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
  • 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: 3
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S3a
SB
214Homo sapiensMutation(s): 0 
Gene Names: RPS3AFTE1MFTL
Find proteins for P61247 (Homo sapiens)
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PHAROS  P61247

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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S3
SD
226Homo 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: 6
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S5
SF
189Homo sapiensMutation(s): 0 
Gene Names: RPS5
Find proteins for P46782 (Homo sapiens)
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PHAROS  P46782

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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S8
SI
204Homo sapiensMutation(s): 0 
Gene Names: RPS8OK/SW-cl.83
Find proteins for P62241 (Homo sapiens)
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PHAROS  P62241

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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S10
SK
98Homo sapiensMutation(s): 0 
Gene Names: RPS10
Find proteins for P46783 (Homo sapiens)
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PHAROS  P46783

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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S11
SL
153Homo sapiensMutation(s): 0 
Gene Names: RPS11
Find proteins for P62280 (Homo sapiens)
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PHAROS  P62280

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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S15
SP
127Homo sapiensMutation(s): 0 
Gene Names: RPS15RIG
Find proteins for P62841 (Homo sapiens)
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PHAROS  P62841

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Entity ID: 12
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S16
SQ
146Homo sapiensMutation(s): 0 
Gene Names: RPS16
Find proteins for P62249 (Homo sapiens)
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PHAROS  P62249

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Entity ID: 13
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S17
SR
134Homo sapiensMutation(s): 0 
Gene Names: RPS17RPS17L
Find proteins for P08708 (Homo sapiens)
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PHAROS  P08708

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Entity ID: 16
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S20
SU
104Homo sapiensMutation(s): 0 
Gene Names: RPS20
Find proteins for P60866 (Homo sapiens)
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PHAROS  P60866

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Entity ID: 18
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S23
SX
141Homo sapiensMutation(s): 0 
Gene Names: RPS23
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PHAROS  P62266

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Entity ID: 19
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S26
Sa
102Homo sapiensMutation(s): 0 
Gene Names: RPS26
Find proteins for P62854 (Homo sapiens)
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PHAROS  P62854

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Entity ID: 21
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S29
Sd
55Homo sapiensMutation(s): 0 
Gene Names: RPS29
Find proteins for P62273 (Homo sapiens)
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PHAROS  P62273

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Entity ID: 22
MoleculeChainsSequence LengthOrganismDetails
Receptor of activated protein C kinase 1
Sg
312Homo sapiensMutation(s): 0 
Gene Names: RACK1GNB2L1HLC7PIG21
Find proteins for P63244 (Homo sapiens)
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PHAROS  P63244

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Entity ID: 23
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S2
SC
220Homo sapiensMutation(s): 0 
Gene Names: RPS2RPS4
Find proteins for P15880 (Homo sapiens)
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PHAROS  P15880

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Entity ID: 24
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S6
SG
237Homo sapiensMutation(s): 0 
Gene Names: RPS6OK/SW-cl.2
Find proteins for P62753 (Homo sapiens)
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PHAROS  P62753

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Entity ID: 26
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S12
SM
118Homo sapiensMutation(s): 0 
Gene Names: RPS12
Find proteins for P25398 (Homo sapiens)
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PHAROS  P25398

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Entity ID: 29
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S15a
SW
129Homo sapiensMutation(s): 0 
Gene Names: RPS15AOK/SW-cl.82
Find proteins for P62244 (Homo sapiens)
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PHAROS  P62244

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Entity ID: 30
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S24
SY
131Homo sapiensMutation(s): 0 
Gene Names: RPS24
Find proteins for P62847 (Homo sapiens)
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PHAROS  P62847

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Entity ID: 34
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S27a
Sf
67Homo sapiensMutation(s): 0 
Gene Names: RPS27AUBA80UBCEP1
Find proteins for P62979 (Homo sapiens)
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PHAROS  P62979

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Entity ID: 35
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L8
A
252Homo sapiensMutation(s): 0 
Gene Names: RPL8
Find proteins for P62917 (Homo sapiens)
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PHAROS  P62917

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Entity ID: 36
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L3
B
397Homo 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: 41
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L6
G
247Homo sapiensMutation(s): 0 
Gene Names: RPL6TXREB1
Find proteins for Q02878 (Homo sapiens)
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PHAROS  Q02878

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Entity ID: 43
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L7a
I
234Homo sapiensMutation(s): 0 
Gene Names: RPL7ASURF-3SURF3
Find proteins for P62424 (Homo sapiens)
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PHAROS  P62424

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Entity ID: 44
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L9
J
191Homo sapiensMutation(s): 0 
Gene Names: RPL9OK/SW-cl.103RPL9P7RPL9P8RPL9P9
Find proteins for P32969 (Homo sapiens)
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PHAROS  P32969

