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- PDB-7aor: mt-SSU from Trypanosoma cruzi in complex with mt-IF-3. -

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Basic information

Entry
Database: PDB / ID: 7aor
Titlemt-SSU from Trypanosoma cruzi in complex with mt-IF-3.
Components
  • 30S Ribosomal protein S17-like protein
  • AKAP7_NLS domain-containing protein
  • MURF5
  • Protein FYV4, mitochondrial
  • RNA (478-MER)
  • Rhodanese domain-containing protein
  • Ribosomal_S5_C domain-containing protein
  • Ribosome protein S12
  • Sod_Fe_C domain-containing protein
  • Superoxide dismutase, putative
  • Trafficking protein particle complex subunit
  • bS16m
  • bS18m
  • bS21m
  • bS6m
  • mS22
  • mS23
  • mS26
  • mS29
  • mS33
  • mS35
  • mS37
  • mS38
  • mS47
  • mS48
  • mS49
  • mS50
  • mS51
  • mS52
  • mS53
  • mS54
  • mS55
  • mS56
  • mS57
  • mS58
  • mS59
  • mS60
  • mS61
  • mS62
  • mS63
  • mS65
  • mS66
  • mS68
  • mS69
  • mS70
  • mS71
  • mS72
  • mS73
  • mt-iF3
  • uS10m
  • uS11m
  • uS14m
  • uS15m
  • uS19
  • uS8m
  • uS9m
KeywordsRIBOSOME / Mitochondria / Kinetoplastid
Function / homology
Function and homology information


