6OLZ

Human ribosome nascent chain complex (PCSK9-RNC) stalled by a drug-like molecule with PP tRNA

  • Classification: RIBOSOME
  • Organism(s): Homo sapiens
  • Mutation(s): No 

  • Deposited: 2019-04-17 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
  • Structures With Same Primary Citation

  • 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: 1
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L8AA248Homo sapiensMutation(s): 0 
Gene Names: RPL8
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PHAROS  P62917
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein SABA215Homo sapiensMutation(s): 0 
Gene Names: RPSALAMBRLAMR1
Find proteins for P08865 (Homo sapiens)
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PHAROS  P08865
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L3AB394Homo sapiensMutation(s): 0 
Gene Names: RPL3OK/SW-cl.32
Find proteins for P39023 (Homo sapiens)
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PHAROS  P39023
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S3aBB212Homo sapiensMutation(s): 0 
Gene Names: RPS3AFTE1MFTL
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PHAROS  P61247
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L4AC363Homo sapiensMutation(s): 0 
Gene Names: RPL4RPL1
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PHAROS  P36578
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S2BC222Homo sapiensMutation(s): 0 
Gene Names: RPS2RPS4
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PHAROS  P15880
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L5AD294Homo sapiensMutation(s): 0 
Gene Names: RPL5MSTP030
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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L7AF234Homo sapiensMutation(s): 0 
Gene Names: RPL7
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Entity ID: 12
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L7aAG234Homo sapiensMutation(s): 0 
Gene Names: RPL7ASURF-3SURF3
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Entity ID: 13
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L9AH191Homo sapiensMutation(s): 0 
Gene Names: RPL9OK/SW-cl.103RPL9P7RPL9P8RPL9P9
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Entity ID: 14
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L10AI211Homo sapiensMutation(s): 0 
Gene Names: RPL10DXS648EQM
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Entity ID: 15
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L11AJ169Homo sapiensMutation(s): 0 
Gene Names: RPL11
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PHAROS  P62913
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Entity ID: 17
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L14AM139Homo sapiensMutation(s): 0 
Gene Names: RPL14
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PHAROS  P50914
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Entity ID: 18
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L15AN203Homo sapiensMutation(s): 0 
Gene Names: RPL15EC45TCBAP0781
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Entity ID: 19
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L13aAO195Homo sapiensMutation(s): 0 
Gene Names: RPL13A
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Entity ID: 22
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L19AR181Homo sapiensMutation(s): 0 
Gene Names: RPL19
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Entity ID: 23
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L18aAS175Homo sapiensMutation(s): 0 
Gene Names: RPL18A
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Entity ID: 24
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L21AT157Homo sapiensMutation(s): 0 
Gene Names: RPL21
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Entity ID: 25
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L22AU99Homo sapiensMutation(s): 0 
Gene Names: RPL22
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Entity ID: 26
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L23AV129Homo sapiensMutation(s): 0 
Gene Names: RPL23
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Entity ID: 27
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L24AW121Homo sapiensMutation(s): 0 
Gene Names: RPL24
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PHAROS  P83731
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Entity ID: 28
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L23aAX117Homo sapiensMutation(s): 0 
Gene Names: RPL23A
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Entity ID: 30
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L27AZ134Homo sapiensMutation(s): 0 
Gene Names: RPL27
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PHAROS  P61353
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Entity ID: 31
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L27aAa147Homo sapiensMutation(s): 0 
Gene Names: RPL27A
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Entity ID: 32
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L29Ab118Homo sapiensMutation(s): 0 
Gene Names: RPL29
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Entity ID: 35
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L32Ae129Homo sapiensMutation(s): 0 
Gene Names: RPL32PP9932
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PHAROS  P62910
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Entity ID: 38
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L35Ah122Homo sapiensMutation(s): 0 
Gene Names: RPL35
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PHAROS  P42766
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Entity ID: 40
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L37Aj84Homo sapiensMutation(s): 0 
Gene Names: RPL37
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PHAROS  P61927
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Entity ID: 41
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L38Ak69Homo sapiensMutation(s): 0 
Gene Names: RPL38