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Entity ID: 46
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L11
L
169Homo sapiensMutation(s): 0 
Gene Names: RPL11
Find proteins for P62913 (Homo sapiens)
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PHAROS  P62913

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Entity ID: 47
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L13
M
205Homo 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: 50
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L13a
P
195Homo sapiensMutation(s): 0 
Gene Names: RPL13A
Find proteins for P40429 (Homo sapiens)
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PHAROS  P40429

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Entity ID: 53
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L19
S
181Homo sapiensMutation(s): 0 
Gene Names: RPL19
Find proteins for P84098 (Homo sapiens)
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PHAROS  P84098

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Entity ID: 56
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L22
V
99Homo sapiensMutation(s): 0 
Gene Names: RPL22
Find proteins for P35268 (Homo sapiens)
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PHAROS  P35268

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Entity ID: 57
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L23
W
129Homo 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 LengthOrganismDetails
60S ribosomal protein L24
X
121Homo sapiensMutation(s): 0 
Gene Names: RPL24
Find proteins for P83731 (Homo sapiens)
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PHAROS  P83731

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Entity ID: 60
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L26
Z
134Homo sapiensMutation(s): 0 
Gene Names: RPL26
Find proteins for P61254 (Homo sapiens)
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PHAROS  P61254

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Entity ID: 62
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L29
c
121Homo sapiensMutation(s): 0 
Gene Names: RPL29
Find proteins for P47914 (Homo sapiens)
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Entity ID: 66
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L35a
g
109Homo 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
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L35
i
122Homo sapiensMutation(s): 0 
Gene Names: RPL35
Find proteins for P42766 (Homo sapiens)
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PHAROS  P42766

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Entity ID: 71
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L38
l
69Homo sapiensMutation(s): 0 
Gene Names: RPL38
Find proteins for P63173 (Homo sapiens)
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PHAROS  P63173

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Entity ID: 72
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L39
m
50Homo 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
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L41
o
25Homo 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
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L37a
q
91Homo sapiensMutation(s): 0 
Gene Names: RPL37A
Find proteins for P61513 (Homo sapiens)
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PHAROS  P61513

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Entity ID: 77
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L28
r
122Homo sapiensMutation(s): 0 
Gene Names: RPL28
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PHAROS  P46779

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Entity ID: 81
MoleculeChainsSequence LengthOrganismDetails
Cadherin-1
y
39Homo sapiensMutation(s): 0 
Gene Names: CDH1CDHEUVO
Find proteins for P12830 (Homo sapiens)
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PHAROS  P12830

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Entity ID: 14
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S18
SS
145Homo sapiensMutation(s): 0 
Gene Names: RPS18D6S218E
Find proteins for P62269 (Homo sapiens)
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PHAROS  P62269

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Entity ID: 15
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S19
ST
143Homo sapiensMutation(s): 0 
Gene Names: RPS19
Find proteins for P39019 (Homo sapiens)
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PHAROS  P39019

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Entity ID: 17
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S21
SV
82Homo sapiensMutation(s): 0 
Gene Names: RPS21
Find proteins for P63220 (Homo sapiens)
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PHAROS  P63220

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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein SA
SA
221Homo sapiensMutation(s): 0 
Gene Names: RPSALAMBRLAMR1
Find proteins for P08865 (Homo sapiens)
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PHAROS  P08865

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Entity ID: 20
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S28
Sc
64Homo sapiensMutation(s): 0 
Gene Names: RPS28
Find proteins for P62857 (Homo sapiens)
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PHAROS  P62857

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Entity ID: 25
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S9
SJ
185Homo sapiensMutation(s): 0 
Gene Names: RPS9
Find proteins for P46781 (Homo sapiens)
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PHAROS  P46781

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Entity ID: 27
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S13
SN
150Homo sapiensMutation(s): 0 
Gene Names: RPS13
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Entity ID: 28
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S14
SO
137Homo sapiensMutation(s): 0 
Gene Names: RPS14PRO2640
Find proteins for P62263 (Homo sapiens)
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PHAROS  P62263

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Entity ID: 31
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S25
SZ
73Homo sapiensMutation(s): 0 
Gene Names: RPS25
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PHAROS  P62851

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Entity ID: 32
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S27
Sb
82Homo sapiensMutation(s): 0 
Gene Names: RPS27MPS1
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PHAROS  P42677

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Entity ID: 33
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S30
Se
57Homo sapiensMutation(s): 0 
Gene Names: FAU
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PHAROS  P62861