regulation of protein kinase A signaling / TRAPP complex / Golgi vesicle transport / thiosulfate-cyanide sulfurtransferase activity / mitochondrial small ribosomal subunit / superoxide dismutase / fatty acid beta-oxidation / protein kinase A regulatory subunit binding / superoxide dismutase activity / rRNA binding ...regulation of protein kinase A signaling / TRAPP complex / Golgi vesicle transport / thiosulfate-cyanide sulfurtransferase activity / mitochondrial small ribosomal subunit / superoxide dismutase / fatty acid beta-oxidation / protein kinase A regulatory subunit binding / superoxide dismutase activity / rRNA binding / ribosome / structural constituent of ribosome / translation / ribonucleoprotein complex / endoplasmic reticulum / Golgi apparatus / mitochondrion / metal ion binding / membrane / cytosol / cytoplasm
Similarity search - Function
Ribosomal protein S12 / Ribosomal protein S12 / Nucleoid-associated protein YbaB-like domain superfamily / : / Protein kinase A anchor protein, nuclear localisation signal domain / AKAP7 2'5' RNA ligase-like domain / Probable Zinc-ribbon domain / Probable Treble clef zinc finger domain / : / TRAPP I complex, subunit 5 ...Ribosomal protein S12 / Ribosomal protein S12 / Nucleoid-associated protein YbaB-like domain superfamily / : / Protein kinase A anchor protein, nuclear localisation signal domain / AKAP7 2'5' RNA ligase-like domain / Probable Zinc-ribbon domain / Probable Treble clef zinc finger domain / : / TRAPP I complex, subunit 5 / Enoyl-CoA hydratase/isomerase domain / Enoyl-CoA hydratase/isomerase / Protein Fyv4 / IGR protein motif / IGR / Cyclic phosphodiesterase / Ribosomal protein S23/S29, mitochondrial / Mitochondrial ribosomal death-associated protein 3 / Rhodanese-like domain / Rhodanese domain profile. / Rhodanese-like domain superfamily / Rhodanese-like domain / LysM domain / Manganese/iron superoxide dismutase, C-terminal / Manganese/iron superoxide dismutase, C-terminal domain superfamily / Manganese/iron superoxide dismutase, N-terminal domain superfamily / Iron/manganese superoxide dismutases, C-terminal domain / LysM domain / ClpP/crotonase-like domain superfamily / Ribosomal protein S18 superfamily / Ribosomal protein S6 superfamily / Translation elongation factor EF1B/ribosomal protein S6 / Ribosomal protein S5, C-terminal / Ribosomal protein S5, C-terminal domain / Ribosomal protein S8 / Ribosomal protein S8 superfamily / Ribosomal protein S8 / Tetratricopeptide-like helical domain superfamily / Ribosomal protein S9 / Ribosomal protein S9/S16 / Ribosomal protein S17/S11 / Ribosomal protein S17 / Ribosomal protein S11 superfamily / S15/NS1, RNA-binding / Ribosomal protein S5 domain 2-type fold, subgroup / Ubiquitin-like domain superfamily / Ribosomal protein S5 domain 2-type fold / Nucleic acid-binding, OB-fold
Similarity search - Domain/homology
GUANOSINE-5'-TRIPHOSPHATE / URIDINE 5'-TRIPHOSPHATE / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Ribosome protein S12 / 30S Ribosomal protein S17-like protein / Superoxide dismutase, putative / Manganese/iron superoxide dismutase C-terminal domain-containing protein ...GUANOSINE-5'-TRIPHOSPHATE / URIDINE 5'-TRIPHOSPHATE / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Ribosome protein S12 / 30S Ribosomal protein S17-like protein / Superoxide dismutase, putative / Manganese/iron superoxide dismutase C-terminal domain-containing protein / Uncharacterized protein / Uncharacterized protein / Uncharacterized protein / Uncharacterized protein / Uncharacterized protein / Uncharacterized protein / Uncharacterized protein / Uncharacterized protein / Uncharacterized protein / Uncharacterized protein / Uncharacterized protein / Uncharacterized protein / Trans-sialidase / Uncharacterized protein / Uncharacterized protein / A-kinase anchor protein 7-like phosphoesterase domain-containing protein / Enoyl-CoA hydratase/isomerase domain-containing protein / LysM domain-containing protein / HMG box domain-containing protein / Ribosomal protein S9 / Mitochondrial SSU ribosomal protein / Uncharacterized protein / Uncharacterized protein / Uncharacterized protein / Uncharacterized protein / Uncharacterized protein / Uncharacterized protein / Uncharacterized protein / Uncharacterized protein / Uncharacterized protein / Uncharacterized protein / Uncharacterized protein / Mitochondrial RNA binding protein 1 / Uncharacterized protein / Small ribosomal subunit protein mS29 / Uncharacterized protein / Uncharacterized protein / Uncharacterized protein / Rhodanese domain-containing protein / 30S ribosomal protein S8 / Small ribosomal subunit protein uS5 C-terminal domain-containing protein / Uncharacterized protein / Small ribosomal subunit protein mS41 / Opioid growth factor receptor (OGFr) conserved domain-containing protein / Probable Zinc-ribbon domain-containing protein / Trafficking protein particle complex subunit / Ubiquitin-like domain-containing protein / Mitochondrial SSU ribosomal protein / Mitochondrial ribosomal protein S18 / Chromosome passenger complex (CPC) protein INCENP N terminal
Similarity search - Component
Biological speciesTrypanosoma cruzi (eukaryote)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.5 Å
AuthorsSoufari, H. / Waltz, F. / Parrot, C. / Bochler, A. / Hashem, Y.
Funding support France, 1items
OrganizationGrant numberCountry
European Research Council (ERC) France
CitationJournal: Proc Natl Acad Sci U S A / Year: 2020
Title: Structure of the mature kinetoplastids mitoribosome and insights into its large subunit biogenesis.
Authors: Heddy Soufari / Florent Waltz / Camila Parrot / Stéphanie Durrieu-Gaillard / Anthony Bochler / Lauriane Kuhn / Marie Sissler / Yaser Hashem /
Abstract: Kinetoplastids are unicellular eukaryotic parasites responsible for such human pathologies as Chagas disease, sleeping sickness, and leishmaniasis. They have a single large mitochondrion, essential ...Kinetoplastids are unicellular eukaryotic parasites responsible for such human pathologies as Chagas disease, sleeping sickness, and leishmaniasis. They have a single large mitochondrion, essential for the parasite survival. In kinetoplastid mitochondria, most of the molecular machineries and gene expression processes have significantly diverged and specialized, with an extreme example being their mitochondrial ribosomes. These large complexes are in charge of translating the few essential mRNAs encoded by mitochondrial genomes. Structural studies performed in already highlighted the numerous peculiarities of these mitoribosomes and the maturation of their small subunit. However, several important aspects mainly related to the large subunit (LSU) remain elusive, such as the structure and maturation of its ribosomal RNA. Here we present a cryo-electron microscopy study of the protozoans and mitoribosomes. For both species, we obtained the structure of their mature mitoribosomes, complete rRNA of the LSU, as well as previously unidentified ribosomal proteins. In addition, we introduce the structure of an LSU assembly intermediate in the presence of 16 identified maturation factors. These maturation factors act on both the intersubunit and the solvent sides of the LSU, where they refold and chemically modify the rRNA and prevent early translation before full maturation of the LSU.
History
DepositionOct 15, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 28, 2021Provider: repository / Type: Initial release
Revision 2.0Jun 23, 2021Group: Advisory / Database references ...Advisory / Database references / Polymer sequence / Source and taxonomy / Structure summary
Category: em_entity_assembly / em_entity_assembly_naturalsource ...em_entity_assembly / em_entity_assembly_naturalsource / entity / entity_name_com / entity_poly / entity_poly_seq / entity_src_nat / pdbx_poly_seq_scheme / pdbx_unobs_or_zero_occ_residues / struct_ref / struct_ref_seq / struct_ref_seq_dif
Item: _entity.formula_weight / _entity_poly.pdbx_seq_one_letter_code ..._entity.formula_weight / _entity_poly.pdbx_seq_one_letter_code / _entity_poly.pdbx_seq_one_letter_code_can / _entity_poly_seq.mon_id / _entity_src_nat.pdbx_ncbi_taxonomy_id / _entity_src_nat.pdbx_organism_scientific / _entity_src_nat.strain / _pdbx_poly_seq_scheme.mon_id / _pdbx_unobs_or_zero_occ_residues.auth_comp_id / _pdbx_unobs_or_zero_occ_residues.label_comp_id / _struct_ref.db_code / _struct_ref.db_name / _struct_ref.pdbx_db_accession / _struct_ref.pdbx_seq_one_letter_code / _struct_ref_seq.pdbx_db_accession
Revision 2.1Nov 20, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / em_admin / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _em_admin.last_update / _pdbx_entry_details.has_protein_modification

