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

  • 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 

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.1 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report


This is version 1.0 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:  

  • 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 Molecular & Cell Biology, University of California, Berkeley, Berkeley, CA, USA.,Department of Chemistry, University of California, Berkeley, Berkeley, CA, USA. jcate@lbl.gov.,Molecular Biophysics and Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.,Pfizer Medicinal Chemistry, Pfizer Worldwide Research and Development, Cambridge, MA, USA.,Cardiovascular, Metabolic and Endocrine Disease Research Unit, Pfizer Worldwide Research and Development, Cambridge, MA, USA.,Molecular Biophysics and Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA. jcate@lbl.gov.,Department of Molecular & Cell Biology, University of California, Berkeley, Berkeley, CA, USA. jcate@lbl.gov.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein SA
SA
221Homo sapiensMutation(s): 0 
Gene Names: RPSA (LAMBR, LAMR1)
Find proteins for P08865 (Homo sapiens)
Go to Gene View: RPSA
Go to UniProtKB:  P08865
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S3a
SB
214Homo sapiensMutation(s): 0 
Gene Names: RPS3A (FTE1, MFTL)
Find proteins for P61247 (Homo sapiens)
Go to Gene View: RPS3A
Go to UniProtKB:  P61247
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S3
SD
226Homo sapiensMutation(s): 0 
Gene Names: RPS3
EC: 4.2.99.18
Find proteins for P23396 (Homo sapiens)
Go to Gene View: RPS3
Go to UniProtKB:  P23396
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S4, X isoform
SE
259Homo sapiensMutation(s): 0 
Gene Names: RPS4X (CCG2, RPS4, SCAR)
Find proteins for P62701 (Homo sapiens)
Go to Gene View: RPS4X
Go to UniProtKB:  P62701
Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S5
SF
189Homo sapiensMutation(s): 0 
Gene Names: RPS5
Find proteins for P46782 (Homo sapiens)
Go to Gene View: RPS5
Go to UniProtKB:  P46782
Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S7
SH
189Homo sapiensMutation(s): 0 
Gene Names: RPS7
Find proteins for P62081 (Homo sapiens)
Go to Gene View: RPS7
Go to UniProtKB:  P62081
Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S8
SI
204Homo sapiensMutation(s): 0 
Gene Names: RPS8
Find proteins for P62241 (Homo sapiens)
Go to Gene View: RPS8
Go to UniProtKB:  P62241
Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S10
SK
98Homo sapiensMutation(s): 0 
Gene Names: RPS10
Find proteins for P46783 (Homo sapiens)
Go to Gene View: RPS10
Go to UniProtKB:  P46783
Entity ID: 10
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S11
SL
153Homo sapiensMutation(s): 0 
Gene Names: RPS11
Find proteins for P62280 (Homo sapiens)
Go to Gene View: RPS11
Go to UniProtKB:  P62280
Entity ID: 11
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S15
SP
127Homo sapiensMutation(s): 0 
Gene Names: RPS15 (RIG)
Find proteins for P62841 (Homo sapiens)
Go to Gene View: RPS15
Go to UniProtKB:  P62841
Entity ID: 12
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S16
SQ
146Homo sapiensMutation(s): 0 
Gene Names: RPS16
Find proteins for P62249 (Homo sapiens)
Go to Gene View: RPS16
Go to UniProtKB:  P62249
Entity ID: 13
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S17
SR
134Homo sapiensMutation(s): 0 
Gene Names: RPS17 (RPS17L)
Find proteins for P08708 (Homo sapiens)
Go to Gene View: RPS17
Go to UniProtKB:  P08708
Entity ID: 14
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S18
SS
145Homo sapiensMutation(s): 0 
Gene Names: RPS18 (D6S218E)
Find proteins for P62269 (Homo sapiens)
Go to Gene View: RPS18
Go to UniProtKB:  P62269
Entity ID: 15
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S19
ST
143Homo sapiensMutation(s): 0 
Gene Names: RPS19
Find proteins for P39019 (Homo sapiens)
Go to Gene View: RPS19
Go to UniProtKB:  P39019
Entity ID: 16
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S20
SU
104Homo sapiensMutation(s): 0 
Gene Names: RPS20
Find proteins for P60866 (Homo sapiens)
Go to Gene View: RPS20
Go to UniProtKB:  P60866
Entity ID: 17
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S21
SV
82Homo sapiensMutation(s): 0 
Gene Names: RPS21
Find proteins for P63220 (Homo sapiens)
Go to Gene View: RPS21
Go to UniProtKB:  P63220
Entity ID: 18
