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- PDB-7ase: 43S preinitiation complex from Trypanosoma cruzi with the kDDX60 ... -

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Basic information

Entry
Database: PDB / ID: 7ase
Title43S preinitiation complex from Trypanosoma cruzi with the kDDX60 helicase
Components
  • (40S ribosomal protein ...) x 26
  • (Eukaryotic translation initiation factor ...) x 6
  • (Putative 40S ribosomal protein ...) x 2
  • (Ribosomal protein ...) x 3
  • 18S
  • 60S ribosomal protein L40
  • CSN8_PSD8_EIF3K domain-containing protein
  • Elongation initiation factor 2 alpha subunit, putative
  • Guanine nucleotide-binding protein subunit beta-like protein
  • JAB_MPN domain-containing protein
  • Protein translation factor SUI1 homolog, putative
  • Putative eukaryotic translation initiation factor 1A
  • RNA-binding protein, putative
  • Translation initiation factor, putative
  • eIF3A
  • eIF3H
  • eL41
  • initiator tRNA-Met
  • kDDX60
KeywordsTRANSLATION / preinitiation / factors / kinetoplastid / helicase
Function / homology
Function and homology information


eukaryotic initiation factor eIF2 binding / eukaryotic translation initiation factor 3 complex, eIF3e / eukaryotic translation initiation factor 3 complex, eIF3m / translation reinitiation / eukaryotic translation initiation factor 2 complex / eukaryotic translation initiation factor 3 complex / formation of cytoplasmic translation initiation complex / multi-eIF complex / eukaryotic 43S preinitiation complex / formation of translation preinitiation complex ...eukaryotic initiation factor eIF2 binding / eukaryotic translation initiation factor 3 complex, eIF3e / eukaryotic translation initiation factor 3 complex, eIF3m / translation reinitiation / eukaryotic translation initiation factor 2 complex / eukaryotic translation initiation factor 3 complex / formation of cytoplasmic translation initiation complex / multi-eIF complex / eukaryotic 43S preinitiation complex / formation of translation preinitiation complex / eukaryotic 48S preinitiation complex / protein-synthesizing GTPase / regulation of translational initiation / GDP-dissociation inhibitor activity / 90S preribosome / translation regulator activity / translation initiation factor binding / translation initiation factor activity / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of SSU-rRNA / small-subunit processome / helicase activity / metallopeptidase activity / rRNA processing / kinase activity / ribosome binding / ribosomal small subunit biogenesis / ribosomal small subunit assembly / small ribosomal subunit / small ribosomal subunit rRNA binding / cytosolic small ribosomal subunit / nucleic acid binding / cytoplasmic translation / tRNA binding / rRNA binding / hydrolase activity / structural constituent of ribosome / ribosome / translation / ribonucleoprotein complex / GTPase activity / mRNA binding / GTP binding / nucleolus / RNA binding / zinc ion binding / ATP binding / nucleus / membrane / cytoplasm / cytosol
Similarity search - Function
: / : / ATP-dependent RNA helicase DDX60, PIN-like domain / Eukaryotic translation initiation factor 3 subunit D / Eukaryotic translation initiation factor 3 subunit 7 (eIF-3) / Translation initiation factor 3 complex subunit L / RNA polymerase I-associated factor PAF67 / Eukaryotic translation initiation factor 3 subunit E / Eukaryotic translation initiation factor 3 subunit E, N-terminal / eIF3 subunit 6 N terminal domain ...: / : / ATP-dependent RNA helicase DDX60, PIN-like domain / Eukaryotic translation initiation factor 3 subunit D / Eukaryotic translation initiation factor 3 subunit 7 (eIF-3) / Translation initiation factor 3 complex subunit L / RNA polymerase I-associated factor PAF67 / Eukaryotic translation initiation factor 3 subunit E / Eukaryotic translation initiation factor 3 subunit E, N-terminal / eIF3 subunit 6 N terminal domain / Eukaryotic translation initiation factor 3 subunit K / Translation initiation factor 3, subunit 12, N-terminal, eukaryotic / Eukaryotic translation initiation factor SUI1 / SUI1 domain superfamily / Translation initiation factor SUI1 / Translation initiation factor SUI1 family profile. / SUI1 domain / Eukaryotic translation initiation factor 3 subunit A / Eukaryotic translation initiation factor 3 subunit C, N-terminal domain / Eukaryotic translation initiation factor 3 subunit C / Eukaryotic translation initiation factor 3 subunit 8 N-terminus / Translation initiation factor IF2/IF5 domain / Translation initiation factor IF2/IF5, N-terminal / Translation initiation factor IF2/IF5, zinc-binding / Translation initiation factor IF2/IF5 / Domain found in IF2B/IF5 / domain present in translation initiation factor eIF2B and eIF5 / W2 domain / W2 domain profile. / eukaryotic translation initiation factor 1A / Translation initiation factor 1A (eIF-1A) / : / Initiation factor eIF2 gamma, C-terminal / Initiation factor eIF2 gamma, domain 2 / Initiation factor eIF2 gamma, GTP-binding domain / Initiation factor eIF2 gamma, C terminal / Translation initiation factor 2, alpha subunit / Translation initiation factor 2, alpha subunit, middle domain superfamily / Translation initiation factor 2, alpha subunit, C-terminal / IF2a, S1-like domain / Eukaryotic translation initiation factor 2 alpha subunit / : / RNA-binding domain, S1, IF1 type / Translation initiation factor 1A / IF-1 / S1 domain IF1 type profile. / CSN8/PSMD8/EIF3K / CSN8/PSMD8/EIF3K family / motif in proteasome subunits, Int-6, Nip-1 and TRIP-15 / PCI domain / Proteasome component (PCI) domain / PCI domain profile. / Translation elongation factor EF1A/initiation factor IF2gamma, C-terminal / JAB1/Mov34/MPN/PAD-1 ubiquitin protease / S1 domain profile. / Ribosomal protein L41 / Ribosomal protein L41 / Ribosomal protein S26e / Ribosomal protein S26e superfamily / Ribosomal protein S26e / : / Ribosomal protein S12e signature. / Ribosomal protein S12e / Small (40S) ribosomal subunit Asc1/RACK1 / Ribosomal protein S5, eukaryotic/archaeal / Ribosomal protein