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Structure visualization

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  • Deposited structure unit
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Assembly

Deposited unit
u: mS35
s: mS33
r: mS29
n: uS19
h: uS14m
e: uS10m
az: mS72
ay: mS71
ax: mS70
aw: mS69
au: Rhodanese domain-containing protein
ak: mS58
aj: mS57
ag: mS55
af: mS54
ae: mS53
l: mS52
ac: mS50
ab: mS49
ad: mS51
m: bS18m
i: uS15m
f: uS11m
c: uS8m
d: uS9m
ba: mS73
av: mS68
at: mS66
ar: AKAP7_NLS domain-containing protein
aq: mS63
ap: mS62
ao: mS61
ai: mS56
an: mS60
z: mS47
y: Sod_Fe_C domain-containing protein
x: Superoxide dismutase, putative
w: Protein FYV4, mitochondrial
v: mS37
bb: mS38
t: Trafficking protein particle complex subunit
al: mS59
q: mS26
p: mS23
Ca: mS22
g: bS21m
j: bS16m
b: bS6m
bd: MURF5
a: Ribosomal_S5_C domain-containing protein
bc: mt-iF3
aa: mS48
k: 30S Ribosomal protein S17-like protein
be: Ribosome protein S12
as: mS65
A: RNA (478-MER)
2: RNA (478-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,881,45564
Polymers7,880,16257
Non-polymers1,2937
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: microscopy
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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Protein , 55 types, 55 molecules usrnheazayaxawauakajagafaelacabadmifcdbaavataraq...

