6OLF

Human ribosome nascent chain complex (CDH1-RNC) stalled by a drug-like molecule with AA 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: 3.90 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 the ribosome exit tunnel in a eukaryotic-specific pocket formed by 28S ribosomal RNA, and alters the path of the nascent polypeptide chain ...

    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 SAB [auth SA]221Homo sapiensMutation(s): 0 
Gene Names: RPSALAMBRLAMR1
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Entity ID: 3
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40S ribosomal protein S3aC [auth SB]214Homo sapiensMutation(s): 0 
Gene Names: RPS3AFTE1MFTL
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S3D [auth SD]226Homo 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 isoformE [auth SE]259Homo sapiensMutation(s): 0 
Gene Names: RPS4XCCG2RPS4SCAR
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S5F [auth SF]189Homo sapiensMutation(s): 0 
Gene Names: RPS5
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Entity ID: 7
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40S ribosomal protein S7G [auth SH]189Homo sapiensMutation(s): 0 
Gene Names: RPS7
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Entity ID: 8
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40S ribosomal protein S8H [auth SI]204Homo sapiensMutation(s): 0 
Gene Names: RPS8OK/SW-cl.83
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Entity ID: 9
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40S ribosomal protein S10I [auth SK]98Homo sapiensMutation(s): 0 
Gene Names: RPS10
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Entity ID: 10
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40S ribosomal protein S11J [auth SL]153Homo sapiensMutation(s): 0 
Gene Names: RPS11
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Entity ID: 11
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40S ribosomal protein S15K [auth SP]127Homo sapiensMutation(s): 0 
Gene Names: RPS15RIG
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Entity ID: 12
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40S ribosomal protein S16L [auth SQ]146Homo sapiensMutation(s): 0 
Gene Names: RPS16
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Entity ID: 13
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40S ribosomal protein S17M [auth SR]134Homo sapiensMutation(s): 0 
Gene Names: RPS17RPS17L
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Entity ID: 14
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40S ribosomal protein S18N [auth SS]145Homo sapiensMutation(s): 0 
Gene Names: RPS18D6S218E
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Entity ID: 15
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40S ribosomal protein S19O [auth ST]143Homo sapiensMutation(s): 0 
Gene Names: RPS19
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Entity ID: 16
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40S ribosomal protein S20P [auth SU]104Homo sapiensMutation(s): 0 
Gene Names: RPS20
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Entity ID: 17
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40S ribosomal protein S21Q [auth SV]82Homo sapiensMutation(s): 0 
Gene Names: RPS21
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Entity ID: 18
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40S ribosomal protein S23R [auth SX]141Homo sapiensMutation(s): 0 
Gene Names: RPS23
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Entity ID: 19
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40S ribosomal protein S26S [auth Sa]102Homo sapiensMutation(s): 0 
Gene Names: RPS26
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Entity ID: 20
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40S ribosomal protein S28T [auth Sc]64Homo sapiensMutation(s): 0 
Gene Names: RPS28
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Entity ID: 21
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40S ribosomal protein S29U [auth Sd]55Homo sapiensMutation(s): 0 
Gene Names: RPS29
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Entity ID: 22
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Receptor of activated protein C kinase 1V [auth Sg]312Homo sapiensMutation(s): 0 
Gene Names: RACK1GNB2L1HLC7PIG21
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Entity ID: 23
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40S ribosomal protein S2W [auth SC]220Homo sapiensMutation(s): 0 
Gene Names: RPS2RPS4
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Entity ID: 24
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40S ribosomal protein S6X [auth SG]237Homo sapiensMutation(s): 0 
Gene Names: RPS6OK/SW-cl.2
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Entity ID: 25
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40S ribosomal protein S9Y [auth SJ]185Homo sapiensMutation(s): 0 
Gene Names: RPS9
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Entity ID: 26
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40S ribosomal protein S12Z [auth SM]118Homo sapiensMutation(s): 0 
Gene Names: RPS12
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Entity ID: 27
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40S ribosomal protein S13AA [auth SN]150Homo sapiensMutation(s): 0 
Gene Names: RPS13
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Entity ID: 28
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40S ribosomal protein S14BA [auth SO]137Homo sapiensMutation(s): 0 
Gene Names: RPS14PRO2640
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Entity ID: 29
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40S ribosomal protein S15aCA [auth SW]129Homo sapiensMutation(s): 0 
Gene Names: RPS15AOK/SW-cl.82
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Entity ID: 30
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S24DA [auth SY]131Homo sapiensMutation(s): 0 
Gene Names: RPS24
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Entity ID: 31
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40S ribosomal protein S25EA [auth SZ]73Homo sapiensMutation(s): 0 
Gene Names: RPS25
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Entity ID: 32
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40S ribosomal protein S27FA [auth Sb]82Homo sapiensMutation(s): 0 
Gene Names: RPS27MPS1
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Entity ID: 33
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40S ribosomal protein S30GA [auth Se]57Homo sapiensMutation(s): 0 
Gene Names: FAU
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Entity ID: 34
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40S ribosomal protein S27aHA [auth Sf]67Homo sapiensMutation(s): 0 
Gene Names: RPS27AUBA80UBCEP1
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Entity ID: 35
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60S ribosomal protein L8IA [auth A]252Homo sapiensMutation(s): 0 
Gene Names: RPL8
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Entity ID: 36
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60S ribosomal protein L3JA [auth B]397Homo sapiensMutation(s): 0 
Gene Names: RPL3OK/SW-cl.32
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Entity ID: 37
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60S ribosomal protein L4KA [auth C]363Homo sapiensMutation(s): 0 
Gene Names: RPL4RPL1
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Entity ID: 40
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60S ribosomal protein L5NA [auth F]294Homo sapiensMutation(s): 0 
Gene Names: RPL5MSTP030
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Entity ID: 41
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60S ribosomal protein L6OA [auth G]247Homo sapiensMutation(s): 0 
Gene Names: RPL6TXREB1
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Entity ID: 42
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60S ribosomal protein L7PA [auth H]225Homo sapiensMutation(s): 0 
Gene Names: RPL7
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Entity ID: 43
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60S ribosomal protein L7aQA [auth I]234Homo sapiensMutation(s): 0 
Gene Names: RPL7ASURF-3SURF3
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Entity ID: 44
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60S ribosomal protein L9RA [auth J]191Homo sapiensMutation(s): 0 
