6OLE

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 1.1 of the entry. See complete history


Literature

Structural basis for selective stalling of human ribosome nascent chain complexes by a drug-like molecule.

Li, W.Ward, F.R.McClure, K.F.Chang, S.T.Montabana, E.Liras, S.Dullea, R.G.Cate, J.H.D.

(2019) Nat Struct Mol Biol 26: 501-509

  • DOI: 10.1038/s41594-019-0236-8
  • Primary Citation of Related Structures:  
    6OM0, 6OLF, 6OLE, 6OLG, 6OLI, 6OM7, 6OLZ

  • 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 th ...

    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 Chemistry, University of California, Berkeley, Berkeley, CA, USA. jcate@lbl.gov.



Macromolecules

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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein SASA221Homo sapiensMutation(s): 0 
Gene Names: RPSALAMBRLAMR1
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S3aSB214Homo sapiensMutation(s): 0 
Gene Names: RPS3AFTE1MFTL
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S3SD226Homo sapiensMutation(s): 0 
Gene Names: RPS3OK/SW-cl.26
EC: 4.2.99.18
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S4, X isoformSE259Homo sapiensMutation(s): 0 
Gene Names: RPS4XCCG2RPS4SCAR
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S5SF189Homo sapiensMutation(s): 0 
Gene Names: RPS5
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S7SH189Homo sapiensMutation(s): 0 
Gene Names: RPS7
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S8SI204Homo sapiensMutation(s): 0 
Gene Names: RPS8OK/SW-cl.83
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S10SK98Homo sapiensMutation(s): 0 
Gene Names: RPS10
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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S11SL153Homo sapiensMutation(s): 0 
Gene Names: RPS11
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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S15SP127Homo sapiensMutation(s): 0 
Gene Names: RPS15RIG
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Entity ID: 12
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S16SQ146Homo sapiensMutation(s): 0 
Gene Names: RPS16
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Entity ID: 13
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40S ribosomal protein S17SR134Homo sapiensMutation(s): 0 
Gene Names: RPS17RPS17L
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Entity ID: 14
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S18SS145Homo sapiensMutation(s): 0 
Gene Names: RPS18D6S218E
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Entity ID: 15
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S19ST143Homo sapiensMutation(s): 0 
Gene Names: RPS19
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Entity ID: 16
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S20SU104Homo sapiensMutation(s): 0 
Gene Names: RPS20
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Entity ID: 17
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40S ribosomal protein S21SV82Homo sapiensMutation(s): 0 
Gene Names: RPS21
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Entity ID: 18
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40S ribosomal protein S23SX141Homo sapiensMutation(s): 0 
Gene Names: RPS23
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Entity ID: 19
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40S ribosomal protein S26Sa102Homo sapiensMutation(s): 0 
Gene Names: RPS26
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Entity ID: 20
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S28Sc64Homo sapiensMutation(s): 0 
Gene Names: RPS28
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Entity ID: 21
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S29Sd55Homo sapiensMutation(s): 0 
Gene Names: RPS29
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Entity ID: 22
MoleculeChainsSequence LengthOrganismDetailsImage
Receptor of activated protein C kinase 1Sg312Homo sapiensMutation(s): 0 
Gene Names: RACK1GNB2L1HLC7PIG21
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Entity ID: 23
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S2SC220Homo sapiensMutation(s): 0 
Gene Names: RPS2RPS4
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Entity ID: 24
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S6SG237Homo sapiensMutation(s): 0 
Gene Names: RPS6OK/SW-cl.2
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Entity ID: 25
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S9SJ185Homo sapiensMutation(s): 0 
Gene Names: RPS9
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Entity ID: 26
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S12SM118Homo sapiensMutation(s): 0 
Gene Names: RPS12
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Entity ID: 27
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S13SN150Homo sapiensMutation(s): 0 
Gene Names: RPS13
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Entity ID: 28
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S14SO137Homo sapiensMutation(s): 0 
Gene Names: RPS14PRO2640
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Entity ID: 29
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S15aSW129Homo sapiensMutation(s): 0 
Gene Names: RPS15AOK/SW-cl.82
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Entity ID: 30
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S24SY131Homo sapiensMutation(s): 0 
Gene Names: RPS24
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Entity ID: 31
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S25SZ73Homo sapiensMutation(s): 0 
Gene Names: RPS25
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Entity ID: 32
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S27Sb82Homo sapiensMutation(s): 0 
Gene Names: RPS27MPS1
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Entity ID: 33
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S30Se57Homo sapiensMutation(s): 0 
Gene Names: FAU
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Entity ID: 34
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S27aSf67Homo sapiensMutation(s): 0 