#1: Protein mS35


Mass: 99238.445 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Trypanosoma cruzi (strain CL Brener) (eukaryote)
Strain: CL Brener / References: UniProt: Q4DIY1
#2: Protein mS33


Mass: 20964.881 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Trypanosoma cruzi (strain CL Brener) (eukaryote)
Strain: CL Brener / References: UniProt: Q4CTU7
#3: Protein mS29


Mass: 57865.008 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Trypanosoma cruzi (strain CL Brener) (eukaryote)
Strain: CL Brener / References: UniProt: Q4DW24
#4: Protein uS19


Mass: 19866.250 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Trypanosoma cruzi (strain CL Brener) (eukaryote)
Strain: CL Brener / References: UniProt: Q4D583
#5: Protein uS14m


Mass: 19805.920 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Trypanosoma cruzi (strain CL Brener) (eukaryote)
Strain: CL Brener / References: UniProt: Q4DRG2
#6: Protein uS10m


Mass: 94283.742 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Trypanosoma cruzi (strain CL Brener) (eukaryote)
Strain: CL Brener / References: UniProt: Q4DEM5
#7: Protein mS72


Mass: 19403.363 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Trypanosoma cruzi (strain CL Brener) (eukaryote)
Strain: CL Brener / References: UniProt: Q4DX04
#8: Protein mS71


Mass: 25866.699 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Trypanosoma cruzi (strain CL Brener) (eukaryote)
Strain: CL Brener / References: UniProt: Q4DX19
#9: Protein mS70


Mass: 20679.938 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Trypanosoma cruzi (strain CL Brener) (eukaryote)
Strain: CL Brener / References: UniProt: Q4DLH4
#10: Protein mS69


Mass: 21672.887 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Trypanosoma cruzi (strain CL Brener) (eukaryote)
Strain: CL Brener / References: UniProt: Q4D0Q8
#11: Protein Rhodanese domain-containing protein


Mass: 30180.223 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Trypanosoma cruzi (strain CL Brener) (eukaryote)
Strain: CL Brener / References: UniProt: Q4DX83
#12: Protein mS58


Mass: 35017.238 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Trypanosoma cruzi (strain CL Brener) (eukaryote)
Strain: CL Brener / References: UniProt: Q4DTE7
#13: Protein mS57


Mass: 46272.082 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Trypanosoma cruzi (strain CL Brener) (eukaryote)
Strain: CL Brener / References: UniProt: Q4DA51
#14: Protein mS55


Mass: 67008.211 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Trypanosoma cruzi (strain CL Brener) (eukaryote)
Strain: CL Brener / References: UniProt: Q4DWR5
#15: Protein mS54


Mass: 77912.539 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Trypanosoma cruzi (strain CL Brener) (eukaryote)
Strain: CL Brener / References: UniProt: Q4CVW1
#16: Protein mS53


Mass: 76246.633 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Trypanosoma cruzi (strain CL Brener) (eukaryote)
Strain: CL Brener / References: UniProt: Q4D651
#17: Protein mS52


Mass: 81423.836 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Trypanosoma cruzi (strain CL Brener) (eukaryote)
Strain: CL Brener / References: UniProt: Q4E2R4
#18: Protein mS50


Mass: 129011.102 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Trypanosoma cruzi (strain CL Brener) (eukaryote)
Strain: CL Brener / References: UniProt: Q4CW80
#19: Protein mS49


Mass: 136204.141 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Trypanosoma cruzi (strain CL Brener) (eukaryote)
Strain: CL Brener / References: UniProt: Q4DNX8
#20: Protein mS51


Mass: 95139.117 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Trypanosoma cruzi (strain CL Brener) (eukaryote)
Strain: CL Brener / References: UniProt: Q4DV41
#21: Protein bS18m


Mass: 37204.203 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Trypanosoma cruzi (strain CL Brener) (eukaryote)
Strain: CL Brener / References: UniProt: Q4E4E0
#22: Protein uS15m


Mass: 50080.918 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Trypanosoma cruzi (strain CL Brener) (eukaryote)
Strain: CL Brener / References: UniProt: Q4DS13
#23: Protein uS11m


Mass: 37723.637 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Trypanosoma cruzi (strain CL Brener) (eukaryote)
Strain: CL Brener / References: UniProt: Q4CT44
#24: Protein uS8m


