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- PDB-5t5h: Structure and assembly model for the Trypanosoma cruzi 60S riboso... -

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Basic information

Entry
Database: PDB / ID: 5t5h
TitleStructure and assembly model for the Trypanosoma cruzi 60S ribosomal subunit
Components
  • (60S ribosomal protein ...) x 23
  • (RNA LARGE SUBUNIT ...) x 2
  • (Ribosomal protein ...) x 13
  • 40S ribosomal protein L14
  • 5.8S rRNA5.8S ribosomal RNA
  • 5S rRNA5S ribosomal RNA
  • 60S ribosomal subunit protein L31
  • srRNA1
  • srRNA2
  • srRNA3
  • srRNA4
KeywordsRIBOSOME / Trypanosoma cruzi / ribosomal subunit / assmebly / multiply fragmented rRNAs / 2.5 angstrom cryo-EM structure
Function / homology
Function and homology information


maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / nucleosome assembly / nucleosome / large ribosomal subunit / 5S rRNA binding / cytosolic large ribosomal subunit / membrane => GO:0016020 / rRNA binding / ribosome / structural constituent of ribosome ...maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / nucleosome assembly / nucleosome / large ribosomal subunit / 5S rRNA binding / cytosolic large ribosomal subunit / membrane => GO:0016020 / rRNA binding / ribosome / structural constituent of ribosome / translation / DNA binding / RNA binding / metal ion binding / cytosol / cytoplasm
Similarity search - Function
Linker histone H1/H5 / Ribosomal protein L30e / Ribosomal protein L28e / Ribosomal L28e/Mak16 / Ribosomal L28e protein family / Ribosomal protein L29e / Ribosomal L29e protein family / Eukaryotic Ribosomal Protein L27, KOW domain / Ribosomal protein L44e / Ribosomal protein L38e ...Linker histone H1/H5 / Ribosomal protein L30e / Ribosomal protein L28e / Ribosomal L28e/Mak16 / Ribosomal L28e protein family / Ribosomal protein L29e / Ribosomal L29e protein family / Eukaryotic Ribosomal Protein L27, KOW domain / Ribosomal protein L44e / Ribosomal protein L38e / Ribosomal protein L38e superfamily / Ribosomal protein L27e / Ribosomal protein L27e superfamily / Ribosomal L38e protein family / 60S ribosomal protein L35 / Ribosomal protein L30e, conserved site / Ribosomal protein L44 / Ribosomal protein L34Ae / Ribosomal protein L13e, conserved site / Ribosomal protein L13e signature. / Ribosomal L27e protein family / Ribosomal Protein L6, KOW domain / Ribosomal protein L22e / Ribosomal protein L22e superfamily / Ribosomal L22e protein family / Ribosomal protein L30/YlxQ / Ribosomal protein L34e / Ribosomal protein L37ae / 60S ribosomal protein L6E / Ribosomal protein L19, eukaryotic / Ribosomal protein L35A / Ribosomal protein L36e / Ribosomal protein L36e domain superfamily / Ribosomal protein L36e / Ribosomal protein L35A superfamily / Ribosomal protein L44e signature. / Ribosomal protein L7A/L8 / Ribosomal protein L13e / Ribosomal protein L13e / 60S ribosomal protein L4, C-terminal domain / 60S ribosomal protein L18a/ L20, eukaryotes / Ribosomal protein L6e / Ribosomal L37ae protein family / Ribosomal protein L35Ae / 50S ribosomal protein L18Ae/60S ribosomal protein L20 and L18a / Ribosomal protein L39e, conserved site / Ribosomal protein 50S-L18Ae/60S-L20/60S-L18A / 60S ribosomal protein L4 C-terminal domain / Ribosomal proteins 50S-L18Ae/60S-L20/60S-L18A / Ribosomal protein L5 eukaryotic, C-terminal / Ribosomal L18 C-terminal region / Ribosomal protein L31e / Ribosomal protein L31e domain superfamily / Ribosomal_L31e / Ribosomal protein L30e signature 1. / Ribosomal protein L21e / Ribosomal protein L21e, conserved site / Ribosomal protein L21 superfamily / Ribosomal protein 60S L18 and 50S L18e / 60S ribosomal protein L19 / Ribosomal protein L4/L1e, eukaryotic/archaeal, conserved site / Ribosomal protein L37e, conserved site / Ribosomal protein L37e / Ribosomal protein L39e signature. / Ribosomal protein L21e / Ribosomal_L15e / Ribosomal protein L15e / Ribosomal protein L15e core domain superfamily / Ribosomal protein L31e / Ribosomal protein L37ae/L37e / Ribosomal protein L24e-related / Ribosomal protein L7, eukaryotic / Ribosomal protein L24e/L24 superfamily / Ribosomal protein L30, N-terminal / Ribosomal L30 N-terminal domain / Ribosomal protein L39e / Ribosomal protein L26/L24, eukaryotic/archaeal / Ribosomal protein L39e domain superfamily / Ribosomal_L19e / Ribosomal protein L13, eukaryotic/archaeal / Ribosomal protein L19/L19e / Ribosomal protein L19/L19e, domain 1 / Ribosomal protein L19/L19e superfamily / Ribosomal protein L4, eukaryotic and archaeal type / Ribosomal protein L19e / Ribosomal protein L18e / Ribosomal L39 protein / Ribosomal protein L37e / Ribosomal protein L24e / Ribosomal protein L22/L17, eukaryotic/archaeal / Ribosomal L15 / Ribosomal protein L14e domain / Ribosomal protein L14 / Ribosomal proteins L26 eukaryotic, L24P archaeal / Ribosomal protein L5 eukaryotic/L18 archaeal / Ribosomal large subunit proteins 60S L5, and 50S L18 / Ribosomal protein L14 / Ribosomal protein L14, KOW motif / Ribosomal protein L1e signature. / Ribosomal protein L21e signature.
