8G5Z

mRNA decoding in human is kinetically and structurally distinct from bacteria (GA state)


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.64 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 2.0 of the entry. See complete history


Literature

mRNA decoding in human is kinetically and structurally distinct from bacteria.

Holm, M.Natchiar, S.K.Rundlet, E.J.Myasnikov, A.G.Watson, Z.L.Altman, R.B.Wang, H.Y.Taunton, J.Blanchard, S.C.

(2023) Nature 617: 200-207

  • DOI: https://doi.org/10.1038/s41586-023-05908-w
  • Primary Citation of Related Structures:  
    8G5Y, 8G5Z, 8G60, 8G61, 8G6J, 8GLP

  • PubMed Abstract: 

    In all species, ribosomes synthesize proteins by faithfully decoding messenger RNA (mRNA) nucleotide sequences using aminoacyl-tRNA substrates. Current knowledge of the decoding mechanism derives principally from studies on bacterial systems 1 . Although key features are conserved across evolution 2 , eukaryotes achieve higher-fidelity mRNA decoding than bacteria 3 . In human, changes in decoding fidelity are linked to ageing and disease and represent a potential point of therapeutic intervention in both viral and cancer treatment 4-6 . Here we combine single-molecule imaging and cryogenic electron microscopy methods to examine the molecular basis of human ribosome fidelity to reveal that the decoding mechanism is both kinetically and structurally distinct from that of bacteria. Although decoding is globally analogous in both species, the reaction coordinate of aminoacyl-tRNA movement is altered on the human ribosome and the process is an order of magnitude slower. These distinctions arise from eukaryote-specific structural elements in the human ribosome and in the elongation factor eukaryotic elongation factor 1A (eEF1A) that together coordinate faithful tRNA incorporation at each mRNA codon. The distinct nature and timing of conformational changes within the ribosome and eEF1A rationalize how increased decoding fidelity is achieved and potentially regulated in eukaryotic species.


  • Organizational Affiliation

    Department of Structural Biology, St Jude Children's Research Hospital, Memphis, TN, USA.