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S23
SX
141Homo sapiensMutation(s): 0 
Gene Names: RPS23
Find proteins for P62266 (Homo sapiens)
Go to Gene View: RPS23
Go to UniProtKB:  P62266
Entity ID: 19
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S26
Sa
102Homo sapiensMutation(s): 0 
Gene Names: RPS26
Find proteins for P62854 (Homo sapiens)
Go to Gene View: RPS26
Go to UniProtKB:  P62854
Entity ID: 20
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S28
Sc
64Homo sapiensMutation(s): 0 
Gene Names: RPS28
Find proteins for P62857 (Homo sapiens)
Go to Gene View: RPS28
Go to UniProtKB:  P62857
Entity ID: 21
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S29
Sd
55Homo sapiensMutation(s): 0 
Gene Names: RPS29
Find proteins for P62273 (Homo sapiens)
Go to Gene View: RPS29
Go to UniProtKB:  P62273
Entity ID: 22
MoleculeChainsSequence LengthOrganismDetails
Receptor of activated protein C kinase 1
Sg
312Homo sapiensMutation(s): 0 
Gene Names: RACK1 (GNB2L1)
Find proteins for P63244 (Homo sapiens)
Go to Gene View: RACK1
Go to UniProtKB:  P63244
Entity ID: 23
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S2
SC
220Homo sapiensMutation(s): 0 
Gene Names: RPS2 (RPS4)
Find proteins for P15880 (Homo sapiens)
Go to Gene View: RPS2
Go to UniProtKB:  P15880
Entity ID: 24
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S6
SG
237Homo sapiensMutation(s): 0 
Gene Names: RPS6
Find proteins for P62753 (Homo sapiens)
Go to Gene View: RPS6
Go to UniProtKB:  P62753
Entity ID: 25
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S9
SJ
185Homo sapiensMutation(s): 0 
Gene Names: RPS9
Find proteins for P46781 (Homo sapiens)
Go to Gene View: RPS9
Go to UniProtKB:  P46781
Entity ID: 26
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S12
SM
118Homo sapiensMutation(s): 0 
Gene Names: RPS12
Find proteins for P25398 (Homo sapiens)
Go to Gene View: RPS12
Go to UniProtKB:  P25398
Entity ID: 27
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S13
SN
150Homo sapiensMutation(s): 0 
Gene Names: RPS13
Find proteins for P62277 (Homo sapiens)
Go to Gene View: RPS13
Go to UniProtKB:  P62277
Entity ID: 28
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S14
SO
137Homo sapiensMutation(s): 0 
Gene Names: RPS14
Find proteins for P62263 (Homo sapiens)
Go to Gene View: RPS14
Go to UniProtKB:  P62263
Entity ID: 29
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S15a
SW
129Homo sapiensMutation(s): 0 
Gene Names: RPS15A
Find proteins for P62244 (Homo sapiens)
Go to Gene View: RPS15A
Go to UniProtKB:  P62244
Entity ID: 30
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S24
SY
131Homo sapiensMutation(s): 0 
Gene Names: RPS24
Find proteins for P62847 (Homo sapiens)
Go to Gene View: RPS24
Go to UniProtKB:  P62847
Entity ID: 31
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S25
SZ
73Homo sapiensMutation(s): 0 
Gene Names: RPS25
Find proteins for P62851 (Homo sapiens)
Go to Gene View: RPS25
Go to UniProtKB:  P62851
Entity ID: 32
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S27
Sb
82Homo sapiensMutation(s): 0 
Gene Names: RPS27 (MPS1)
Find proteins for P42677 (Homo sapiens)
Go to Gene View: RPS27
Go to UniProtKB:  P42677
Entity ID: 33
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S30
Se
57Homo sapiensMutation(s): 0 
Gene Names: FAU
Find proteins for E9PR30 (Homo sapiens)
Go to Gene View: FAU
Go to UniProtKB:  E9PR30
Entity ID: 34
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S27a
Sf
67Homo sapiensMutation(s): 0 
Gene Names: RPS27A (UBA80, UBCEP1)
Find proteins for P62979 (Homo sapiens)
Go to Gene View: RPS27A
Go to UniProtKB:  P62979
Entity ID: 35
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L8
A
252Homo sapiensMutation(s): 0 
Gene Names: RPL8
Find proteins for P62917 (Homo sapiens)
Go to Gene View: RPL8
Go to UniProtKB:  P62917
Entity ID: 36
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L3
B
397Homo sapiensMutation(s): 0 
Gene Names: RPL3
Find proteins for P39023 (Homo sapiens)
Go to Gene View: RPL3
Go to UniProtKB:  P39023
Entity ID: 37
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L4
C
363Homo sapiensMutation(s): 0 
Gene Names: RPL4 (RPL1)
Find proteins for P36578 (Homo sapiens)
Go to Gene View: RPL4
Go to UniProtKB:  P36578
Entity ID: 40
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L5
F
294Homo sapiensMutation(s): 0 
Gene Names: RPL5
Find proteins for P46777 (Homo sapiens)
Go to Gene View: RPL5