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PHAROS  P63173
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Entity ID: 44
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L41An25Homo sapiensMutation(s): 0 
Gene Names: RPL41
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Entity ID: 45
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L36aAo105Homo sapiensMutation(s): 0 
Gene Names: RPL36ARPL44GIG15MIG6
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PHAROS  P83881
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Entity ID: 47
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L28At122Homo sapiensMutation(s): 0 
Gene Names: RPL28
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Entity ID: 52
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S5BF190Homo sapiensMutation(s): 0 
Gene Names: RPS5
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Entity ID: 54
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S7BH183Homo sapiensMutation(s): 0 
Gene Names: RPS7
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Entity ID: 55
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S8BI207Homo sapiensMutation(s): 0 
Gene Names: RPS8OK/SW-cl.83
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Entity ID: 56
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S9BJ179Homo sapiensMutation(s): 0 
Gene Names: RPS9
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Entity ID: 57
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S10BK98Homo sapiensMutation(s): 0 
Gene Names: RPS10
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Entity ID: 58
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S11BL153Homo sapiensMutation(s): 0 
Gene Names: RPS11
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Entity ID: 59
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S12BM120Homo sapiensMutation(s): 0 
Gene Names: RPS12
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Entity ID: 60
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S13BN149Homo sapiensMutation(s): 0 
Gene Names: RPS13
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Entity ID: 61
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S14BO136Homo sapiensMutation(s): 0 
Gene Names: RPS14PRO2640
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Entity ID: 62
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S15BP120Homo sapiensMutation(s): 0 
Gene Names: RPS15RIG
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Entity ID: 63
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S16BQ139Homo sapiensMutation(s): 0 
Gene Names: RPS16
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Entity ID: 64
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S17BR125Homo sapiensMutation(s): 0 
Gene Names: RPS17RPS17L
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Entity ID: 66
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S19BT143Homo sapiensMutation(s): 0 
Gene Names: RPS19
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Entity ID: 67
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S20BU97Homo sapiensMutation(s): 0 
Gene Names: RPS20
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Entity ID: 68
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S21BV81Homo sapiensMutation(s): 0 
Gene Names: RPS21
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Entity ID: 69
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S15aBW129Homo sapiensMutation(s): 0 
Gene Names: RPS15AOK/SW-cl.82
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Entity ID: 70
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S23BX139Homo sapiensMutation(s): 0 
Gene Names: RPS23
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Entity ID: 71
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S24BY125Homo sapiensMutation(s): 0 
Gene Names: RPS24
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Entity ID: 72
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S25BZ86Homo sapiensMutation(s): 0 
Gene Names: RPS25
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Entity ID: 75
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S28Bc62Homo sapiensMutation(s): 0 
Gene Names: RPS28
Find proteins for P62857 (Homo sapiens)
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PHAROS  P62857
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Entity ID: 76
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S29Bd51Homo sapiensMutation(s): 0 
Gene Names: RPS29
Find proteins for P62273 (Homo sapiens)
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PHAROS  P62273
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Entity ID: 77
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S30Be55Homo sapiensMutation(s): 0 
Gene Names: FAU
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PHAROS  P62861
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Entity ID: 78
MoleculeChainsSequence LengthOrganismDetails
Ubiquitin-40S ribosomal protein S27aBf73Homo sapiensMutation(s): 0 
Gene Names: RPS27AUBA80UBCEP1
Find proteins for P62979 (Homo sapiens)
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PHAROS  P62979
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Entity ID: 82
MoleculeChainsSequence LengthOrganismDetails
Proprotein convertase subtilisin/kexin type 9A26Homo sapiensMutation(s): 0 
Gene Names: PCSK9NARC1PSEC0052
EC: 3.4.21
Find proteins for Q8NBP7 (Homo sapiens)
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PHAROS  Q8NBP7
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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L6AE247Homo sapiensMutation(s): 0 
Gene Names: RPL6TXREB1
Find proteins for Q02878 (Homo sapiens)
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PHAROS  Q02878
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Entity ID: 16
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L13AL205Homo sapiensMutation(s): 0 
Gene Names: RPL13BBC1OK/SW-cl.46
Find proteins for P26373 (Homo sapiens)
