6OLE | pdb_00006ole

Human ribosome nascent chain complex (CDH1-RNC) stalled by a drug-like molecule with AP 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: 3.10 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.2 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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UniProt GroupP08865
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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 
EC: 4.2.99.18
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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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UniProt GroupP62424
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Entity ID: 44
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L9RA [auth J]191Homo sapiensMutation(s): 0 
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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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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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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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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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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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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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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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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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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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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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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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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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GTEx:  ENSG00000125691 
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Entity ID: 58
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L24FB [auth X]61Homo sapiensMutation(s): 0 
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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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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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GTEx:  ENSG00000161970 
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Entity ID: 61
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L27IB [auth a]134Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000131469 
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Entity ID: 62
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L27aJB [auth b]147Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000166441 
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Entity ID: 63
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L29KB [auth c]121Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000162244 
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Entity ID: 64
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L30LB [auth d]103Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000156482 
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Entity ID: 65
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L31MB [auth e]106Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000071082 
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Entity ID: 66
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L32NB [auth f]129Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000144713 
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Entity ID: 67
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L35aOB [auth g]109Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000182899 
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Entity ID: 68
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L34PB [auth h]114Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000109475 
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Entity ID: 69
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L35QB [auth i]122Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000136942 
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Entity ID: 70
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L36RB [auth j]97Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000130255 
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Entity ID: 71
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L37SB [auth k]84Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000145592 
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Entity ID: 72
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L38TB [auth l]69Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000172809 
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Entity ID: 73
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L39UB [auth m]50Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000198918 
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Entity ID: 74
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L40VB [auth n]50Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000221983 
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Entity ID: 75
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L41WB [auth o]25Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000229117 
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Entity ID: 76
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L36aXB [auth p]105Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000241343 
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Entity ID: 77
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L37aYB [auth q]91Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000197756 
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Entity ID: 78
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L28ZB [auth r]122Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000108107 
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Entity ID: 83
MoleculeChains Sequence LengthOrganismDetailsImage
Cadherin-1EC [auth y]39Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000039068 
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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]121Homo sapiens
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Entity ID: 79
MoleculeChains LengthOrganismImage
28S ribosomal RNAAC [auth t]3,607Homo sapiens
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Entity ID: 80
MoleculeChains LengthOrganismImage
AP RNABC [auth u]76Homo sapiens
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Entity ID: 81
MoleculeChains LengthOrganismImage
PE RNACC [auth v]76Homo sapiens
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Entity ID: 82
MoleculeChains LengthOrganismImage
mRNADC [auth w]10Homo sapiens
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Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
MVM
Query on MVM
Download Ideal Coordinates CCD File 
QD [auth y]N-(3-chloropyridin-2-yl)-N-[(3R)-piperidin-3-yl]-4-(3H-[1,2,3]triazolo[4,5-b]pyridin-3-yl)benzamide
C22 H20 Cl N7 O
FDTXHWQFIXYHCL-QGZVFWFLSA-N
ZN
Query on ZN
Download Ideal Coordinates CCD File 
GC [auth S2]
HD [auth k]
ID [auth p]
JC [auth Sa]
JD [auth q]
GC [auth S2],
HD [auth k],
ID [auth p],
JC [auth Sa],
JD [auth q],
KC [auth Sf]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
MG
Query on MG
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AD [auth E]
BD [auth E]
CD [auth E]
DD [auth E]
ED [auth O]
AD [auth E],
BD [auth E],
CD [auth E],
DD [auth E],
ED [auth O],
FC [auth S2],
FD [auth Z],
GD [auth b],
HC [auth S2],
IC [auth S2],
KD [auth t],
LC [auth A],
LD [auth t],
MC [auth B],
MD [auth t],
NC [auth D],
ND [auth t],
OC [auth D],
OD [auth t],
PC [auth D],
PD [auth t],
QC [auth D],
RC [auth D],
SC [auth D],
TC [auth D],
UC [auth D],
VC [auth E],
WC [auth E],
XC [auth E],
YC [auth E],
ZC [auth E]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.10 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)United StatesR01-GM065050

Revision History  (Full details and data files)

  • Version 1.0: 2019-06-19
    Type: Initial release
  • Version 1.1: 2019-12-18
    Changes: Author supporting evidence
  • Version 1.2: 2024-10-23
    Changes: Data collection, Database references, Derived calculations, Structure summary