Similarity search - Domain/homology
RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / 60S ribosomal protein L28 / 60S ribosomal protein L11, putative / 60S ribosomal protein L29 / 60S ribosomal protein L4, putative / Ribosomal protein L15 / 60S ribosomal protein L5, putative ...RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / 60S ribosomal protein L28 / 60S ribosomal protein L11, putative / 60S ribosomal protein L29 / 60S ribosomal protein L4, putative / Ribosomal protein L15 / 60S ribosomal protein L5, putative / 60S ribosomal protein L44, putative / 60S ribosomal protein L32, putative / 60S ribosomal protein L37a, putative / 60S ribosomal protein L34, putative / 60S ribosomal protein L17, putative / Ribosomal protein L21E (60S), putative / 60S ribosomal protein L26, putative / 60S ribosomal protein L30, putative / 60S ribosomal protein L6, putative / 60S ribosomal protein L7, putative / 60S ribosomal protein L2, putative / 40S ribosomal protein L14, putative / Ribosomal protein L38, putative / Ribosomal protein L39, putative / Ribosomal protein L37 / 60S ribosomal protein L18a / 60S ribosomal protein L22, putative / 60S ribosomal protein L18 / Ribosomal protein L24, putative / 60S ribosomal protein L35, putative / 60S ribosomal protein L23a, putative / 60S ribosomal protein L27A/L29, putative / 60S ribosomal protein L23, putative / Ribosomal protein L35A, putative / 60S ribosomal protein L13 / 60S ribosomal protein L7a / Ribosomal protein L19-like protein / 60S ribosomal protein L27 / Ribosomal protein L13 / Ribosomal protein L36 / 60S ribosomal subunit protein L31 / 60S ribosomal protein L13a
Similarity search - Component
Biological speciesTrypanosoma cruzi (eukaryote)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.54 Å
AuthorsLiu, Z. / Gutierrez-Vargas, C. / Wei, J. / Grassucci, R.A. / Ramesh, M. / Espina, N. / Sun, M. / Tutuncuoglu, B. / Madison-Antenucci, S. / Woolford Jr., J.L. ...Liu, Z. / Gutierrez-Vargas, C. / Wei, J. / Grassucci, R.A. / Ramesh, M. / Espina, N. / Sun, M. / Tutuncuoglu, B. / Madison-Antenucci, S. / Woolford Jr., J.L. / Tong, L. / Frank, J.
Funding support United States, 5items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM29169 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)35GM118093 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM028301 United States
National Science Foundation (NSF, United States)GRFP DGE-11-44155 United States
Howard Hughes Medical Institute (HHMI)HHMI United States
CitationJournal: Proc Natl Acad Sci U S A / Year: 2016
Title: Structure and assembly model for the Trypanosoma cruzi 60S ribosomal subunit.
Authors: Zheng Liu / Cristina Gutierrez-Vargas / Jia Wei / Robert A Grassucci / Madhumitha Ramesh / Noel Espina / Ming Sun / Beril Tutuncuoglu / Susan Madison-Antenucci / John L Woolford / Liang Tong / Joachim Frank /
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 ...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.
History
DepositionAug 31, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 12, 2016Provider: repository / Type: Initial release
Revision 1.1Nov 16, 2016Group: Database references
Revision 1.2Sep 20, 2017Group: Author supporting evidence / Data collection ...Author supporting evidence / Data collection / Database references / Derived calculations
Category: citation / em_image_scans ...citation / em_image_scans / pdbx_audit_support / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Mar 28, 2018Group: Advisory / Data collection ...Advisory / Data collection / Other / Structure summary
Category: cell / database_PDB_caveat ...cell / database_PDB_caveat / em_entity_assembly / entity
Item: _cell.length_a / _cell.length_b ..._cell.length_a / _cell.length_b / _cell.length_c / _em_entity_assembly.name / _entity.pdbx_description
Revision 1.4Nov 20, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Dec 18, 2019Group: Advisory / Derived calculations / Other
Category: atom_sites / cell ...atom_sites / cell / pdbx_validate_close_contact / struct_conn
Item: _atom_sites.fract_transf_matrix[1][1] / _atom_sites.fract_transf_matrix[2][2] ..._atom_sites.fract_transf_matrix[1][1] / _atom_sites.fract_transf_matrix[2][2] / _atom_sites.fract_transf_matrix[3][3] / _cell.length_a / _cell.length_b / _cell.length_c

