6QZP

High-resolution cryo-EM structure of the human 80S ribosome


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.90 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 3.0 of the entry. See complete history


Literature

Visualization of chemical modifications in the human 80S ribosome structure.

Natchiar, S.K.Myasnikov, A.G.Kratzat, H.Hazemann, I.Klaholz, B.P.

(2017) Nature 551: 472-477

  • DOI: https://doi.org/10.1038/nature24482
  • Primary Citation of Related Structures:  
    6QZP

  • PubMed Abstract: 

    Chemical modifications of human ribosomal RNA (rRNA) are introduced during biogenesis and have been implicated in the dysregulation of protein synthesis, as is found in cancer and other diseases. However, their role in this phenomenon is unknown. Here we visualize more than 130 individual rRNA modifications in the three-dimensional structure of the human ribosome, explaining their structural and functional roles. In addition to a small number of universally conserved sites, we identify many eukaryote- or human-specific modifications and unique sites that form an extended shell in comparison to bacterial ribosomes, and which stabilize the RNA. Several of the modifications are associated with the binding sites of three ribosome-targeting antibiotics, or are associated with degenerate states in cancer, such as keto alkylations on nucleotide bases reminiscent of specialized ribosomes. This high-resolution structure of the human 80S ribosome paves the way towards understanding the role of epigenetic rRNA modifications in human diseases and suggests new possibilities for designing selective inhibitors and therapeutic drugs.


  • Organizational Affiliation

    Institute of Genetics and of Molecular and Cellular Biology (IGBMC), 1 rue Laurent Fries, Illkirch, France.


Macromolecules

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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L8D [auth LA]248Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000161016 
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L3E [auth LB]402Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000100316 
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L4F [auth LC]368Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000174444 
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L5G [auth LD]293Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000122406 
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L6H [auth LE]236Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000089009 
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L7I [auth LF]225Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000147604 
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L7aJ [auth LG]241Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000148303 
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L9K [auth LH]190Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000163682 
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L10-likeL [auth LI]213Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000165496 
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L11M [auth LJ]176Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000142676 
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L13N [auth LL]210Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000167526 
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L14O [auth LM]139Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000188846 
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L15P [auth LN]203Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000174748 
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L13aQ [auth LO]201Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000142541 
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L17R [auth LP]153Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000265681 
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L18S [auth LQ]187Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000063177 
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L19T [auth LR]187Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000108298 
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L18aU [auth LS]175Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000105640 
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Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L21V [auth LT]159Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000122026 
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Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L22W [auth LU]101Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000116251 
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Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L23X [auth LV]131Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000125691 
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Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L24Y [auth LW]124Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000114391 
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Entity ID: 26
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L23aZ [auth LX]120Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000198242 
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Entity ID: 27
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L26AA [auth LY]134Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000161970 
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Entity ID: 28
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L27BA [auth LZ]135Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000131469 
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Entity ID: 29
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L27aCA [auth La]147Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000166441 
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Entity ID: 30
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L29DA [auth Lb]109Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000162244 
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Entity ID: 31
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L30EA [auth Lc]98Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000156482 
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Entity ID: 32
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L31FA [auth Ld]107Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000071082 
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Entity ID: 33
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L32GA [auth Le]128Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000144713 
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Entity ID: 34
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L35aHA [auth Lf]109Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000182899 
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Entity ID: 35
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L34IA [auth Lg]114Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000109475 
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Entity ID: 36
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L35JA [auth Lh]122Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000136942 
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Entity ID: 37
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L36KA [auth Li]102Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000130255 
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Entity ID: 38
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L37LA [auth Lj]86Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000145592 
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Entity ID: 39
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L38MA [auth Lk]69Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000172809 
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Entity ID: 40
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L39NA [auth Ll]50Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000198918 
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Entity ID: 41
MoleculeChains Sequence LengthOrganismDetailsImage
Ubiquitin-60S ribosomal protein L40OA [auth Lm]52Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000221983 
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Entity ID: 42
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L41PA [auth Ln]24Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000229117 
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Entity ID: 43
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L36aQA [auth Lo]105Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000241343 
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Entity ID: 44
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L37aRA [auth Lp]91Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000197756 
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UniProt GroupP61513
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Entity ID: 45
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L28SA [auth Lr]125Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000108107 
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Entity ID: 46
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L10aTA [auth Lz]217Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000198755 
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Entity ID: 49
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein SAWA [auth SA]221Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000168028 
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UniProt GroupP08865
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Entity ID: 50
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S3aXA [auth SB]214Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000145425 
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UniProt GroupP61247
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Entity ID: 51
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S3YA [auth SD]227Homo sapiensMutation(s): 0 
EC: 4.2.99.18
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GTEx:  ENSG00000149273 
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UniProt GroupP23396
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Entity ID: 52
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S4, X isoformZA [auth SE]262Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000198034 
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Entity ID: 53
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S5AB [auth SF]189Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000083845 
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UniProt GroupP46782
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Entity ID: 54
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S7BB [auth SH]186Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000171863 
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Entity ID: 55
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S8CB [auth SI]206Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000142937 
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UniProt GroupP62241
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Entity ID: 56
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S10DB [auth SK]98Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000124614 
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Entity ID: 57
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S11EB [auth SL]153Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000142534 
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Entity ID: 58
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S15FB [auth SP]127Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000115268 
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Entity ID: 59
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S16GB [auth SQ]141Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000105193 
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Entity ID: 60
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S17HB [auth SR]135Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000182774 
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Entity ID: 61
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S18IB [auth SS]145Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000231500 
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UniProt GroupP62269
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Entity ID: 62
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S19JB [auth ST]143Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000105372 
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Entity ID: 63
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S20KB [auth SU]103Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000008988 
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Entity ID: 64
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S21LB [auth SV]83Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000171858 
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Entity ID: 65
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S23MB [auth SX]141Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000186468 
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UniProt GroupP62266
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Entity ID: 66
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S26NB [auth Sa]102Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000197728 
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Entity ID: 67
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S28OB [auth Sc]64Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000233927 
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Entity ID: 68
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S29PB [auth Sd]55Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000213741 
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UniProt GroupP62273
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Entity ID: 69
MoleculeChains Sequence LengthOrganismDetailsImage
Receptor of activated protein C kinase 1QB [auth Sg]313Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000204628 
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Entity ID: 70
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S2RB [auth SC]222Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000140988 
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Entity ID: 71
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S6SB [auth SG]237Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000137154 
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Entity ID: 72
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S9TB [auth SJ]185Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000170889 
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Entity ID: 73
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S12UB [auth SM]122Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000112306 
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Entity ID: 74
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S13VB [auth SN]150Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000110700 
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Entity ID: 75
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S14WB [auth SO]140Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000164587 
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Entity ID: 76
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S15aXB [auth SW]129Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000134419 
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Entity ID: 77
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S24YB [auth SY]131Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000138326 
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Entity ID: 78
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S25ZB [auth SZ]75Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000118181 
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Entity ID: 79
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S27AC [auth Sb]83Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000177954 
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Entity ID: 80
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S30BC [auth Se]58Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000149806 
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Entity ID: 81
MoleculeChains Sequence LengthOrganismDetailsImage
Ubiquitin-40S ribosomal protein S27aCC [auth Sf]67Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000143947 
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Entity ID: 1
MoleculeChains LengthOrganismImage
28S rRNA (3773-MER)A [auth L5]3,773Homo sapiens
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Entity ID: 2
MoleculeChains