Go to UniProtKB:  P46777
Entity ID: 41
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L6
G
247Homo sapiensMutation(s): 0 
Gene Names: RPL6 (TXREB1)
Find proteins for Q02878 (Homo sapiens)
Go to Gene View: RPL6
Go to UniProtKB:  Q02878
Entity ID: 42
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L7
H
225Homo sapiensMutation(s): 0 
Gene Names: RPL7
Find proteins for P18124 (Homo sapiens)
Go to Gene View: RPL7
Go to UniProtKB:  P18124
Entity ID: 43
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L7a
I
234Homo sapiensMutation(s): 0 
Gene Names: RPL7A (SURF-3, SURF3)
Find proteins for P62424 (Homo sapiens)
Go to Gene View: RPL7A
Go to UniProtKB:  P62424
Entity ID: 44
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L9
J
191Homo sapiensMutation(s): 0 
Gene Names: RPL9, RPL9P7, RPL9P8, RPL9P9
Find proteins for P32969 (Homo sapiens)
Go to Gene View: RPL9
Go to UniProtKB:  P32969
Entity ID: 45
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L10
K
211Homo sapiensMutation(s): 0 
Gene Names: RPL10 (DXS648E, QM)
Find proteins for P27635 (Homo sapiens)
Go to Gene View: RPL10
Go to UniProtKB:  P27635
Entity ID: 46
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L11
L
169Homo sapiensMutation(s): 0 
Gene Names: RPL11
Find proteins for P62913 (Homo sapiens)
Go to Gene View: RPL11
Go to UniProtKB:  P62913
Entity ID: 47
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L13
M
205Homo sapiensMutation(s): 0 
Gene Names: RPL13 (BBC1)
Find proteins for P26373 (Homo sapiens)
Go to Gene View: RPL13
Go to UniProtKB:  P26373
Entity ID: 48
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L14
N
139Homo sapiensMutation(s): 0 
Gene Names: RPL14
Find proteins for P50914 (Homo sapiens)
Go to Gene View: RPL14
Go to UniProtKB:  P50914
Entity ID: 49
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L15
O
203Homo sapiensMutation(s): 0 
Gene Names: RPL15 (EC45)
Find proteins for P61313 (Homo sapiens)
Go to Gene View: RPL15
Go to UniProtKB:  P61313
Entity ID: 50
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L13a
P
195Homo sapiensMutation(s): 0 
Gene Names: RPL13A
Find proteins for P40429 (Homo sapiens)
Go to Gene View: RPL13A
Go to UniProtKB:  P40429
Entity ID: 51
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L17
Q
153Homo sapiensMutation(s): 0 
Gene Names: RPL17
Find proteins for P18621 (Homo sapiens)
Go to Gene View: RPL17
Go to UniProtKB:  P18621
Entity ID: 52
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L18
R
187Homo sapiensMutation(s): 0 
Gene Names: RPL18
Find proteins for Q07020 (Homo sapiens)
Go to Gene View: RPL18
Go to UniProtKB:  Q07020
Entity ID: 53
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L19
S
181Homo sapiensMutation(s): 0 
Gene Names: RPL19
Find proteins for P84098 (Homo sapiens)
Go to Gene View: RPL19
Go to UniProtKB:  P84098
Entity ID: 54
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L18a
T
175Homo sapiensMutation(s): 0 
Gene Names: RPL18A
Find proteins for Q02543 (Homo sapiens)
Go to Gene View: RPL18A
Go to UniProtKB:  Q02543
Entity ID: 55
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L21
U
157Homo sapiensMutation(s): 0 
Gene Names: RPL21
Find proteins for P46778 (Homo sapiens)
Go to Gene View: RPL21
Go to UniProtKB:  P46778
Entity ID: 56
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L22
V
99Homo sapiensMutation(s): 0 
Gene Names: RPL22
Find proteins for P35268 (Homo sapiens)
Go to Gene View: RPL22
Go to UniProtKB:  P35268
Entity ID: 57
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L23
W
129Homo sapiensMutation(s): 0 
Find proteins for Q9BTQ7 (Homo sapiens)
Go to UniProtKB:  Q9BTQ7
Entity ID: 58
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L24
X
61Homo sapiensMutation(s): 0 
Gene Names: RPL24
Find proteins for P83731 (Homo sapiens)
Go to Gene View: RPL24
Go to UniProtKB:  P83731
Entity ID: 59
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L23a
Y
117Homo sapiensMutation(s): 0 
Gene Names: RPL23A
Find proteins for P62750 (Homo sapiens)
Go to Gene View: RPL23A
Go to UniProtKB:  P62750
Entity ID: 60
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L26
Z
134Homo sapiensMutation(s): 0 
Gene Names: RPL26
Find proteins for P61254 (Homo sapiens)
Go to Gene View: RPL26
Go to UniProtKB:  P61254
Entity ID: 61
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L27
a
134Homo sapiensMutation(s): 0 
Gene Names: RPL27
Find proteins for P61353 (Homo sapiens)