Macromolecules

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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S3aE [auth SB]223Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000145425 
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein SAF [auth SA]222Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000168028 
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S3G [auth SD]226Homo sapiensMutation(s): 0 
EC: 4.2.99.18
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GTEx:  ENSG00000149273 
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S9H [auth SJ]185Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000170889 
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
eS4I [auth SE]262Homo sapiensMutation(s): 0 
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S2J [auth SC]222Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000140988 
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S6K [auth SG]237Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000137154 
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S5L [auth SF]189Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000083845 
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S7M [auth SH]189Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000171863 
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S15aN [auth SW]129Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000134419 
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S8O [auth SI]206Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000142937 
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
uS9P [auth SQ]141Homo sapiensMutation(s): 0 
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
uS10Q [auth SU]101Homo sapiensMutation(s): 0 
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
eS10R [auth SK]96Homo sapiensMutation(s): 0 
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
uS11S [auth SO]135Homo sapiensMutation(s): 0 
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
uS12T [auth SX]142Homo sapiensMutation(s): 0 
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
eS12U [auth SM]122Homo sapiensMutation(s): 0 
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Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
uS13V [auth SS]148Homo sapiensMutation(s): 0 
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Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S29W [auth Sd]55Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000213741 
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Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S13X [auth SN]150Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000110700 
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Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
uS17Y [auth SL]143Homo sapiensMutation(s): 0 
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Entity ID: 26
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S17Z [auth SR]134Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000182774 
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Entity ID: 27
MoleculeChains Sequence LengthOrganismDetailsImage
uS19AA [auth SP]133Homo sapiensMutation(s): 0 
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Entity ID: 28
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S19BA [auth ST]143Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000105372 
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Entity ID: 29
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S21CA [auth SV]83Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000171858 
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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
eS25EA [auth SZ]84Homo sapiensMutation(s): 0 
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Entity ID: 32
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S26FA [auth Sa]99Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000197728 
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Entity ID: 33
MoleculeChains Sequence LengthOrganismDetailsImage
eS27GA [auth Sb]83Homo sapiensMutation(s): 0 
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Entity ID: 34
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S28HA [auth Sc]64Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000233927 
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Entity ID: 35
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S30IA [auth Se]59Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000149806 
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Entity ID: 36
MoleculeChains Sequence LengthOrganismDetailsImage
eS31JA [auth Sf]75Homo sapiensMutation(s): 0 
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Entity ID: 37
MoleculeChains Sequence LengthOrganismDetailsImage
Receptor of activated protein C kinase 1KA [auth Sg]313Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000204628 
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Entity ID: 38
MoleculeChains Sequence LengthOrganismDetailsImage
uL1LA [auth Lz]211Homo sapiensMutation(s): 0 
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Entity ID: 39
MoleculeChains Sequence LengthOrganismDetailsImage
uL2MA [auth LA]251Homo sapiensMutation(s): 0 
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Entity ID: 40
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L3NA [auth LB]402Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000100316 
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Entity ID: 41
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L4OA [auth LC]368Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000174444 
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Entity ID: 42
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L11PA [auth LJ]169Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000142676 
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Entity ID: 43
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L9QA [auth LH]190Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000163682 
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Entity ID: 44
MoleculeChains Sequence LengthOrganismDetailsImage
eL6RA [auth LE]223Homo sapiensMutation(s): 0 
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Entity ID: 45
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L7aSA [auth LG]239Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000148303 
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Entity ID: 46
MoleculeChains Sequence LengthOrganismDetailsImage
60S acidic ribosomal protein P0TA [auth Lq]196Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000089157 
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Entity ID: 47
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L12UA [auth LK]147Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000197958 
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Entity ID: 48
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L13aVA [auth LO]201Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000142541 
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Entity ID: 49
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L13WA [auth LL]206Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000167526 
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Entity ID: 50
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L23XA [auth LV]140Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000125691 
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Entity ID: 51
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L14YA [auth LM]136Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000188846 
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Entity ID: 52
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L27aZA [auth La]147Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000166441 
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Entity ID: 53
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L15AB [auth LN]203Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000174748 
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Entity ID: 54
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L10BB [auth LI]205Homo sapiensMutation(s): 0 
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Find proteins for P27635 (Homo sapiens)
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GTEx:  ENSG00000147403 
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Entity ID: 55
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L5CB [auth LD]294Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000122406 
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Entity ID: 56
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L18DB [auth LQ]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: 57
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L19EB [auth LR]187Homo 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: 58
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L18aFB [auth LS]176Homo 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: 59
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L21GB [auth LT]159Homo 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: 60
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L17HB [auth LP]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: 61
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L22IB [auth LU]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: 62
MoleculeChains Sequence LengthOrganismDetailsImage
uL23JB [auth LX]118Homo sapiensMutation(s): 0 
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Entity ID: 63
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L26KB [auth LY]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: 64
MoleculeChains Sequence LengthOrganismDetailsImage
eL24LB [auth LW]118Homo sapiensMutation(s): 0 
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Entity ID: 65
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L27MB [auth LZ]135Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000131469 
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Entity ID: 66
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L28NB [auth Lr]125Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000108107 
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Entity ID: 67
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L35OB [auth Lh]122Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000136942 
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Entity ID: 68
MoleculeChains Sequence LengthOrganismDetailsImage
eL29PB [auth Lb]109Homo sapiensMutation(s): 0 
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Entity ID: 69
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L7QB [auth LF]225Homo sapiensMutation(s): 0 
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Find proteins for P18124 (Homo sapiens)
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GTEx:  ENSG00000147604 
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Entity ID: 70
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L30RB [auth Lc]98Homo 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: 71
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L31SB [auth Ld]107Homo 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: 72
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L32TB [auth Le]128Homo sapiensMutation(s): 0 
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Find proteins for P62910 (Homo sapiens)
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PHAROS:  P62910
GTEx:  ENSG00000144713 
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Entity ID: 73
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L35aUB [auth Lf]109Homo sapiensMutation(s): 0 
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Find proteins for P18077 (Homo sapiens)
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PHAROS:  P18077
GTEx:  ENSG00000182899 
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Entity ID: 74
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L34VB [auth Lg]114Homo sapiensMutation(s): 0 
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Find proteins for P49207 (Homo sapiens)
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PHAROS:  P49207
GTEx:  ENSG00000109475 
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UniProt GroupP49207
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Entity ID: 75
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L36WB [auth Li]102Homo sapiensMutation(s): 0 
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Find proteins for Q9Y3U8 (Homo sapiens)
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PHAROS:  Q9Y3U8
GTEx:  ENSG00000130255 
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Entity ID: 76
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L37XB [auth Lj]86Homo sapiensMutation(s): 0 
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Find proteins for P61927 (Homo sapiens)
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PHAROS:  P61927
GTEx:  ENSG00000145592 
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Entity ID: 77
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L38YB [auth Lk]69Homo sapiensMutation(s): 0 
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Find proteins for P63173 (Homo sapiens)
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PHAROS:  P63173
GTEx:  ENSG00000172809 
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UniProt GroupP63173
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Entity ID: 78
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L39ZB [auth Ll]50Homo sapiensMutation(s): 0 
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Find proteins for P62891 (Homo sapiens)
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GTEx:  ENSG00000198918 
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