Gene Names: RPL9OK/SW-cl.103RPL9P7RPL9P8RPL9P9
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Entity ID: 45
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60S ribosomal protein L10SA [auth K]211Homo sapiensMutation(s): 0 
Gene Names: RPL10DXS648EQM
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Entity ID: 46
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60S ribosomal protein L11TA [auth L]169Homo sapiensMutation(s): 0 
Gene Names: RPL11
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Entity ID: 47
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60S ribosomal protein L13UA [auth M]205Homo sapiensMutation(s): 0 
Gene Names: RPL13BBC1OK/SW-cl.46
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Entity ID: 48
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60S ribosomal protein L14VA [auth N]139Homo sapiensMutation(s): 0 
Gene Names: RPL14
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Entity ID: 49
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60S ribosomal protein L15WA [auth O]203Homo sapiensMutation(s): 0 
Gene Names: RPL15EC45TCBAP0781
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Entity ID: 50
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60S ribosomal protein L13aXA [auth P]195Homo sapiensMutation(s): 0 
Gene Names: RPL13A
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Entity ID: 51
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60S ribosomal protein L17YA [auth Q]153Homo sapiensMutation(s): 0 
Gene Names: RPL17
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Entity ID: 52
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60S ribosomal protein L18ZA [auth R]187Homo sapiensMutation(s): 0 
Gene Names: RPL18
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Entity ID: 53
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60S ribosomal protein L19AB [auth S]181Homo sapiensMutation(s): 0 
Gene Names: RPL19
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Entity ID: 54
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60S ribosomal protein L18aBB [auth T]175Homo sapiensMutation(s): 0 
Gene Names: RPL18A
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Entity ID: 55
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L21CB [auth U]157Homo sapiensMutation(s): 0 
Gene Names: RPL21
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Entity ID: 56
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60S ribosomal protein L22DB [auth V]99Homo sapiensMutation(s): 0 
Gene Names: RPL22
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Entity ID: 57
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60S ribosomal protein L23EB [auth W]129Homo sapiensMutation(s): 0 
Gene Names: RPL23
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Entity ID: 58
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60S ribosomal protein L24FB [auth X]121Homo sapiensMutation(s): 0 
Gene Names: RPL24
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Entity ID: 59
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60S ribosomal protein L23aGB [auth Y]117Homo sapiensMutation(s): 0 
Gene Names: RPL23A
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Entity ID: 60
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L26HB [auth Z]134Homo sapiensMutation(s): 0 
Gene Names: RPL26
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Entity ID: 61
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60S ribosomal protein L27aIB [auth b]147Homo sapiensMutation(s): 0 
Gene Names: RPL27A
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Entity ID: 62
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L29JB [auth c]121Homo sapiensMutation(s): 0 
Gene Names: RPL29
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Entity ID: 63
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60S ribosomal protein L30KB [auth d]103Homo sapiensMutation(s): 0 
Gene Names: RPL30
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Entity ID: 64
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60S ribosomal protein L31LB [auth e]106Homo sapiensMutation(s): 0 
Gene Names: RPL31
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Entity ID: 65
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60S ribosomal protein L32MB [auth f]129Homo sapiensMutation(s): 0 
Gene Names: RPL32PP9932
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Entity ID: 66
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60S ribosomal protein L35aNB [auth g]109Homo sapiensMutation(s): 0 
Gene Names: RPL35AGIG33
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Entity ID: 67
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60S ribosomal protein L34OB [auth h]114Homo sapiensMutation(s): 0 
Gene Names: RPL34
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Entity ID: 68
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60S ribosomal protein L35PB [auth i]122Homo sapiensMutation(s): 0 
Gene Names: RPL35
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Entity ID: 69
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60S ribosomal protein L36QB [auth j]97Homo sapiensMutation(s): 0 
Gene Names: RPL36
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Entity ID: 70
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60S ribosomal protein L37RB [auth k]84Homo sapiensMutation(s): 0 
Gene Names: RPL37
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Entity ID: 71
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60S ribosomal protein L38SB [auth l]69Homo sapiensMutation(s): 0 
Gene Names: RPL38
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Entity ID: 72
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60S ribosomal protein L39TB [auth m]50Homo sapiensMutation(s): 0 
Gene Names: RPL39
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Entity ID: 73
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60S ribosomal protein L40UB [auth n]50Homo sapiensMutation(s): 0 
Gene Names: UBA52UBCEP2
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Entity ID: 74
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60S ribosomal protein L41VB [auth o]25Homo sapiensMutation(s): 0 
Gene Names: RPL41
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Entity ID: 75
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L36aWB [auth p]105Homo sapiensMutation(s): 0 
Gene Names: RPL36ARPL44GIG15MIG6
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Entity ID: 76
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60S ribosomal protein L37aXB [auth q]91Homo sapiensMutation(s): 0 
Gene Names: RPL37A
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Entity ID: 77
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L28YB [auth r]122Homo sapiensMutation(s): 0 
Gene Names: RPL28
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Entity ID: 81
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Cadherin-1CC [auth y]39Homo sapiensMutation(s): 0 
Gene Names: CDH1CDHEUVO
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Entity ID: 83
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60S ribosomal protein L27EC [auth a]134Homo sapiensMutation(s): 0 
Gene Names: RPL27
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Entity ID: 1
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18S ribosomal RNAA [auth S2]1714Homo sapiens
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Entity ID: 38
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5.8S ribosomal RNALA [auth D]157Homo sapiens
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Entity ID: 39
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5S ribosomal RNAMA [auth E]119Homo sapiens
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Entity ID: 78
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28S ribosomal RNAZB [auth t]3607Homo sapiens
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Entity ID: 79
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AA tRNAAC [auth v]76Homo sapiens
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  • Entity ID: 80
    MoleculeChainsLengthOrganismImage
    mRNABC [auth w]10Homo sapiens
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    Entity ID: 82
    MoleculeChainsLengthOrganismImage
    PE tRNADC [auth u]76Homo sapiens
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    Small Molecules
    Ligands 3 Unique
    IDChainsName / Formula / InChI Key2D Diagram3D Interactions
    MVM
    Query on MVM