Go to Gene View: RPL27
Go to UniProtKB:  P61353
Entity ID: 62
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L27a
b
147Homo sapiensMutation(s): 0 
Gene Names: RPL27A
Find proteins for P46776 (Homo sapiens)
Go to Gene View: RPL27A
Go to UniProtKB:  P46776
Entity ID: 63
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L29
c
121Homo sapiensMutation(s): 0 
Gene Names: RPL29
Find proteins for P47914 (Homo sapiens)
Go to Gene View: RPL29
Go to UniProtKB:  P47914
Entity ID: 64
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L30
d
103Homo sapiensMutation(s): 0 
Gene Names: RPL30
Find proteins for P62888 (Homo sapiens)
Go to Gene View: RPL30
Go to UniProtKB:  P62888
Entity ID: 65
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L31
e
106Homo sapiensMutation(s): 0 
Gene Names: RPL31
Find proteins for P62899 (Homo sapiens)
Go to Gene View: RPL31
Go to UniProtKB:  P62899
Entity ID: 66
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L32
f
129Homo sapiensMutation(s): 0 
Gene Names: RPL32
Find proteins for P62910 (Homo sapiens)
Go to Gene View: RPL32
Go to UniProtKB:  P62910
Entity ID: 67
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L35a
g
109Homo sapiensMutation(s): 0 
Gene Names: RPL35A
Find proteins for P18077 (Homo sapiens)
Go to Gene View: RPL35A
Go to UniProtKB:  P18077
Entity ID: 68
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L34
h
114Homo sapiensMutation(s): 0 
Gene Names: RPL34
Find proteins for P49207 (Homo sapiens)
Go to Gene View: RPL34
Go to UniProtKB:  P49207
Entity ID: 69
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L35
i
122Homo sapiensMutation(s): 0 
Gene Names: RPL35
Find proteins for P42766 (Homo sapiens)
Go to Gene View: RPL35
Go to UniProtKB:  P42766
Entity ID: 70
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L36
j
97Homo sapiensMutation(s): 0 
Gene Names: RPL36
Find proteins for Q9Y3U8 (Homo sapiens)
Go to Gene View: RPL36
Go to UniProtKB:  Q9Y3U8
Entity ID: 71
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L37
k
84Homo sapiensMutation(s): 0 
Gene Names: RPL37
Find proteins for P61927 (Homo sapiens)
Go to Gene View: RPL37
Go to UniProtKB:  P61927
Entity ID: 72
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L38
l
69Homo sapiensMutation(s): 0 
Gene Names: RPL38
Find proteins for P63173 (Homo sapiens)
Go to Gene View: RPL38
Go to UniProtKB:  P63173
Entity ID: 73
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L39
m
50Homo sapiensMutation(s): 0 
Gene Names: RPL39
Find proteins for P62891 (Homo sapiens)
Go to Gene View: RPL39
Go to UniProtKB:  P62891
Entity ID: 74
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L40
n
50Homo sapiensMutation(s): 0 
Gene Names: UBA52 (UBCEP2)
Find proteins for P62987 (Homo sapiens)
Go to Gene View: UBA52
Go to UniProtKB:  P62987
Entity ID: 75
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L41
o
25Homo sapiensMutation(s): 0 
Gene Names: RPL41
Find proteins for P62945 (Homo sapiens)
Go to Gene View: RPL41
Go to UniProtKB:  P62945
Entity ID: 76
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L36a
p
105Homo sapiensMutation(s): 0 
Gene Names: RPL36A (RPL44)
Find proteins for P83881 (Homo sapiens)
Go to Gene View: RPL36A
Go to UniProtKB:  P83881
Entity ID: 77
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L37a
q
91Homo sapiensMutation(s): 0 
Gene Names: RPL37A
Find proteins for P61513 (Homo sapiens)
Go to Gene View: RPL37A
Go to UniProtKB:  P61513
Entity ID: 78
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L28
r
122Homo sapiensMutation(s): 0 
Gene Names: RPL28
Find proteins for P46779 (Homo sapiens)
Go to Gene View: RPL28
Go to UniProtKB:  P46779
Entity ID: 83
MoleculeChainsSequence LengthOrganismDetails
Cadherin-1
y
39Homo sapiensMutation(s): 0 
Gene Names: CDH1 (CDHE, UVO)
Find proteins for P12830 (Homo sapiens)
Go to Gene View: CDH1
Go to UniProtKB:  P12830
Entity ID: 1
MoleculeChainsLengthOrganism
18S ribosomal RNAS21714Homo sapiens
Entity ID: 38
MoleculeChainsLengthOrganism
5.8S ribosomal RNAD157Homo sapiens
Entity ID: 39
MoleculeChainsLengthOrganism
5S ribosomal RNAE121Homo sapiens
Entity ID: 79
MoleculeChainsLengthOrganism
28S ribosomal RNAt3607Homo sapiens
Entity ID: 80
MoleculeChainsLengthOrganism
AP RNAu76Homo sapiens
Entity ID: 81
MoleculeChainsLengthOrganism
PE RNAv76Homo sapiens
Entity ID: 82
MoleculeChainsLengthOrganism
mRNAw10Homo sapiens
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

