 0 
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Find proteins for P46778 (Homo sapiens)
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GTEx:  ENSG00000122026 
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Entity ID: 56
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L22DB [auth V]99Homo sapiensMutation(s): 0 
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Find proteins for P35268 (Homo sapiens)
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GTEx:  ENSG00000116251 
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Entity ID: 57
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L23EB [auth W]129Homo sapiensMutation(s): 0 
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Find proteins for P62829 (Homo sapiens)
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GTEx:  ENSG00000125691 
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Entity ID: 58
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L24FB [auth X]121Homo sapiensMutation(s): 0 
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Find proteins for P83731 (Homo sapiens)
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GTEx:  ENSG00000114391 
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Entity ID: 59
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L23aGB [auth Y]117Homo sapiensMutation(s): 0 
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Find proteins for P62750 (Homo sapiens)
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GTEx:  ENSG00000198242 
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Entity ID: 60
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L26HB [auth Z]134Homo sapiensMutation(s): 0 
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Find proteins for P61254 (Homo sapiens)
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GTEx:  ENSG00000161970 
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Entity ID: 61
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L27aIB [auth b]147Homo sapiensMutation(s): 0 
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Find proteins for P46776 (Homo sapiens)
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GTEx:  ENSG00000166441 
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Entity ID: 62
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L29JB [auth c]121Homo sapiensMutation(s): 0 
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Find proteins for P47914 (Homo sapiens)
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GTEx:  ENSG00000162244 
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Entity ID: 63
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L30KB [auth d]103Homo sapiensMutation(s): 0 
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Find proteins for P62888 (Homo sapiens)
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GTEx:  ENSG00000156482 
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Entity ID: 64
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L31LB [auth e]106Homo sapiensMutation(s): 0 
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Find proteins for P62899 (Homo sapiens)
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GTEx:  ENSG00000071082 
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Entity ID: 65
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L32MB [auth f]129Homo sapiensMutation(s): 0 
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Find proteins for P62910 (Homo sapiens)
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GTEx:  ENSG00000144713 
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Entity ID: 66
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L35aNB [auth g]109Homo sapiensMutation(s): 0 
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Find proteins for P18077 (Homo sapiens)
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GTEx:  ENSG00000182899 
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Entity ID: 67
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L34OB [auth h]114Homo sapiensMutation(s): 0 
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Find proteins for P49207 (Homo sapiens)
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GTEx:  ENSG00000109475 
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Entity ID: 68
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L35PB [auth i]122Homo sapiensMutation(s): 0 
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Find proteins for P42766 (Homo sapiens)
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GTEx:  ENSG00000136942 
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Entity ID: 69
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L36QB [auth j]97Homo sapiensMutation(s): 0 
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Find proteins for Q9Y3U8 (Homo sapiens)
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GTEx:  ENSG00000130255 
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Entity ID: 70
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L37RB [auth k]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: 71
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L38SB [auth l]69Homo sapiensMutation(s): 0 
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Find proteins for P63173 (Homo sapiens)
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GTEx:  ENSG00000172809 
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Entity ID: 72
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L39TB [auth m]50Homo sapiensMutation(s): 0 
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Find proteins for P62891 (Homo sapiens)
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GTEx:  ENSG00000198918 
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Entity ID: 73
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L40UB [auth n]50Homo sapiensMutation(s): 0 
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Find proteins for P62987 (Homo sapiens)
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GTEx:  ENSG00000221983 
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Entity ID: 74
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L41VB [auth o]25Homo sapiensMutation(s): 0 
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Find proteins for P62945 (Homo sapiens)
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GTEx:  ENSG00000229117 
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Entity ID: 75
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L36aWB [auth p]105Homo sapiensMutation(s): 0 
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Find proteins for P83881 (Homo sapiens)
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GTEx:  ENSG00000241343 
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Entity ID: 76
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L37aXB [auth q]91Homo sapiensMutation(s): 0 
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Find proteins for P61513 (Homo sapiens)
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GTEx:  ENSG00000197756 
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UniProt GroupP61513
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Entity ID: 77
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L28YB [auth r]122Homo sapiensMutation(s): 0 
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Find proteins for P46779 (Homo sapiens)
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GTEx:  ENSG00000108107 
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Entity ID: 81
MoleculeChains Sequence LengthOrganismDetailsImage
Cadherin-1CC [auth y]39Homo sapiensMutation(s): 0 
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Find proteins for P12830 (Homo sapiens)
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GTEx:  ENSG00000039068 
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Entity ID: 83
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L27EC [auth a]134Homo sapiensMutation(s): 0 
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Find proteins for P61353 (Homo sapiens)
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GTEx:  ENSG00000131469 
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Entity ID: 1
MoleculeChains LengthOrganismImage
18S ribosomal RNAA [auth S2]1,714Homo sapiens
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Entity ID: 38
MoleculeChains LengthOrganismImage
5.8S ribosomal RNALA [auth D]157Homo sapiens
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Entity ID: 39
MoleculeChains LengthOrganismImage
5S ribosomal RNAMA [auth E]119Homo sapiens
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