5T5H

Structure and assembly model for the Trypanosoma cruzi 60S ribosomal subunit


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.54 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Structure and assembly model for the Trypanosoma cruzi 60S ribosomal subunit.

Liu, Z.Gutierrez-Vargas, C.Wei, J.Grassucci, R.A.Ramesh, M.Espina, N.Sun, M.Tutuncuoglu, B.Madison-Antenucci, S.Woolford, J.L.Tong, L.Frank, J.

(2016) Proc.Natl.Acad.Sci.USA 113: 12174-12179

  • DOI: 10.1073/pnas.1614594113

  • PubMed Abstract: 
  • Ribosomes of trypanosomatids, a family of protozoan parasites causing debilitating human diseases, possess multiply fragmented rRNAs that together are analogous to 28S rRNA, unusually large rRNA expansion segments, and r-protein variations compared w ...

    Ribosomes of trypanosomatids, a family of protozoan parasites causing debilitating human diseases, possess multiply fragmented rRNAs that together are analogous to 28S rRNA, unusually large rRNA expansion segments, and r-protein variations compared with other eukaryotic ribosomes. To investigate the architecture of the trypanosomatid ribosomes, we determined the 2.5-Å structure of the Trypanosoma cruzi ribosome large subunit by single-particle cryo-EM. Examination of this structure and comparative analysis of the yeast ribosomal assembly pathway allowed us to develop a stepwise assembly model for the eight pieces of the large subunit rRNAs and a number of ancillary "glue" proteins. This model can be applied to the characterization of Trypanosoma brucei and Leishmania spp. ribosomes as well. Together with other details, our atomic-level structure may provide a foundation for structure-based design of antitrypanosome drugs.