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PHAROS  P26373
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Entity ID: 20
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L17AP153Homo sapiensMutation(s): 0 
Gene Names: RPL17
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PHAROS  P18621
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Entity ID: 21
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L18AQ187Homo sapiensMutation(s): 0 
Gene Names: RPL18
Find proteins for Q07020 (Homo sapiens)
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PHAROS  Q07020
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Entity ID: 29
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L26AY127Homo sapiensMutation(s): 0 
Gene Names: RPL26
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PHAROS  P61254
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Entity ID: 33
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L30Ac103Homo sapiensMutation(s): 0 
Gene Names: RPL30
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PHAROS  P62888
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Entity ID: 34
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L31Ad106Homo sapiensMutation(s): 0 
Gene Names: RPL31
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PHAROS  P62899
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Entity ID: 36
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L35aAf109Homo sapiensMutation(s): 0 
Gene Names: RPL35AGIG33
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PHAROS  P18077
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Entity ID: 37
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L34Ag114Homo sapiensMutation(s): 0 
Gene Names: RPL34
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PHAROS  P49207
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Entity ID: 39
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L36Ai97Homo sapiensMutation(s): 0 
Gene Names: RPL36
Find proteins for Q9Y3U8 (Homo sapiens)
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PHAROS  Q9Y3U8
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Entity ID: 42
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L39Al50Homo sapiensMutation(s): 0 
Gene Names: RPL39
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PHAROS  P62891
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Entity ID: 43
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L40Am50Homo sapiensMutation(s): 0 
Gene Names: UBA52UBCEP2
Find proteins for P62987 (Homo sapiens)
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PHAROS  P62987
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Entity ID: 46
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L37aAp91Homo sapiensMutation(s): 0 
Gene Names: RPL37A
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PHAROS  P61513
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Entity ID: 50
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S3BD220Homo sapiensMutation(s): 0 
Gene Names: RPS3OK/SW-cl.26
EC: 4.2.99.18
Find proteins for P23396 (Homo sapiens)
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PHAROS  P23396
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Entity ID: 51
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S4, Y isoform 1BE257Homo sapiensMutation(s): 0 
Gene Names: RPS4Y1RPS4YPRO2646
Find proteins for P22090 (Homo sapiens)
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PHAROS  P22090
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Entity ID: 53
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S6BG232Homo sapiensMutation(s): 0 
Gene Names: RPS6OK/SW-cl.2
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PHAROS  P62753
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Entity ID: 65
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S18BS139Homo sapiensMutation(s): 0 
Gene Names: RPS18D6S218E
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PHAROS  P62269
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Entity ID: 73
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S26Ba97Homo sapiensMutation(s): 0 
Gene Names: RPS26
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PHAROS  P62854
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Entity ID: 74
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S27Bb80Homo sapiensMutation(s): 0 
Gene Names: RPS27MPS1
Find proteins for P42677 (Homo sapiens)
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PHAROS  P42677
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Entity ID: 79
MoleculeChainsSequence LengthOrganismDetails
Receptor of activated protein C kinase 1Bg314Homo sapiensMutation(s): 0 
Gene Names: RACK1GNB2L1HLC7PIG21
Find proteins for P63244 (Homo sapiens)
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PHAROS  P63244
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Entity ID: 7
MoleculeChainsLengthOrganism
5.8S ribosomal RNAA3157Homo sapiens

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Entity ID: 8
MoleculeChainsLengthOrganism
5S ribosomal RNAA4119Homo sapiens

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Entity ID: 48
MoleculeChainsLengthOrganism
28S ribosomal RNAA23643Homo sapiens

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Entity ID: 49
MoleculeChainsLengthOrganism
18S ribosomal RNAB11708Homo sapiens

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Entity ID: 80
MoleculeChainsLengthOrganism
tRNABv76Homo sapiens
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Entity ID: 81
MoleculeChainsLengthOrganism
mRNABx16Homo sapiens
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MVM
Query on MVM

Download CCD File 
A
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 CCD File 
Aj, Ao, Ap, Ba, Bd
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

Download CCD File 
A2, A3, A4, AA, AB, AN, AP, Aa, Ae, Aj, Al, An, B1, BC, BI, Bv
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: 2019-04-17 
  • 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