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 1.5 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 U S A 113: 12174-12179

  • DOI: https://doi.org/10.1073/pnas.1614594113
  • Primary Citation of Related Structures:  
    5T5H

  • 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 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

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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L18192Trypanosoma cruziMutation(s): 0 
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L11J [auth L]65Trypanosoma cruziMutation(s): 0 
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L13K [auth N]205Trypanosoma cruziMutation(s): 0 
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L13aL [auth O]203Trypanosoma cruziMutation(s): 0 
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein L14M [auth P]149Trypanosoma cruziMutation(s): 0 
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein L15N [auth Q]203Trypanosoma cruziMutation(s): 0 
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L17O [auth R]152Trypanosoma cruziMutation(s): 0 
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L18aP [auth S]177Trypanosoma cruziMutation(s): 0 
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein L19-like proteinQ [auth T]150Trypanosoma cruziMutation(s): 0 
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein L21E (60S)R [auth U]146Trypanosoma cruziMutation(s): 0 
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L22S [auth V]99Trypanosoma cruziMutation(s): 0 
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L23T [auth W]127Trypanosoma cruziMutation(s): 0 
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L23aU [auth X]116Trypanosoma cruziMutation(s): 0 
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Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein L24V [auth Y]61Trypanosoma cruziMutation(s): 0 
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Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L26W [auth Z]113Trypanosoma cruziMutation(s): 0 
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Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein L27X [auth a]132Trypanosoma cruziMutation(s): 0 
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Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L27A/L29Y [auth b]144Trypanosoma cruziMutation(s): 0 
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Entity ID: 26
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L28Z [auth c]125Trypanosoma cruziMutation(s): 0 
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Find proteins for O00822 (Trypanosoma cruzi)
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Entity ID: 27
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein L29AA [auth d]63Trypanosoma cruziMutation(s): 0 
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Entity ID: 28
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L2BA [auth e]245Trypanosoma cruziMutation(s): 0 
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Entity ID: 29
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein L13CA [auth f]397Trypanosoma cruziMutation(s): 0 
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Entity ID: 30
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L30DA [auth g]66Trypanosoma cruziMutation(s): 0 
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Entity ID: 31
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal subunit protein L31EA [auth h]169Trypanosoma cruziMutation(s): 0 
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Find proteins for V5C333 (Trypanosoma cruzi Dm28c)
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Entity ID: 32
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L32FA [auth i]113Trypanosoma cruziMutation(s): 0 
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Entity ID: 33
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L34GA [auth j]104Trypanosoma cruziMutation(s): 0 
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Entity ID: 34
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L35HA [auth k]120Trypanosoma cruziMutation(s): 0 
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Entity ID: 35
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein L35AIA [auth l]136Trypanosoma cruziMutation(s): 0 
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Entity ID: 36
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein L36JA [auth m]95Trypanosoma cruziMutation(s): 0 
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Entity ID: 37
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein L37KA [auth n]81Trypanosoma cruziMutation(s): 0 
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Entity ID: 38
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L37aLA [auth o]85Trypanosoma cruziMutation(s): 0 
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Entity ID: 39
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein L38MA [auth p]58Trypanosoma cruziMutation(s): 0 
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Entity ID: 40
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein L39NA [auth q]50Trypanosoma cruziMutation(s): 0 
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Entity ID: 41
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L4OA [auth r]337Trypanosoma cruziMutation(s): 0 
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Entity ID: 42
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L44PA [auth t]93Trypanosoma cruziMutation(s): 0 
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Entity ID: 43
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L5QA [auth u]254Trypanosoma cruziMutation(s): 0 
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Entity ID: 44
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L6RA [auth v]171Trypanosoma cruziMutation(s): 0 
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Entity ID: 45
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L7SA [auth w]215Trypanosoma cruziMutation(s): 0 
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Entity ID: 46
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein L7a-like proteinTA [auth x]223Trypanosoma cruziMutation(s): 0 
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Entity ID: 1
MoleculeChains LengthOrganismImage
RNA LARGE SUBUNIT ALPHA1,278Trypanosoma cruzi
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Entity ID: 2
MoleculeChains LengthOrganismImage
RNA LARGE SUBUNIT BETA941Trypanosoma cruzi
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Entity ID: 3
MoleculeChains LengthOrganismImage
5.8S rRNA169Trypanosoma cruzi
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MoleculeChains LengthOrganismImage
5S rRNA118Trypanosoma cruzi
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Entity ID: 5
MoleculeChains LengthOrganismImage
srRNA1146Trypanosoma cruzi
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Entity ID: 6
MoleculeChains LengthOrganismImage
srRNA346Trypanosoma cruzi
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Entity ID: 7
MoleculeChains LengthOrganismImage
srRNA2123Trypanosoma cruzi
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Entity ID: 8
MoleculeChains LengthOrganismImage
srRNA491Trypanosoma cruzi
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Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download Ideal Coordinates CCD File 
VE [auth n],
WE [auth o],
XE [auth t]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
MG
Query on MG

