6Y0G

Structure of human ribosome in classical-PRE state


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.20 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

Dynamics of uS19 C-Terminal Tail during the Translation Elongation Cycle in Human Ribosomes.

Bhaskar, V.Graff-Meyer, A.Schenk, A.D.Cavadini, S.von Loeffelholz, O.Natchiar, S.K.Artus-Revel, C.G.Hotz, H.R.Bretones, G.Klaholz, B.P.Chao, J.A.

(2020) Cell Rep 31: 107473-107473

  • DOI: https://doi.org/10.1016/j.celrep.2020.03.037
  • Primary Citation of Related Structures:  
    6Y0G, 6Y2L, 6Y57

  • PubMed Abstract: 

    Ribosomes undergo multiple conformational transitions during translation elongation. Here, we report the high-resolution cryoelectron microscopy (cryo-EM) structure of the human 80S ribosome in the post-decoding pre-translocation state (classical-PRE) at 3.3-Å resolution along with the rotated (hybrid-PRE) and the post-translocation states (POST). The classical-PRE state ribosome structure reveals a previously unobserved interaction between the C-terminal region of the conserved ribosomal protein uS19 and the A- and P-site tRNAs and the mRNA in the decoding site. In addition to changes in the inter-subunit bridges, analysis of different ribosomal conformations reveals the dynamic nature of this domain and suggests a role in tRNA accommodation and translocation during elongation. Furthermore, we show that disease-associated mutations in uS19 result in increased frameshifting. Together, this structure-function analysis provides mechanistic insights into the role of the uS19 C-terminal tail in the context of mammalian ribosomes.


  • Organizational Affiliation

    Friedrich Miescher Institute for Biomedical Research, 4058 Basel, Switzerland.


Macromolecules

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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Nascent peptideC [auth C4]2Homo sapiensMutation(s): 0 
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L8H [auth LA]257Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000161016 
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UniProt GroupP62917
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L3I [auth LB]403Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000100316 
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L4J [auth LC]427Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000174444 
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L5K [auth LD]297Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000122406 
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L6L [auth LE]288Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000089009 
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L7M [auth LF]248Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000147604 
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L7aN [auth LG]266Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000148303 
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L9O [auth LH]192Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000163682 
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L10-likeP [auth LI]214Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000165496 
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L11Q [auth LJ]178Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000142676 
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L13R [auth LL]211Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000167526 
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L14S [auth LM]215Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000188846 
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L15T [auth LN]204Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000174748 
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L13aU [auth LO]203Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000142541 
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L17V [auth LP]184Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000265681 
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Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L18W [auth LQ]188Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000063177 
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Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L19X [auth LR]196Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000108298 
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Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L18aY [auth LS]176Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000105640 
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Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L21Z [auth LT]160Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000122026 
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Entity ID: 26
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L22AA [auth LU]128Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000116251 
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Entity ID: 27
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L23BA [auth LV]140Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000125691 
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Entity ID: 28
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L24CA [auth LW]157Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000114391 
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Entity ID: 29
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L23aDA [auth LX]156Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000198242 
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Entity ID: 30
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L26EA [auth LY]145Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000161970 
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Entity ID: 31
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L27FA [auth LZ]136Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000131469 
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Entity ID: 32
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L27aGA [auth La]148Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000166441 
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Entity ID: 33
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L29HA [auth Lb]159Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000162244 
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Entity ID: 34
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L30IA [auth Lc]115Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000156482 
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Entity ID: 35
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L31JA [auth Ld]125Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000071082 
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Entity ID: 36
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L32KA [auth Le]135Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000144713 
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Entity ID: 37
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L35aLA [auth Lf]110Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000182899 
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Entity ID: 38
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L34MA [auth Lg]117Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000109475 
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Entity ID: 39
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L35NA [auth Lh]123Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000136942 
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Entity ID: 40
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L36OA [auth Li]105Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000130255 
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Entity ID: 41
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L37PA [auth Lj]97Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000145592 
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Entity ID: 42
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L38QA [auth Lk]70Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000172809 
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Entity ID: 43
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L39RA [auth Ll]51Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000198918 
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Entity ID: 44
MoleculeChains Sequence LengthOrganismDetailsImage
Ubiquitin-60S ribosomal protein L40SA [auth Lm]128Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000221983 
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Entity ID: 45
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L41TA [auth Ln]25Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000229117 
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Entity ID: 46
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L36aUA [auth Lo]106Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000241343 
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Entity ID: 47
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L37aVA [auth Lp]92Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000197756 
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Entity ID: 48
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L28WA [auth Lr]137Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000108107 
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Entity ID: 50
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein SAYA [auth SA]295Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000168028 
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Entity ID: 51
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S3aZA [auth SB]264Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000145425 
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Entity ID: 52
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S2AB [auth SC]293Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000140988 
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Entity ID: 53
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S3BB [auth SD]243Homo sapiensMutation(s): 0 
EC: 4.2.99.18
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GTEx:  ENSG00000149273 
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Entity ID: 54
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S4, X isoformCB [auth SE]263Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000198034 
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Entity ID: 55
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S5DB [auth SF]204Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000083845 
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Entity ID: 56
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S6EB [auth SG]249Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000137154 
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Entity ID: 57
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S7FB [auth SH]194Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000171863 
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Entity ID: 58
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S8GB [auth SI]208Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000142937 
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Entity ID: 59
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S9HB [auth SJ]194Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000170889 
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Entity ID: 60
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S10IB [auth SK]165Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000124614 
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Entity ID: 61
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S11JB [auth SL]158Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000142534 
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Entity ID: 62
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S12KB [auth SM]132Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000112306 
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Entity ID: 63
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S13LB [auth SN]151Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000110700 
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Entity ID: 64
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S14MB [auth SO]151Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000164587 
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Entity ID: 65
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S15NB [auth SP]145Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000115268 
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Entity ID: 66
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S16OB [auth SQ]146Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000105193 
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Entity ID: 67
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S17PB [auth SR]135Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000182774 
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Entity ID: 68
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S18QB [auth SS]152Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000231500 
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Entity ID: 69
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S19RB [auth ST]145Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000105372 
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Entity ID: 70
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S20SB [auth SU]119Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000008988 
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Entity ID: 71
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S21TB [auth SV]83Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000171858 
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Entity ID: 72
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S15aUB [auth SW]130Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000134419 
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Entity ID: 73
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S23VB [auth SX]143Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000186468 
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Entity ID: 74
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S24WB [auth SY]133Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000138326 
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Entity ID: 75
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S25XB [auth SZ]125Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000118181 
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Entity ID: 76
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S26YB [auth Sa]115Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000197728 
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Entity ID: 77
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S27ZB [auth Sb]84Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000177954 
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Entity ID: 78
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S28AC [auth Sc]69Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000233927 
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Entity ID: 79
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S29BC [auth Sd]56Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000213741 
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Entity ID: 80
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S30CC [auth Se]59Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000149806 
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Entity ID: 81
MoleculeChains Sequence LengthOrganismDetailsImage
Ubiquitin-40S ribosomal protein S27aDC [auth Sf]156Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000143947 
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Entity ID: 82
MoleculeChains Sequence LengthOrganismDetailsImage
Receptor of activated protein C kinase 1EC [auth Sg]317Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000204628 
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Entity ID: 1
MoleculeChains LengthOrganismImage
mRNAA [auth A4]28Homo sapiens
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Entity ID: 2
MoleculeChains LengthOrganismImage
tRNAB [auth B4],
D [auth D4]
76Homo sapiens
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Entity ID: 4
MoleculeChains LengthOrganismImage
28S ribosomal RNAE [auth L5]5,070Homo sapiens
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Entity ID: 5
MoleculeChains LengthOrganismImage
5S rRNAF [auth L7]120Homo sapiens
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Entity ID: 6
MoleculeChains LengthOrganismImage
5.8S ribosomal RNAG [auth L8]156Homo sapiens
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Entity ID: 49
MoleculeChains LengthOrganismImage
18S ribosomal RNAXA [auth S2]1,869Homo sapiens
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Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
3HE
Query on 3HE

