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: 10.1073/pnas.1614594113
  • Structures With Same Primary Citation

  • 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; Department of Biological Sciences, Columbia University, New York, NY 10027; Howard Hughes Medical Institute, Columbia University, New York, NY 10027; jf2192@cumc.columbia.edu.



Macromolecules

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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L11L65Trypanosoma cruziMutation(s): 0 
Find proteins for Q4CNF4 (Trypanosoma cruzi (strain CL Brener))
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Entity ID: 17
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein L19-like proteinT150Trypanosoma cruziMutation(s): 0 
Gene Names: RpL19
Find proteins for Q9BMP1 (Trypanosoma cruzi)
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Entity ID: 20
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L23W127Trypanosoma cruziMutation(s): 0 
Find proteins for Q4E4R0 (Trypanosoma cruzi (strain CL Brener))
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Entity ID: 23
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L26Z113Trypanosoma cruziMutation(s): 0 
Find proteins for Q4DG45 (Trypanosoma cruzi (strain CL Brener))
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Entity ID: 28
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L2e245Trypanosoma cruziMutation(s): 0 
Find proteins for Q4DPQ8 (Trypanosoma cruzi (strain CL Brener))
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Entity ID: 32
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L32i113Trypanosoma cruziMutation(s): 0 
Find proteins for Q4D1H8 (Trypanosoma cruzi (strain CL Brener))
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Entity ID: 35
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein L35Al136Trypanosoma cruziMutation(s): 0 
Find proteins for Q4E581 (Trypanosoma cruzi (strain CL Brener))
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Entity ID: 37
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein L37n81Trypanosoma cruziMutation(s): 0 
Find proteins for Q4DXW6 (Trypanosoma cruzi (strain CL Brener))
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Entity ID: 38
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L37ao85Trypanosoma cruziMutation(s): 0 
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Entity ID: 39
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein L38p58Trypanosoma cruziMutation(s): 0 
Find proteins for Q4DQ60 (Trypanosoma cruzi (strain CL Brener))
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Entity ID: 43
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L5u254Trypanosoma cruziMutation(s): 0 
Find proteins for Q4CU61 (Trypanosoma cruzi (strain CL Brener))
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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L13N205Trypanosoma cruziMutation(s): 0 
Find proteins for Q4E661 (Trypanosoma cruzi (strain CL Brener))
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Entity ID: 12
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L13aO203Trypanosoma cruziMutation(s): 0 
Find proteins for V5DCT1 (Trypanosoma cruzi Dm28c)
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Entity ID: 13
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein L14P149Trypanosoma cruziMutation(s): 0 
Find proteins for Q4DQ35 (Trypanosoma cruzi (strain CL Brener))
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Entity ID: 14
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein L15Q203Trypanosoma cruziMutation(s): 0 
Find proteins for Q4CTG9 (Trypanosoma cruzi (strain CL Brener))
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Entity ID: 15
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L17R152Trypanosoma cruziMutation(s): 0 
Find proteins for Q4DC23 (Trypanosoma cruzi (strain CL Brener))
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Entity ID: 16
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L18aS177Trypanosoma cruziMutation(s): 0 
Find proteins for Q4DZ31 (Trypanosoma cruzi (strain CL Brener))
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Entity ID: 18
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein L21E (60S)U146Trypanosoma cruziMutation(s): 0 
Find proteins for Q4DED2 (Trypanosoma cruzi (strain CL Brener))
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Entity ID: 19
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L22V99Trypanosoma cruziMutation(s): 0 
Find proteins for Q4DZN3 (Trypanosoma cruzi (strain CL Brener))
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Entity ID: 21
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L23aX116Trypanosoma cruziMutation(s): 0 
Find proteins for Q4E2Y1 (Trypanosoma cruzi (strain CL Brener))
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Entity ID: 22
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein L24Y61Trypanosoma cruziMutation(s): 0 
Find proteins for Q4E078 (Trypanosoma cruzi (strain CL Brener))
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Entity ID: 24