Mass: 33219.047 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Trypanosoma cruzi (strain CL Brener) (eukaryote)
Strain: CL Brener / References: UniProt: Q4DY17
#25: Protein uS9m


Mass: 50335.250 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Trypanosoma cruzi (strain CL Brener) (eukaryote)
Strain: CL Brener / References: UniProt: Q4DEW9
#26: Protein mS73


Mass: 24784.449 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Trypanosoma cruzi (strain CL Brener) (eukaryote)
Strain: CL Brener / References: UniProt: Q4D7F8
#27: Protein mS68


Mass: 27692.355 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Trypanosoma cruzi (strain CL Brener) (eukaryote)
Strain: CL Brener / References: UniProt: Q4E2I9
#28: Protein mS66


Mass: 29834.234 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Trypanosoma cruzi (strain CL Brener) (eukaryote)
Strain: CL Brener / References: UniProt: Q4E1X5
#29: Protein AKAP7_NLS domain-containing protein


Mass: 30783.395 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Trypanosoma cruzi (strain CL Brener) (eukaryote)
Strain: CL Brener / References: UniProt: Q4DBB7
#30: Protein mS63


Mass: 34337.473 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Trypanosoma cruzi (strain CL Brener) (eukaryote)
Strain: CL Brener / References: UniProt: Q4E0X6
#31: Protein mS62


Mass: 31623.609 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Trypanosoma cruzi (strain CL Brener) (eukaryote)
Strain: CL Brener / References: UniProt: Q4D014
#32: Protein mS61


Mass: 32920.785 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Trypanosoma cruzi (strain CL Brener) (eukaryote)
Strain: CL Brener / References: UniProt: Q4D7Y5
#33: Protein mS56


Mass: 47860.852 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Trypanosoma cruzi (strain CL Brener) (eukaryote)
Strain: CL Brener / References: UniProt: Q4D4C7
#34: Protein mS60


Mass: 34410.688 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Trypanosoma cruzi (strain CL Brener) (eukaryote)
Strain: CL Brener / References: UniProt: Q4DJ95
#35: Protein mS47


Mass: 134734.562 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Trypanosoma cruzi (strain CL Brener) (eukaryote)
Strain: CL Brener / References: UniProt: Q4DD80
#36: Protein Sod_Fe_C domain-containing protein


Mass: 49030.516 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Trypanosoma cruzi (strain CL Brener) (eukaryote)
Strain: CL Brener / References: UniProt: Q4CSF0
#37: Protein Superoxide dismutase, putative


Mass: 38998.422 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Trypanosoma cruzi (strain CL Brener) (eukaryote)
Strain: CL Brener / References: UniProt: Q4CPX3, superoxide dismutase
#38: Protein Protein FYV4, mitochondrial


Mass: 22392.725 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Trypanosoma cruzi (strain CL Brener) (eukaryote)
Strain: CL Brener / References: UniProt: Q4DZS3
#39: Protein mS37


Mass: 24565.621 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Trypanosoma cruzi (strain CL Brener) (eukaryote)
Strain: CL Brener / References: UniProt: Q4DRC8
#40: Protein mS38


Mass: 26499.914 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Trypanosoma cruzi (strain CL Brener) (eukaryote)
Strain: CL Brener / References: UniProt: Q4DMI0
#41: Protein Trafficking protein particle complex subunit


Mass: 28870.480 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Trypanosoma cruzi (strain CL Brener) (eukaryote)
Strain: CL Brener / References: UniProt: Q4E2D1
#42: Protein mS59


Mass: 35605.117 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Trypanosoma cruzi (strain CL Brener) (eukaryote)
Strain: CL Brener / References: UniProt: Q4DRU1
#43: Protein mS26


Mass: 51718.258 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Trypanosoma cruzi (strain CL Brener) (eukaryote)
Strain: CL Brener / References: UniProt: Q4DUA8
#44: Protein mS23


Mass: 34869.160 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Trypanosoma cruzi (strain CL Brener) (eukaryote)
Strain: CL Brener / References: UniProt: Q4DRR8
#45: Protein mS22