S21e / Ribosomal protein S21e superfamily / Ribosomal protein S21e / Ribosomal protein S2, eukaryotic / S27a-like superfamily / 40S Ribosomal protein S10 / Plectin/S10, N-terminal / Plectin/S10 domain / Ribosomal protein S10, eukaryotic/archaeal / Ribosomal protein S30 / Ribosomal protein S30 / Ribosomal protein S25 / S25 ribosomal protein / Ribosomal protein S27a / Ribosomal protein S27a / Ribosomal protein S27a / Ribosomal protein S2, eukaryotic/archaeal / JAB1/MPN/MOV34 metalloenzyme domain / 40S ribosomal protein S29/30S ribosomal protein S14 type Z / Ribosomal protein S3, eukaryotic/archaeal / 40S ribosomal protein S4, C-terminal domain / 40S ribosomal protein S4 C-terminus / Ribosomal protein S19A/S15e / Ribosomal protein S8e, conserved site / Ribosomal protein S8e signature. / Ribosomal protein S19e / Ribosomal protein S19e / Ribosomal_S19e / Ribosomal protein S17e / Ribosomal protein S17e-like superfamily / Ribosomal S17 / Ribosomal protein S6, eukaryotic / Ribosomal protein S7e / Ribosomal protein S7e / 40S ribosomal protein S1/3, eukaryotes / 40S ribosomal protein S11, N-terminal
Similarity search - Domain/homology
PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / 40S ribosomal protein S33 / Putative 40S ribosomal protein S21 / Ubiquitin-ribosomal protein eL40 fusion protein / Small ribosomal subunit protein uS4 ...PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / 40S ribosomal protein S33 / Putative 40S ribosomal protein S21 / Ubiquitin-ribosomal protein eL40 fusion protein / Small ribosomal subunit protein uS4 / Putative eukaryotic translation initiation factor 1A / 60S ribosomal protein L41 / 40S ribosomal protein S4 / protein-synthesizing GTPase / Small ribosomal subunit protein uS2 / 40S ribosomal protein S12 / 40S ribosomal protein S7 / Ribosomal protein S29, putative / 40S ribosomal protein S15a, putative / 40S ribosomal protein S26 / 40S ribosomal protein S11, putative / Eukaryotic translation initiation factor 3 (eIF-3) interacting protein, putative / Small ribosomal subunit protein uS10 / 40S ribosomal protein S14, putative / Eukaryotic translation initiation factor 3 subunit E / 40S ribosomal protein S30 / 40S ribosomal protein S13, putative / Eukaryotic translation initiation factor 3 subunit 7-like protein, putative / CSN8/PSMD8/EIF3K domain-containing protein / 40S ribosomal protein S16, putative / 40S ribosomal protein S15, putative / Translation initiation factor, putative / Small ribosomal subunit protein uS5 / Ribosomal protein S19, putative / 40S ribosomal protein S17, putative / Eukaryotic translation initiation factor 3 subunit a / Protein translation factor SUI1 homolog, putative / 40S ribosomal protein S3 / Ribosomal protein S27, putative / JAB1/MPN/MOV34 metalloenzyme domain-containing protein / Eukaryotic translation initiation factor 3 subunit h / 40S ribosomal protein S6 / Activated protein kinase C receptor homolog / 40S ribosomal protein S23, putative / 40S ribosomal protein S25 / 40S ribosomal protein S8 / 40S ribosomal protein S24 / RNA-binding protein, putative / Small ribosomal subunit protein eS1B / Eukaryotic translation initiation factor 5, putative / 40S ribosomal protein S10, putative / 40S ribosomal protein S18, putative / 40S ribosomal protein S5, putative / Eukaryotic translation initiation factor 3 subunit 8, putative / ATP-dependent DEAD/H RNA helicase / Elongation initiation factor 2 alpha subunit, putative
Similarity search - Component
Biological speciesTrypanosoma cruzi (eukaryote)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.33 Å
AuthorsBochler, A. / Brito Querido, J. / Prilepskaja, T. / Soufari, H. / Del Cistia, M.L. / Kuhn, L. / Rimoldi Ribeiro, A. / Valasek, L.S. / Hashem, Y.
Funding support France, Czech Republic, 4items
OrganizationGrant numberCountry
European Research Council (ERC)ERC-2017-STG#759120TransTryp France
Laboratories of Excellence (LabEx)ANR10LABX0036NETRNA France
Laboratories of Excellence (LabEx)ANR 14 ACHN0024 CryoEM80S France
Czech Science FoundationGrant of Excellence in Basic Research (EXPRO2019) Czech Republic
CitationJournal: Cell Rep / Year: 2020
Title: Structural Differences in Translation Initiation between Pathogenic Trypanosomatids and Their Mammalian Hosts.
Authors: Anthony Bochler / Jailson Brito Querido / Terezie Prilepskaja / Heddy Soufari / Angelita Simonetti / Mayara Lucia Del Cistia / Lauriane Kuhn / Aline Rimoldi Ribeiro / Leoš Shivaya Valášek / Yaser Hashem /
Abstract: Canonical mRNA translation in eukaryotes begins with the formation of the 43S pre-initiation complex (PIC). Its assembly requires binding of initiator Met-tRNA and several eukaryotic initiation ...Canonical mRNA translation in eukaryotes begins with the formation of the 43S pre-initiation complex (PIC). Its assembly requires binding of initiator Met-tRNA and several eukaryotic initiation factors (eIFs) to the small ribosomal subunit (40S). Compared to their mammalian hosts, trypanosomatids present significant structural differences in their 40S, suggesting substantial variability in translation initiation. Here, we determine the structure of the 43S PIC from Trypanosoma cruzi, the parasite causing Chagas disease. Our structure shows numerous specific features, such as the variant eIF3 structure and its unique interactions with the large rRNA expansion segments (ESs) 9, 7, and 6, and the association of a kinetoplastid-specific DDX60-like helicase. It also reveals the 40S-binding site of the eIF5 C-terminal domain and structures of key terminal tails of several conserved eIFs underlying their activities within the PIC. Our results are corroborated by glutathione S-transferase (GST) pull-down assays in both human and T. cruzi and mass spectrometry data.
History
DepositionOct 27, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 14, 2021Provider: repository / Type: Initial release
Revision 1.1Apr 21, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Oct 16, 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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Assembly