Gene Names: RPS27AUBA80UBCEP1
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Entity ID: 35
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60S ribosomal protein L8A252Homo sapiensMutation(s): 0 
Gene Names: RPL8
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Entity ID: 36
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60S ribosomal protein L3B397Homo sapiensMutation(s): 0 
Gene Names: RPL3OK/SW-cl.32
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Entity ID: 37
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60S ribosomal protein L4C363Homo sapiensMutation(s): 0 
Gene Names: RPL4RPL1
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Entity ID: 40
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60S ribosomal protein L5F294Homo sapiensMutation(s): 0 
Gene Names: RPL5MSTP030
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Entity ID: 41
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L6G247Homo sapiensMutation(s): 0 
Gene Names: RPL6TXREB1
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Entity ID: 42
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L7H225Homo sapiensMutation(s): 0 
Gene Names: RPL7
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Entity ID: 43
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60S ribosomal protein L7aI234Homo sapiensMutation(s): 0 
Gene Names: RPL7ASURF-3SURF3
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Entity ID: 44
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60S ribosomal protein L9J191Homo sapiensMutation(s): 0 
Gene Names: RPL9OK/SW-cl.103RPL9P7RPL9P8RPL9P9
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Entity ID: 45
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60S ribosomal protein L10K211Homo sapiensMutation(s): 0 
Gene Names: RPL10DXS648EQM
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Entity ID: 46
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60S ribosomal protein L11L169Homo sapiensMutation(s): 0 
Gene Names: RPL11
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Entity ID: 47
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60S ribosomal protein L13M205Homo sapiensMutation(s): 0 
Gene Names: RPL13BBC1OK/SW-cl.46
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Entity ID: 48
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60S ribosomal protein L14N139Homo sapiensMutation(s): 0 
Gene Names: RPL14
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Entity ID: 49
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60S ribosomal protein L15O203Homo sapiensMutation(s): 0 
Gene Names: RPL15EC45TCBAP0781
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Entity ID: 50
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60S ribosomal protein L13aP195Homo sapiensMutation(s): 0 
Gene Names: RPL13A
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Entity ID: 51
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60S ribosomal protein L17Q153Homo sapiensMutation(s): 0 
Gene Names: RPL17
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Entity ID: 52
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60S ribosomal protein L18R187Homo sapiensMutation(s): 0 
Gene Names: RPL18
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Entity ID: 53
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60S ribosomal protein L19S181Homo sapiensMutation(s): 0 
Gene Names: RPL19
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Entity ID: 54
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60S ribosomal protein L18aT175Homo sapiensMutation(s): 0 
Gene Names: RPL18A
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Entity ID: 55
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60S ribosomal protein L21U157Homo sapiensMutation(s): 0 
Gene Names: RPL21
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Entity ID: 56
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60S ribosomal protein L22V99Homo sapiensMutation(s): 0 
Gene Names: RPL22
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Entity ID: 57
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60S ribosomal protein L23W129Homo sapiensMutation(s): 0 
Gene Names: RPL23
Find proteins for P62829 (Homo sapiens)
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PHAROS  P62829
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Entity ID: 58
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L24X61Homo sapiensMutation(s): 0 
Gene Names: RPL24
Find proteins for P83731 (Homo sapiens)
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Entity ID: 59
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L23aY117Homo sapiensMutation(s): 0 
Gene Names: RPL23A
Find proteins for P62750 (Homo sapiens)
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Entity ID: 60
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L26Z134Homo sapiensMutation(s): 0 
Gene Names: RPL26
Find proteins for P61254 (Homo sapiens)
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PHAROS  P61254
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Entity ID: 61
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L27a134Homo sapiensMutation(s): 0 
Gene Names: RPL27
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PHAROS  P61353
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Entity ID: 62
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L27ab147Homo sapiensMutation(s): 0 
Gene Names: RPL27A
Find proteins for P46776 (Homo sapiens)
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PHAROS  P46776
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Entity ID: 63
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L29c121Homo sapiensMutation(s): 0 
Gene Names: RPL29
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Entity ID: 64
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L30d103Homo sapiensMutation(s): 0 
Gene Names: RPL30
Find proteins for P62888 (Homo sapiens)
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Entity ID: 65
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60S ribosomal protein L31e106Homo sapiensMutation(s): 0 