Mass: 73123.039 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Trypanosoma cruzi (strain CL Brener) (eukaryote)
Strain: CL Brener / References: UniProt: Q4E4S6
#46: Protein bS21m


Mass: 23030.959 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Trypanosoma cruzi (strain CL Brener) (eukaryote)
Strain: CL Brener / References: UniProt: Q4DET1
#47: Protein bS16m


Mass: 22422.164 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Trypanosoma cruzi (strain CL Brener) (eukaryote)
Strain: CL Brener / References: UniProt: Q4D6Y0
#48: Protein bS6m


Mass: 19189.016 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Trypanosoma cruzi (strain CL Brener) (eukaryote)
Strain: CL Brener / References: UniProt: Q4DZA7
#49: Protein MURF5 / Maxicircle unassigned reading frame 5


Mass: 10806.988 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Trypanosoma cruzi (strain CL Brener) (eukaryote)
Strain: CL Brener
#50: Protein Ribosomal_S5_C domain-containing protein


Mass: 49823.090 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Trypanosoma cruzi (strain CL Brener) (eukaryote)
Strain: CL Brener / References: UniProt: Q4DYR0
#51: Protein mt-iF3


Mass: 42914.078 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Trypanosoma cruzi (strain CL Brener) (eukaryote)
Strain: CL Brener / References: UniProt: Q4D913
#52: Protein mS48


Mass: 206534.984 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Trypanosoma cruzi (strain CL Brener) (eukaryote)
Strain: CL Brener / References: UniProt: Q4DVD2
#53: Protein 30S Ribosomal protein S17-like protein


Mass: 35840.910 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma cruzi (eukaryote) / References: UniProt: A0A2V2XQ88
#54: Protein Ribosome protein S12


Mass: 9806.853 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma cruzi (eukaryote) / References: UniProt: A0A2H4T2H0
#55: Protein mS65


Mass: 29683.416 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Trypanosoma cruzi (strain CL Brener) (eukaryote)
Strain: CL Brener / References: UniProt: Q4D4G1

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RNA chain , 1 types, 2 molecules A2

#56: RNA chain RNA (478-MER)


Mass: 2616414.250 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Trypanosoma cruzi (strain CL Brener) (eukaryote)
Strain: CL Brener

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Non-polymers , 4 types, 7 molecules

#57: Chemical ChemComp-GTP / GUANOSINE-5'-TRIPHOSPHATE


Mass: 523.180 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O14P3 / Comment: GTP, energy-carrying molecule*YM
#58: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#59: Chemical ChemComp-UTP / URIDINE 5'-TRIPHOSPHATE


Mass: 484.141 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H15N2O15P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: UTP*YM
#60: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn

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Details

Has ligand of interestY
Has protein modificationY

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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

Component
IDNameTypeEntity IDParent-IDSource
1mt-SSU from Trypanosoma cruzi in complex with mt-IF-3.RIBOSOME#1-#560NATURAL
2mt-SSU from Trypanosoma cruzi in complex with mt-IF-3.RIBOSOME#1-#52, #55-#561NATURAL
3mt-SSU from Trypanosoma cruzi in complex with mt-IF-3.RIBOSOME#53-#541NATURAL
Molecular weightExperimental value: NO
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
12Trypanosoma cruzi (strain CL Brener) (eukaryote)353153
23Trypanosoma cruzi (eukaryote)5693
Buffer solutionpH: 7
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company
MicroscopyModel: FEI TALOS ARCTICA
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD
Image recordingElectron dose: 60 e/Å2 / Film or detector model: FEI FALCON III (4k x 4k)

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Processing

Software
NameVersionClassification
phenix.real_space_refinedev_3699refinement
PHENIXdev_3699refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 148180 / Symmetry type: POINT
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 30.74 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0119179733
ELECTRON MICROSCOPYf_angle_d0.9808246276
ELECTRON MICROSCOPYf_chiral_restr0.05526387
ELECTRON MICROSCOPYf_plane_restr0.006529865
ELECTRON MICROSCOPYf_dihedral_angle_d23.665429644

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