Download Ideal Coordinates CCD File 
AB [auth A]
AC [auth A]
AD [auth A]
AE [auth B]
BB [auth A]
AB [auth A],
AC [auth A],
AD [auth A],
AE [auth B],
BB [auth A],
BC [auth A],
BD [auth A],
BE [auth B],
CB [auth A],
CC [auth A],
CD [auth A],
CE [auth B],
DB [auth A],
DC [auth A],
DD [auth A],
DE [auth B],
EB [auth A],
EC [auth A],
ED [auth A],
EE [auth B],
FB [auth A],
FC [auth A],
FD [auth A],
FE [auth B],
GB [auth A],
GC [auth A],
GD [auth A],
GE [auth B],
HB [auth A],
HC [auth A],
HD [auth A],
HE [auth B],
IB [auth A],
IC [auth A],
ID [auth B],
IE [auth B],
JB [auth A],
JC [auth A],
JD [auth B],
JE [auth B],
KB [auth A],
KC [auth A],
KD [auth B],
KE [auth B],
LB [auth A],
LC [auth A],
LD [auth B],
LE [auth B],
MB [auth A],
MC [auth A],
MD [auth B],
ME [auth B],
NB [auth A],
NC [auth A],
ND [auth B],
NE [auth B],
OB [auth A],
OC [auth A],
OD [auth B],
OE [auth C],
PB [auth A],
PC [auth A],
PD [auth B],
PE [auth C],
QB [auth A],
QC [auth A],
QD [auth B],
QE [auth D],
RB [auth A],
RC [auth A],
RD [auth B],
RE [auth E],
SB [auth A],
SC [auth A],
SD [auth B],
SE [auth F],
TB [auth A],
TC [auth A],
TD [auth B],
TE [auth G],
UA [auth A],
UB [auth A],
UC [auth A],
UD [auth B],
UE [auth H],
VA [auth A],
VB [auth A],
VC [auth A],
VD [auth B],
WA [auth A],
WB [auth A],
WC [auth A],
WD [auth B],
XA [auth A],
XB [auth A],
XC [auth A],
XD [auth B],
YA [auth A],
YB [auth A],
YC [auth A],
YD [auth B],
ZA [auth A],
ZB [auth A],
ZC [auth A],
ZD [auth B]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
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



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM29169
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United States35GM118093
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM028301
National Science Foundation (NSF, United States)United StatesGRFP DGE-11-44155
Howard Hughes Medical Institute (HHMI)United StatesHHMI

Revision History  (Full details and data files)

  • Version 1.0: 2016-10-12
    Type: Initial release
  • Version 1.1: 2016-11-16
    Changes: Database references
  • Version 1.2: 2017-09-20
    Changes: Author supporting evidence, Data collection, Database references, Derived calculations
  • Version 1.3: 2018-03-28
    Changes: Advisory, Data collection, Other, Structure summary
  • Version 1.4: 2019-11-20
    Changes: Author supporting evidence
  • Version 1.5: 2019-12-18
    Changes: Advisory, Derived calculations, Other