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Structure visualization

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Assembly

Deposited unit
A: RNA LARGE SUBUNIT ALPHA
B: RNA LARGE SUBUNIT BETA
C: 5.8S rRNA
D: 5S rRNA
E: srRNA1
F: srRNA3
G: srRNA2
H: srRNA4
I: 60S ribosomal protein L18
L: 60S ribosomal protein L11
N: 60S ribosomal protein L13
O: 60S ribosomal protein L13a
P: 40S ribosomal protein L14
Q: Ribosomal protein L15
R: 60S ribosomal protein L17
S: 60S ribosomal protein L18a
T: Ribosomal protein L19-like protein
U: Ribosomal protein L21E (60S)
V: 60S ribosomal protein L22
W: 60S ribosomal protein L23
X: 60S ribosomal protein L23a
Y: Ribosomal protein L24
Z: 60S ribosomal protein L26
a: Ribosomal protein L27
b: 60S ribosomal protein L27A/L29
c: 60S ribosomal protein L28
d: Ribosomal protein L29
e: 60S ribosomal protein L2
f: Ribosomal protein L13
g: 60S ribosomal protein L30
h: 60S ribosomal subunit protein L31
i: 60S ribosomal protein L32
j: 60S ribosomal protein L34
k: 60S ribosomal protein L35
l: Ribosomal protein L35A
m: Ribosomal protein L36
n: Ribosomal protein L37
o: 60S ribosomal protein L37a
p: Ribosomal protein L38
q: Ribosomal protein L39
r: 60S ribosomal protein L4
t: 60S ribosomal protein L44
u: 60S ribosomal protein L5
v: 60S ribosomal protein L6
w: 60S ribosomal protein L7
x: Ribosomal protein L7a-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,591,694154
Polymers1,588,94646
Non-polymers2,748108
Water1,49583
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

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RNA LARGE SUBUNIT ... , 2 types, 2 molecules AB