Gene Names: RPL31
Find proteins for P62899 (Homo sapiens)
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Entity ID: 66
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L32f129Homo sapiensMutation(s): 0 
Gene Names: RPL32PP9932
Find proteins for P62910 (Homo sapiens)
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PHAROS  P62910
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Entity ID: 67
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L35ag109Homo sapiensMutation(s): 0 
Gene Names: RPL35AGIG33
Find proteins for P18077 (Homo sapiens)
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PHAROS  P18077
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Entity ID: 68
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60S ribosomal protein L34h114Homo sapiensMutation(s): 0 
Gene Names: RPL34
Find proteins for P49207 (Homo sapiens)
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PHAROS  P49207
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Entity ID: 69
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60S ribosomal protein L35i122Homo sapiensMutation(s): 0 
Gene Names: RPL35
Find proteins for P42766 (Homo sapiens)
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PHAROS  P42766
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Entity ID: 70
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60S ribosomal protein L36j97Homo sapiensMutation(s): 0 
Gene Names: RPL36
Find proteins for Q9Y3U8 (Homo sapiens)
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PHAROS  Q9Y3U8
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Entity ID: 71
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60S ribosomal protein L37k84Homo sapiensMutation(s): 0 
Gene Names: RPL37
Find proteins for P61927 (Homo sapiens)
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Entity ID: 72
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L38l69Homo sapiensMutation(s): 0 
Gene Names: RPL38
Find proteins for P63173 (Homo sapiens)
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Entity ID: 73
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60S ribosomal protein L39m50Homo sapiensMutation(s): 0 
Gene Names: RPL39
Find proteins for P62891 (Homo sapiens)
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PHAROS  P62891
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Entity ID: 74
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60S ribosomal protein L40n50Homo sapiensMutation(s): 0 
Gene Names: UBA52UBCEP2
Find proteins for P62987 (Homo sapiens)
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PHAROS  P62987
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Entity ID: 75
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L41o25Homo sapiensMutation(s): 0 
Gene Names: RPL41
Find proteins for P62945 (Homo sapiens)
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PHAROS  P62945
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Entity ID: 76
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60S ribosomal protein L36ap105Homo sapiensMutation(s): 0 
Gene Names: RPL36ARPL44GIG15MIG6
Find proteins for P83881 (Homo sapiens)
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PHAROS  P83881
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Entity ID: 77
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L37aq91Homo sapiensMutation(s): 0 
Gene Names: RPL37A
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PHAROS  P61513
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Entity ID: 78
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60S ribosomal protein L28r122Homo sapiensMutation(s): 0 
Gene Names: RPL28
Find proteins for P46779 (Homo sapiens)
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PHAROS  P46779
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Entity ID: 83
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Cadherin-1y39Homo sapiensMutation(s): 0 
Gene Names: CDH1CDHEUVO
Find proteins for P12830 (Homo sapiens)
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Entity ID: 1
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18S ribosomal RNAS21714Homo sapiens
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Entity ID: 38
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5.8S ribosomal RNAD157Homo sapiens
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Entity ID: 39
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5S ribosomal RNAE121Homo sapiens
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Entity ID: 79
MoleculeChainsLengthOrganismImage
28S ribosomal RNAt3607Homo sapiens
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Entity ID: 80
MoleculeChainsLengthOrganismImage
AP RNAu76Homo sapiens
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Entity ID: 81
MoleculeChainsLengthOrganismImage
PE RNAv76Homo sapiens
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  • Entity ID: 82
    MoleculeChainsLengthOrganismImage
    mRNAw10Homo sapiens
    Small Molecules
    Ligands 3 Unique
    IDChainsName / Formula / InChI Key2D Diagram3D Interactions
    MVM
    Query on MVM

    Download CCD File 
    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
     Ligand Interaction
    ZN
    Query on ZN

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    S2, Sa, Sf, k, p, q
    ZINC ION
    Zn
    PTFCDOFLOPIGGS-UHFFFAOYSA-N
     Ligand Interaction
    MG
    Query on MG

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    A, B, D, E, O, S2, Z, b, t
    MAGNESIUM ION
    Mg
    JLVVSXFLKOJNIY-UHFFFAOYSA-N
     Ligand Interaction
    Experimental Data & Validation

    Experimental Data

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

    Structure Validation

    View Full Validation Report



    Entry History & Funding Information

    Deposition Data

    • Deposited Date: 2019-04-16 
    • Released Date: 2019-06-19 
    • Deposition Author(s): Li, W., Cate, J.H.D.

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

    Revision History 

    • Version 1.0: 2019-06-19
      Type: Initial release
    • Version 1.1: 2019-12-18
      Changes: Author supporting evidence