    Download Ideal Coordinates CCD File 
    QD [auth t]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

    Download Ideal Coordinates CCD File 
    CD [auth k], DD [auth p], ED [auth q], FC [auth S2], JC [auth Sa], KC [auth Sf]ZINC ION
    Zn
    PTFCDOFLOPIGGS-UHFFFAOYSA-N
     Ligand Interaction
    MG
    Query on MG

    Download Ideal Coordinates CCD File 
    AD [auth b] , BD [auth b] , FD [auth t] , GC [auth S2] , GD [auth t] , HC [auth S2] , HD [auth t] , IC [auth S2] , 
    AD [auth b],  BD [auth b],  FD [auth t],  GC [auth S2],  GD [auth t],  HC [auth S2],  HD [auth t],  IC [auth S2],  ID [auth t],  JD [auth t],  KD [auth t],  LC [auth D],  LD [auth t],  MC [auth D],  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 E],  SC [auth E],  TC [auth E],  UC [auth E],  VC [auth E],  WC [auth E],  XC [auth E],  YC [auth E],  ZC [auth E]
    MAGNESIUM ION
    Mg
    JLVVSXFLKOJNIY-UHFFFAOYSA-N
     Ligand Interaction
    Experimental Data & Validation

    Experimental Data

    • Method: ELECTRON MICROSCOPY
    • Resolution: 3.90 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  (Full details and data files)

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