    Organizational Affiliation

    Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L18
I
192Trypanosoma cruzi (strain CL Brener)Mutation(s): 0 
Gene Names: RPL18
Find proteins for Q4DZP2 (Trypanosoma cruzi (strain CL Brener))
Go to Gene View: RPL18
Go to UniProtKB:  Q4DZP2
Entity ID: 10
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L11
L
65Trypanosoma cruzi (strain CL Brener)Mutation(s): 0 
Find proteins for Q4CNF4 (Trypanosoma cruzi (strain CL Brener))
Go to UniProtKB:  Q4CNF4
Entity ID: 11
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L13
N
205Trypanosoma cruzi (strain CL Brener)Mutation(s): 0 
Find proteins for Q4E661 (Trypanosoma cruzi (strain CL Brener))
Go to UniProtKB:  Q4E661
Entity ID: 12
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L13a
O
203Trypanosoma cruzi Dm28cMutation(s): 0 
Find proteins for V5DCT1 (Trypanosoma cruzi Dm28c)
Go to UniProtKB:  V5DCT1
Entity ID: 13
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein L14
P
149Trypanosoma cruzi (strain CL Brener)Mutation(s): 0 
Find proteins for Q4DQ35 (Trypanosoma cruzi (strain CL Brener))
Go to UniProtKB:  Q4DQ35
Entity ID: 14
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein L15
Q
203Trypanosoma cruzi (strain CL Brener)Mutation(s): 0 
Find proteins for Q4CTG9 (Trypanosoma cruzi (strain CL Brener))
Go to UniProtKB:  Q4CTG9
Entity ID: 15
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L17
R
152Trypanosoma cruzi (strain CL Brener)Mutation(s): 0 
Find proteins for Q4DC23 (Trypanosoma cruzi (strain CL Brener))
Go to UniProtKB:  Q4DC23
Entity ID: 16
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L18a
S
177Trypanosoma cruzi (strain CL Brener)Mutation(s): 0 
Find proteins for Q4DZ31 (Trypanosoma cruzi (strain CL Brener))
Go to UniProtKB:  Q4DZ31
Entity ID: 17
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein L19-like protein
T
150Trypanosoma cruziMutation(s): 0 
Gene Names: RpL19
Find proteins for Q9BMP1 (Trypanosoma cruzi)
Go to UniProtKB:  Q9BMP1
Entity ID: 18
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein L21E (60S)
U
146Trypanosoma cruzi (strain CL Brener)Mutation(s): 0 
Find proteins for Q4DED2 (Trypanosoma cruzi (strain CL Brener))
Go to UniProtKB:  Q4DED2
Entity ID: 19
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L22
V
99Trypanosoma cruzi (strain CL Brener)Mutation(s): 0 
Find proteins for Q4DZN3 (Trypanosoma cruzi (strain CL Brener))
Go to UniProtKB:  Q4DZN3
Entity ID: 20
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L23
W
127Trypanosoma cruzi (strain CL Brener)Mutation(s): 0 
Find proteins for Q4E4R0 (Trypanosoma cruzi (strain CL Brener))
Go to UniProtKB:  Q4E4R0
Entity ID: 21
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L23a
X
116Trypanosoma cruzi (strain CL Brener)Mutation(s): 0 
Find proteins for Q4E2Y1 (Trypanosoma cruzi (strain CL Brener))
Go to UniProtKB:  Q4E2Y1
Entity ID: 22
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein L24
Y
61Trypanosoma cruzi (strain CL Brener)Mutation(s): 0 
Find proteins for Q4E078 (Trypanosoma cruzi (strain CL Brener))
Go to UniProtKB:  Q4E078
Entity ID: 23
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L26
Z
113Trypanosoma cruzi (strain CL Brener)Mutation(s): 0 
Find proteins for Q4DG45 (Trypanosoma cruzi (strain CL Brener))
Go to UniProtKB:  Q4DG45
Entity ID: 24
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein L27
a
132Trypanosoma cruziMutation(s): 0 
Find proteins for Q9U4H7 (Trypanosoma cruzi)
Go to UniProtKB:  Q9U4H7
Entity ID: 25
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L27A/L29
b
144Trypanosoma cruzi (strain CL Brener)Mutation(s): 0 
Find proteins for Q4E4Q8 (Trypanosoma cruzi (strain CL Brener))
Go to UniProtKB:  Q4E4Q8
Entity ID: 26
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L28
c
125Trypanosoma cruziMutation(s): 0 
Find proteins for O00822 (Trypanosoma cruzi)
Go to UniProtKB:  O00822
Entity ID: 27
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein L29
d
63Trypanosoma cruzi (strain CL Brener)Mutation(s): 0 
Find proteins for Q4CPD8 (Trypanosoma cruzi (strain CL Brener))
Go to UniProtKB:  Q4CPD8
Entity ID: 28
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L2
e
245Trypanosoma cruzi (strain CL Brener)Mutation(s): 0 
Find proteins for Q4DPQ8 (Trypanosoma cruzi (strain CL Brener))
Go to UniProtKB:  Q4DPQ8
Entity ID: 29
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein L13
f
397Trypanosoma cruzi Dm28cMutation(s): 0 
Find proteins for V5B599 (Trypanosoma cruzi Dm28c)
Go to UniProtKB:  V5B599
Entity ID: 30
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L30
g
66Trypanosoma cruzi (strain CL Brener)Mutation(s): 0 
Find proteins for Q4DIC9 (Trypanosoma cruzi (strain CL Brener))
Go to UniProtKB:  Q4DIC9
Entity ID: 31
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal subunit protein L31
h
169Trypanosoma cruzi Dm28cMutation(s): 0 
Find proteins for V5C333 (Trypanosoma cruzi Dm28c)
Go to UniProtKB:  V5C333
Entity ID: 32
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L32
i
113Trypanosoma cruzi (strain CL Brener)Mutation(s): 0 
Find proteins for Q4D1H8 (Trypanosoma cruzi (strain CL Brener))
Go to UniProtKB:  Q4D1H8
Entity ID: 33
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L34
j
104Trypanosoma cruzi (strain CL Brener)Mutation(s): 0 
Find proteins for Q4DB26 (Trypanosoma cruzi (strain CL Brener))
Go to UniProtKB:  Q4DB26
Entity ID: 34
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L35
k
120Trypanosoma cruzi (strain CL Brener)Mutation(s): 0 
Find proteins for Q4E2E0 (Trypanosoma cruzi (strain CL Brener))
Go to UniProtKB:  Q4E2E0
Entity ID: 35
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein L35A
l
136Trypanosoma cruzi (strain CL Brener)Mutation(s): 0 
Find proteins for Q4E581 (Trypanosoma cruzi (strain CL Brener))
Go to UniProtKB:  Q4E581
Entity ID: 36
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein L36
m
95Trypanosoma cruzi Dm28cMutation(s): 0 
Find proteins for V5BDJ2 (Trypanosoma cruzi Dm28c)
Go to UniProtKB:  V5BDJ2
Entity ID: 37
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein L37
n
81Trypanosoma cruzi (strain CL Brener)Mutation(s): 0 
Find proteins for Q4DXW6 (Trypanosoma cruzi (strain CL Brener))
Go to UniProtKB:  Q4DXW6
Entity ID: 38
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L37a
o
85Trypanosoma cruzi (strain CL Brener)Mutation(s): 0 
Find proteins for Q4DAV9 (Trypanosoma cruzi (strain CL Brener))
Go to UniProtKB:  Q4DAV9
Entity ID: 39
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein L38
p
58Trypanosoma cruzi (strain CL Brener)Mutation(s): 0 
Find proteins for Q4DQ60 (Trypanosoma cruzi (strain CL Brener))
Go to UniProtKB:  Q4DQ60
Entity ID: 40
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein L39
q
50Trypanosoma cruzi (strain CL Brener)Mutation(s): 0 
Find proteins for Q4DVC6 (Trypanosoma cruzi (strain CL Brener))
Go to UniProtKB:  Q4DVC6
Entity ID: 41
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L4
r
337Trypanosoma cruzi (strain CL Brener)Mutation(s): 0 
Find proteins for Q4CQW2 (Trypanosoma cruzi (strain CL Brener))
Go to UniProtKB:  Q4CQW2
Entity ID: 42
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L44
t
93Trypanosoma cruzi (strain CL Brener)Mutation(s): 0 
Find proteins for Q4CV79 (Trypanosoma cruzi (strain CL Brener))
Go to UniProtKB:  Q4CV79
Entity ID: 43
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L5
u
254Trypanosoma cruzi (strain CL Brener)Mutation(s): 0 
Find proteins for Q4CU61 (Trypanosoma cruzi (strain CL Brener))
Go to UniProtKB:  Q4CU61
Entity ID: 44
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L6
v
171Trypanosoma cruzi (strain CL Brener)Mutation(s): 0 
Find proteins for Q4DIV9 (Trypanosoma cruzi (strain CL Brener))
Go to UniProtKB:  Q4DIV9
Entity ID: 45
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L7
w
215Trypanosoma cruzi (strain CL Brener)Mutation(s): 0 
Find proteins for Q4DNZ7 (Trypanosoma cruzi (strain CL Brener))
Go to UniProtKB:  Q4DNZ7
Entity ID: 46
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein L7a-like protein
x
223Trypanosoma cruziMutation(s): 0 
Gene Names: RpL7a
Find proteins for Q9BMP0 (Trypanosoma cruzi)
Go to UniProtKB:  Q9BMP0
Entity ID: 1
MoleculeChainsLengthOrganism
RNA LARGE SUBUNIT ALPHAA1278Trypanosoma cruzi
Entity ID: 2
MoleculeChainsLengthOrganism
RNA LARGE SUBUNIT BETAB941Trypanosoma cruzi
Entity ID: 3
MoleculeChainsLengthOrganism
5.8S rRNAC169Trypanosoma cruzi
Entity ID: 4
MoleculeChainsLengthOrganism
5S rRNAD118Trypanosoma cruzi
Entity ID: 5
MoleculeChainsLengthOrganism
srRNA1E146Trypanosoma cruzi
Entity ID: 6
MoleculeChainsLengthOrganism
srRNA3F46Trypanosoma cruzi
Entity ID: 7
MoleculeChainsLengthOrganism
srRNA2G123Trypanosoma cruzi
Entity ID: 8
MoleculeChainsLengthOrganism
srRNA4H91Trypanosoma cruzi
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
n, o, t
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