Download Ideal Coordinates CCD File 
GC [auth L5]4-{(2R)-2-[(1S,3S,5S)-3,5-dimethyl-2-oxocyclohexyl]-2-hydroxyethyl}piperidine-2,6-dione
C15 H23 N O4
YPHMISFOHDHNIV-FSZOTQKASA-N
ZN
Query on ZN

Download Ideal Coordinates CCD File 
AE [auth Lm]
BE [auth Lo]
CE [auth Lp]
FF [auth Sa]
GF [auth Sd]
AE [auth Lm],
BE [auth Lo],
CE [auth Lp],
FF [auth Sa],
GF [auth Sd],
YD [auth Lg],
ZD [auth Lj]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
MG
Query on MG

Download Ideal Coordinates CCD File 
AD [auth L5]
AF [auth S2]
BD [auth L5]
BF [auth S2]
CD [auth L5]
AD [auth L5],
AF [auth S2],
BD [auth L5],
BF [auth S2],
CD [auth L5],
CF [auth S2],
DD [auth L5],
DE [auth S2],
DF [auth S2],
ED [auth L5],
EE [auth S2],
EF [auth S2],
FC [auth A4],
FD [auth L5],
FE [auth S2],
GD [auth L5],
GE [auth S2],
HC [auth L5],
HD [auth L5],
HE [auth S2],
IC [auth L5],
ID [auth L5],
IE [auth S2],
JC [auth L5],
JD [auth L5],
JE [auth S2],
KC [auth L5],
KD [auth L5],
KE [auth S2],
LC [auth L5],
LD [auth L5],
LE [auth S2],
MC [auth L5],
MD [auth L5],
ME [auth S2],
NC [auth L5],
ND [auth L5],
NE [auth S2],
OC [auth L5],
OD [auth L5],
OE [auth S2],
PC [auth L5],
PD [auth L5],
PE [auth S2],
QC [auth L5],
QD [auth L5],
QE [auth S2],
RC [auth L5],
RD [auth L7],
RE [auth S2],
SC [auth L5],
SD [auth L7],
SE [auth S2],
TC [auth L5],
TD [auth L8],
TE [auth S2],
UC [auth L5],
UD [auth L8],
UE [auth S2],
VC [auth L5],
VD [auth L8],
VE [auth S2],
WC [auth L5],
WD [auth L8],
WE [auth S2],
XC [auth L5],
XD [auth LI],
XE [auth S2],
YC [auth L5],
YE [auth S2],
ZC [auth L5],
ZE [auth S2]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.20 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION2.1
MODEL REFINEMENTPHENIX1.16

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Swiss National Science FoundationSwitzerland31003A_182314
French Infrastructure for Integrated Structural Biology (FRISBI)FranceANR-10-INSB-05-01
Centre National de la Recherche Scientifique (CNRS)France--

Revision History  (Full details and data files)

  • Version 1.0: 2020-04-15
    Type: Initial release
  • Version 1.1: 2020-04-22
    Changes: Database references