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

Download SDF File 
Download CCD File 
A, B, b, D, E, O, S2, t, Z
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
MVM
Query on MVM

Download SDF File 
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
Modified Residues  15 Unique
IDChainsTypeFormula2D DiagramParent
A2M
Query on A2M
S2
RNA LINKINGC11 H16 N5 O7 PA
PSU
Query on PSU
S2
RNA LINKINGC9 H13 N2 O9 PU
5MC
Query on 5MC
S2
RNA LINKINGC10 H16 N3 O8 PC
6MZ
Query on 6MZ
S2
RNA LINKINGC11 H16 N5 O7 PA
OMU
Query on OMU
S2
RNA LINKINGC10 H15 N2 O9 PU
M7A
Query on M7A
S2
RNA linkingC11 H18 N5 O7 PA
B8N
Query on B8N
S2
RNA linkingC14 H22 N3 O11 P

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B8Q
Query on B8Q
S2
RNA linkingC10 H18 N3 O8 PC
OMC
Query on OMC
S2
RNA LINKINGC10 H16 N3 O8 PC
MA6
Query on MA6
S2
RNA LINKINGC12 H18 N5 O7 PA
UR3
Query on UR3
S2
RNA LINKINGC10 H15 N2 O9 PU
E3C
Query on E3C
S2
RNA linkingC11 H20 N3 O8 PC
OMG
Query on OMG
S2
RNA LINKINGC11 H16 N5 O8 PG
5MU
Query on 5MU
S2
RNA LINKINGC10 H15 N2 O9 PU
4AC
Query on 4AC
S2
RNA LINKINGC11 H16 N3 O9 P

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Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.1 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report or Ramachandran Plots



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 InstituteUnited StatesR01-GM065050

Revision History 

  • Version 1.0: 2019-06-19
    Type: Initial release