Deposited unit
f: kDDX60
1: initiator tRNA-Met
0: 18S
y: 40S ribosomal protein S24
s: Elongation initiation factor 2 alpha subunit, putative
j: 60S ribosomal protein L40
n: Translation initiation factor, putative
p: Guanine nucleotide-binding protein subunit beta-like protein
r: 40S ribosomal protein S16, putative
u: 40S ribosomal protein S18, putative
m: 40S ribosomal protein S23, putative
Z: 40S ribosomal protein S8
o: 40S ribosomal protein S5, putative
q: 40S ribosomal protein S7
R: 40S ribosomal protein S13, putative
S: 40S ribosomal protein S27, putative
t: 40S ribosomal protein S26
U: 40S ribosomal protein S33
v: 40S ribosomal protein S14, putative
X: 40S ribosomal protein S11, putative
B: Putative 40S ribosomal protein S9
F: 40S ribosomal protein SA
d: 40S ribosomal protein S2, putative
g: Putative 40S ribosomal protein S21
a: 40S ribosomal protein S25
J: RNA-binding protein, putative
h: 40S ribosomal protein S12
5: Eukaryotic translation initiation factor 2 subunit, putative
P: 40S ribosomal protein S6
i: 40S ribosomal protein S17, putative
L: Ribosomal protein S20, putative
M: 40S ribosomal protein S3, putative
N: 40S ribosomal protein S10, putative
O: Ribosomal protein S19, putative
b: 40S ribosomal protein S15a, putative
c: 40S ribosomal protein S30
V: Protein translation factor SUI1 homolog, putative
w: Putative eukaryotic translation initiation factor 1A
E: Eukaryotic translation initiation factor 3 subunit E
Y: Eukaryotic translation initiation factor 5, putative
Q: Ribosomal protein S29, putative
D: eL41
G: JAB_MPN domain-containing protein
K: CSN8_PSD8_EIF3K domain-containing protein
T: 40S ribosomal protein S15, putative
C: Eukaryotic translation initiation factor 3 subunit 8, putative
8: eIF3A
W: 40S ribosomal protein S3a-2
I: Eukaryotic translation initiation factor 3 (EIF-3) interacting protein, putative
H: eIF3H
A: Eukaryotic translation initiation factor 3 subunit 7-like protein, putative
l: 40S ribosomal protein S4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)2,328,33455
Polymers2,327,72252
Non-polymers6123
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: mass spectrometry, microscopy
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area306030 Å2
ΔGint-2013 kcal/mol
Surface area777730 Å2
MethodPISA