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Entity ID: 37
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L4
C
363Homo sapiensMutation(s): 0 
Gene Names: RPL4RPL1
Find proteins for P36578 (Homo sapiens)
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PHAROS  P36578

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Entity ID: 40
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L5
F
294Homo sapiensMutation(s): 0 
Gene Names: RPL5MSTP030
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PHAROS  P46777

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Entity ID: 42
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L7
H
225Homo sapiensMutation(s): 0 
Gene Names: RPL7
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PHAROS  P18124

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Entity ID: 45
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L10
K
211Homo sapiensMutation(s): 0 
Gene Names: RPL10DXS648EQM
Find proteins for P27635 (Homo sapiens)
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PHAROS  P27635

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Entity ID: 48
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L14
N
139Homo sapiensMutation(s): 0 
Gene Names: RPL14
Find proteins for P50914 (Homo sapiens)
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PHAROS  P50914

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Entity ID: 49
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L15
O
203Homo sapiensMutation(s): 0 
Gene Names: RPL15EC45TCBAP0781
Find proteins for P61313 (Homo sapiens)
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PHAROS  P61313

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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S4, X isoform
SE
259Homo sapiensMutation(s): 0 
Gene Names: RPS4XCCG2RPS4SCAR
Find proteins for P62701 (Homo sapiens)
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PHAROS  P62701

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Entity ID: 51
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L17
Q
153Homo sapiensMutation(s): 0 
Gene Names: RPL17
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PHAROS  P18621

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Entity ID: 52
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L18
R
187Homo sapiensMutation(s): 0 
Gene Names: RPL18
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PHAROS  Q07020

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Entity ID: 54
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L18a
T
175Homo sapiensMutation(s): 0 
Gene Names: RPL18A
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Entity ID: 55
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L21
U
157Homo sapiensMutation(s): 0 
Gene Names: RPL21
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Entity ID: 59
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L23a
Y
117Homo sapiensMutation(s): 0 
Gene Names: RPL23A
Find proteins for P62750 (Homo sapiens)
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PHAROS  P62750

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Entity ID: 61
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L27a
b
147Homo 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 LengthOrganismDetails
60S ribosomal protein L30
d
103Homo sapiensMutation(s): 0 
Gene Names: RPL30
Find proteins for P62888 (Homo sapiens)
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PHAROS  P62888

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Entity ID: 64
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L31
e
106Homo sapiensMutation(s): 0 
Gene Names: RPL31
Find proteins for P62899 (Homo sapiens)
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PHAROS  P62899

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Entity ID: 65
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L32
f
129Homo sapiensMutation(s): 0 
Gene Names: RPL32PP9932
Find proteins for P62910 (Homo sapiens)
Go to UniProtKB:  P62910
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PHAROS  P62910

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Entity ID: 67
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L34
h
114Homo 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
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L36
j
97Homo sapiensMutation(s): 0 
Gene Names: RPL36
Find proteins for Q9Y3U8 (Homo sapiens)
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PHAROS  Q9Y3U8

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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S7
SH
189Homo sapiensMutation(s): 0 
Gene Names: RPS7
Find proteins for P62081 (Homo sapiens)
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PHAROS  P62081

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Entity ID: 70
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L37
k
84Homo sapiensMutation(s): 0 
Gene Names: RPL37
Find proteins for P61927 (Homo sapiens)
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PHAROS  P61927

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Entity ID: 73
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L40
n
50Homo 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 LengthOrganismDetails
60S ribosomal protein L36a
p
105Homo sapiensMutation(s): 0 
Gene Names: RPL36ARPL44GIG15MIG6
Find proteins for P83881 (Homo sapiens)
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PHAROS  P83881

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Entity ID: 83
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L27
a
134Homo sapiensMutation(s): 0 
Gene Names: RPL27
Find proteins for P61353 (Homo sapiens)
Go to UniProtKB:  P61353
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PHAROS  P61353

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Entity ID: 38
MoleculeChainsLengthOrganism
5.8S ribosomal RNAD157Homo sapiens

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Entity ID: 39
MoleculeChainsLengthOrganism
5S ribosomal RNAE119Homo sapiens

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Entity ID: 78
MoleculeChainsLengthOrganism
28S ribosomal RNAt3607Homo sapiens

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Entity ID: 1
MoleculeChainsLengthOrganism
18S ribosomal RNAS21714Homo sapiens

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Entity ID: 79
MoleculeChainsLengthOrganism
AA tRNAv76Homo sapiens
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Entity ID: 80
MoleculeChainsLengthOrganism
mRNAw10Homo sapiens

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Entity ID: 82
MoleculeChainsLengthOrganism
PE tRNAu76Homo sapiens
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MVM
Query on MVM

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

Download CCD File 
D, E, S2, b, t
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 

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