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein L27a132Trypanosoma cruziMutation(s): 0 
Gene Names: C3747_12g1558cC3747_12g1559cC4B63_9g2155cC4B63_9g2158c
Find proteins for Q9U4H7 (Trypanosoma cruzi)
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Entity ID: 25
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L27A/L29b144Trypanosoma cruziMutation(s): 0 
Find proteins for Q4E4Q8 (Trypanosoma cruzi (strain CL Brener))
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Entity ID: 26
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L28c125Trypanosoma cruziMutation(s): 0 
Find proteins for O00822 (Trypanosoma cruzi)
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Entity ID: 27
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein L29d63Trypanosoma cruziMutation(s): 0 
Find proteins for Q4CPD8 (Trypanosoma cruzi (strain CL Brener))
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Entity ID: 29
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein L13f397Trypanosoma cruziMutation(s): 0 
Find proteins for V5B599 (Trypanosoma cruzi Dm28c)
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Entity ID: 30
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L30g66Trypanosoma cruziMutation(s): 0 
Find proteins for Q4DIC9 (Trypanosoma cruzi (strain CL Brener))
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Entity ID: 31
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal subunit protein L31h169Trypanosoma cruziMutation(s): 0 
Find proteins for V5C333 (Trypanosoma cruzi Dm28c)
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Entity ID: 33
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L34j104Trypanosoma cruziMutation(s): 0 
Find proteins for Q4DB26 (Trypanosoma cruzi (strain CL Brener))
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Entity ID: 34
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L35k120Trypanosoma cruziMutation(s): 0 
Find proteins for Q4E2E0 (Trypanosoma cruzi (strain CL Brener))
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Entity ID: 36
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein L36m95Trypanosoma cruziMutation(s): 0 
Find proteins for V5BDJ2 (Trypanosoma cruzi Dm28c)
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Entity ID: 40
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein L39q50Trypanosoma cruziMutation(s): 0 
Find proteins for Q4DVC6 (Trypanosoma cruzi (strain CL Brener))
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Entity ID: 41
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L4r337Trypanosoma cruziMutation(s): 0 
Find proteins for Q4CQW2 (Trypanosoma cruzi (strain CL Brener))
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Entity ID: 42
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L44t93Trypanosoma cruziMutation(s): 0 
Find proteins for Q4CV79 (Trypanosoma cruzi (strain CL Brener))
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Entity ID: 44
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L6v171Trypanosoma cruziMutation(s): 0 
Find proteins for Q4DIV9 (Trypanosoma cruzi (strain CL Brener))
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Entity ID: 45
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L7w215Trypanosoma cruziMutation(s): 0 
Find proteins for Q4DNZ7 (Trypanosoma cruzi (strain CL Brener))
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Entity ID: 46
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein L7a-like proteinx223Trypanosoma cruziMutation(s): 0 
Gene Names: RpL7aC3747_15g157
Find proteins for Q9BMP0 (Trypanosoma cruzi)
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L18I192Trypanosoma cruziMutation(s): 0 
Find proteins for Q4DZP2 (Trypanosoma cruzi (strain CL Brener))
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Entity ID: 2
MoleculeChainsLengthOrganism
RNA LARGE SUBUNIT BETAB941Trypanosoma cruzi

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Entity ID: 1
MoleculeChainsLengthOrganism
RNA LARGE SUBUNIT ALPHAA1278Trypanosoma cruzi

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Entity ID: 3
MoleculeChainsLengthOrganism
5.8S rRNAC169Trypanosoma cruzi

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Entity ID: 4
MoleculeChainsLengthOrganism
5S rRNAD118Trypanosoma cruzi

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Entity ID: 5
MoleculeChainsLengthOrganism
srRNA1E146Trypanosoma cruzi

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Entity ID: 6
MoleculeChainsLengthOrganism
srRNA3F46Trypanosoma cruzi

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Entity ID: 7
MoleculeChainsLengthOrganism
srRNA2G123Trypanosoma cruzi

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Entity ID: 8
MoleculeChainsLengthOrganism
srRNA4H91Trypanosoma cruzi
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

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

Download CCD File 
A, B, C, D, E, F, G, H
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
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 

  • 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