Download SDF File 
Download CCD File 
A, B, C, D, E, F, G, H
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  6 Unique
IDChainsTypeFormula2D DiagramParent
A2M
Query on A2M
A, B, C
RNA LINKINGC11 H16 N5 O7 PA
5MC
Query on 5MC
A, B
RNA LINKINGC10 H16 N3 O8 PC
OMU
Query on OMU
A, B, C
RNA LINKINGC10 H15 N2 O9 PU
OMC
Query on OMC
A, B, C
RNA LINKINGC10 H16 N3 O8 PC
OMG
Query on OMG
A, B, C, G
RNA LINKINGC11 H16 N5 O8 PG
7MG
Query on 7MG
A, B, C
RNA LINKINGC11 H18 N5 O8 PG
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.54 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical SciencesUnited StatesGM29169
National Institutes of Health/National Institute of General Medical SciencesUnited States35GM118093
National Institutes of Health/National Institute of General Medical SciencesUnited StatesGM028301
National Science Foundation (United States)United StatesGRFP DGE-11-44155
Howard Hughes Medical InstituteUnited StatesHHMI

Revision History 

  • Version 1.0: 2016-10-12
    Type: Initial release
  • Version 1.1: 2016-11-16
    Type: Database references
  • Version 1.2: 2017-09-20
    Type: Author supporting evidence, Data collection, Database references, Derived calculations
  • Version 1.3: 2018-03-28
    Type: Advisory, Data collection, Other, Structure summary