#1: RNA chain RNA LARGE SUBUNIT ALPHA /


Mass: 414400.031 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma cruzi (eukaryote)
#2: RNA chain RNA LARGE SUBUNIT BETA / / Trypanosoma cruzi 5.8S ribosomal RNA / internal transcribed spacers 1-7 (ITS1-ITS7) / and 28S ribosomal RNA


Mass: 303899.750 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma cruzi (eukaryote)

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RNA chain , 6 types, 6 molecules CDEFGH

#3: RNA chain 5.8S rRNA / 5.8S ribosomal RNA


Mass: 54425.363 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma cruzi (eukaryote)
#4: RNA chain 5S rRNA / 5S ribosomal RNA


Mass: 38047.582 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma cruzi (eukaryote)
#5: RNA chain srRNA1


Mass: 46982.832 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma cruzi (eukaryote)
#6: RNA chain srRNA3


Mass: 14572.682 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma cruzi (eukaryote)
#7: RNA chain srRNA2


Mass: 39608.434 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma cruzi (eukaryote)
#8: RNA chain srRNA4


Mass: 29374.498 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma cruzi (eukaryote)

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60S ribosomal protein ... , 23 types, 23 molecules ILNORSVWXZbcegijkortuvw

#9: Protein 60S ribosomal protein L18 /


Mass: 21595.504 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma cruzi (eukaryote) / References: UniProt: Q4DZP2
#10: Protein 60S ribosomal protein L11 /


Mass: 7672.055 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma cruzi (eukaryote) / References: UniProt: Q4CNF4
#11: Protein 60S ribosomal protein L13 /


Mass: 23690.836 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma cruzi (eukaryote) / References: UniProt: Q4E661
#12: Protein 60S ribosomal protein L13a /


Mass: 23412.801 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma cruzi (eukaryote) / References: UniProt: V5DCT1
#15: Protein 60S ribosomal protein L17 /


Mass: 17545.625 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma cruzi (eukaryote) / References: UniProt: Q4DC23
#16: Protein 60S ribosomal protein L18a /


Mass: 20595.014 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma cruzi (eukaryote) / References: UniProt: Q4DZ31
#19: Protein 60S ribosomal protein L22 /


Mass: 11872.974 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma cruzi (eukaryote) / References: UniProt: Q4DZN3
#20: Protein 60S ribosomal protein L23 /


Mass: 13651.026 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma cruzi (eukaryote) / References: UniProt: Q4E4R0
#21: Protein 60S ribosomal protein L23a /


Mass: 13444.673 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma cruzi (eukaryote) / References: UniProt: Q4E2Y1
#23: Protein 60S ribosomal protein L26 /


Mass: 13107.445 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma cruzi (eukaryote) / References: UniProt: Q4DG45
#25: Protein 60S ribosomal protein L27A/L29 / Ribosome


Mass: 16103.848 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma cruzi (eukaryote) / References: UniProt: Q4E4Q8
#26: Protein 60S ribosomal protein L28 /


Mass: 13836.174 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma cruzi (eukaryote) / References: UniProt: O00822
#28: Protein 60S ribosomal protein L2 /


Mass: 26737.242 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma cruzi (eukaryote) / References: UniProt: Q4DPQ8
#30: Protein 60S ribosomal protein L30 /


Mass: 7508.954 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma cruzi (eukaryote) / References: UniProt: Q4DIC9
#32: Protein 60S ribosomal protein L32 /


Mass: 13218.489 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma cruzi (eukaryote) / References: UniProt: Q4D1H8
#33: Protein 60S ribosomal protein L34 /


Mass: 12302.434 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma cruzi (eukaryote) / References: UniProt: Q4DB26
#34: Protein 60S ribosomal protein L35 /


Mass: 14526.508 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma cruzi (eukaryote) / References: UniProt: Q4E2E0
#38: Protein 60S ribosomal protein L37a / / Ribosomal proteins L37 / putative


Mass: 9609.315 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma cruzi (eukaryote) / References: UniProt: Q4DAV9
#41: Protein 60S ribosomal protein L4 /


Mass: 37228.363 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma cruzi (eukaryote) / References: UniProt: Q4CQW2
#42: Protein 60S ribosomal protein L44 /


Mass: 10908.060 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma cruzi (eukaryote) / References: UniProt: Q4CV79
#43: Protein 60S ribosomal protein L5 /


Mass: 28665.885 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma cruzi (eukaryote) / References: UniProt: Q4CU61
#44: Protein 60S ribosomal protein L6 /


Mass: 19042.512 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma cruzi (eukaryote) / References: UniProt: Q4DIV9
#45: Protein 60S ribosomal protein L7 /


Mass: 24898.406 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma cruzi (eukaryote) / References: UniProt: Q4DNZ7

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Protein , 2 types, 2 molecules Ph

#13: Protein 40S ribosomal protein L14 /


Mass: 17483.592 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma cruzi (eukaryote) / References: UniProt: Q4DQ35
#31: Protein 60S ribosomal subunit protein L31 /


Mass: 19483.080 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma cruzi (eukaryote) / References: UniProt: V5C333

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Ribosomal protein ... , 13 types, 13 molecules QTUYadflmnpqx

#14: Protein Ribosomal protein L15 /


Mass: 24154.484 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma cruzi (eukaryote) / References: UniProt: Q4CTG9
#17: Protein Ribosomal protein L19-like protein / Ribosome


Mass: 18187.561 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma cruzi (eukaryote) / References: UniProt: Q9BMP1
#18: Protein Ribosomal protein L21E (60S) / Ribosome


Mass: 16584.541 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma cruzi (eukaryote) / References: UniProt: Q4DED2
#22: Protein Ribosomal protein L24 /


Mass: 7363.689 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma cruzi (eukaryote) / References: UniProt: Q4E078
#24: Protein Ribosomal protein L27 /


Mass: 15419.276 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma cruzi (eukaryote) / References: UniProt: Q9U4H7
#27: Protein Ribosomal protein L29 /


Mass: 7378.556 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma cruzi (eukaryote) / References: UniProt: Q4CPD8
#29: Protein Ribosomal protein L13 / 60S ribosomal protein L13


Mass: 45359.961 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma cruzi (eukaryote) / References: UniProt: V5B599
#35: Protein Ribosomal protein L35A / Ribosome


Mass: 15513.169 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma cruzi (eukaryote) / References: UniProt: Q4E581
#36: Protein Ribosomal protein L36 /


Mass: 10819.966 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma cruzi (eukaryote) / References: UniProt: V5BDJ2
#37: Protein Ribosomal protein L37 /


Mass: 9734.394 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma cruzi (eukaryote) / References: UniProt: Q4DXW6
#39: Protein Ribosomal protein L38 /


Mass: 6840.182 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma cruzi (eukaryote) / References: UniProt: Q4DQ60
#40: Protein/peptide Ribosomal protein L39 /


Mass: 6436.773 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma cruzi (eukaryote) / References: UniProt: Q4DVC6
#46: Protein Ribosomal protein L7a-like protein / Ribosome


Mass: 25701.291 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma cruzi (eukaryote) / References: UniProt: Q9BMP0

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Non-polymers , 3 types, 191 molecules

#47: Chemical...
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 105 / Source method: obtained synthetically / Formula: Mg
#48: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn
#49: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 83 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: trypanosoma cruzi 60S ribosomal subunit / Type: RIBOSOME / Entity ID: #1-#46 / Source: NATURAL
Source (natural)Organism: Trypanosoma cruzi (eukaryote)
Buffer solutionpH: 7.2
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 400 divisions/in. / Grid type: Quantfoil
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy
Image recordingElectron dose: 27 e/Å2 / Film or detector model: FEI FALCON II (4k x 4k)

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Processing

EM softwareName: EPU / Category: image acquisition
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.54 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 235000 / Symmetry type: POINT
Atomic model buildingB value: 56 / Space: REAL

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  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

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