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Components

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Protein , 12 types, 12 molecules fsjnpJVwGK8H

#1: Protein kDDX60


Mass: 246749.875 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma cruzi (eukaryote) / References: UniProt: Q4E5Z1
#5: Protein Elongation initiation factor 2 alpha subunit, putative


Mass: 47700.223 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma cruzi (eukaryote) / References: UniProt: Q4E620
#6: Protein 60S ribosomal protein L40 / Ubiquitin-60S ribosomal protein L40


Mass: 16624.496 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma cruzi (eukaryote) / References: UniProt: A0A2V2VP49
#7: Protein Translation initiation factor, putative


Mass: 38227.219 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma cruzi (eukaryote) / References: UniProt: Q4DH88
#8: Protein Guanine nucleotide-binding protein subunit beta-like protein


Mass: 35070.312 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma cruzi (eukaryote) / References: UniProt: Q4DTN2
#26: Protein RNA-binding protein, putative


Mass: 27676.303 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma cruzi (eukaryote) / References: UniProt: Q4DY32
#37: Protein Protein translation factor SUI1 homolog, putative / Translation factor SUI1 / putative


Mass: 12577.262 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma cruzi (eukaryote) / References: UniProt: Q4DM75
#38: Protein Putative eukaryotic translation initiation factor 1A


Mass: 18418.516 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma cruzi (eukaryote) / References: UniProt: A0A2V2WGW5
#43: Protein JAB_MPN domain-containing protein


Mass: 38589.625 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma cruzi (eukaryote) / References: UniProt: Q4DQZ2
#44: Protein CSN8_PSD8_EIF3K domain-containing protein


Mass: 22458.547 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma cruzi (eukaryote) / References: UniProt: Q4DDK1
#47: Protein eIF3A


Mass: 87439.898 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma cruzi (eukaryote) / References: UniProt: Q4DL69
#50: Protein eIF3H


Mass: 38408.816 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma cruzi (eukaryote) / References: UniProt: Q4DSJ1

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RNA chain , 2 types, 2 molecules 10

#2: RNA chain initiator tRNA-Met


Mass: 24255.533 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma cruzi (eukaryote)
#3: RNA chain 18S


Mass: 746696.125 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma cruzi (eukaryote) / References: GenBank: 320364483

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40S ribosomal protein ... , 26 types, 26 molecules yrumZoqRStUvXFdahPiMNbcTWl

#4: Protein 40S ribosomal protein S24


Mass: 15706.745 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma cruzi (eukaryote) / References: UniProt: Q4DW38
#9: Protein 40S ribosomal protein S16, putative


Mass: 16841.643 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma cruzi (eukaryote) / References: UniProt: Q4DEK4
#10: Protein 40S ribosomal protein S18, putative


Mass: 17585.469 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma cruzi (eukaryote) / References: UniProt: Q4E093
#11: Protein 40S ribosomal protein S23, putative


Mass: 15960.672 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma cruzi (eukaryote) / References: UniProt: Q4DTQ1
#12: Protein 40S ribosomal protein S8


Mass: 25246.783 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma cruzi (eukaryote) / References: UniProt: Q4DU83
#13: Protein 40S ribosomal protein S5, putative


Mass: 21292.715 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma cruzi (eukaryote) / References: UniProt: Q4E0Q3
#14: Protein 40S ribosomal protein S7


Mass: 24896.504 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma cruzi (eukaryote) / References: UniProt: Q4CUC7
#15: Protein 40S ribosomal protein S13, putative


Mass: 17295.621 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma cruzi (eukaryote) / References: UniProt: Q4DC38
#16: Protein 40S ribosomal protein S27, putative / Ribosomal protein S27 / putative


Mass: 9581.131 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma cruzi (eukaryote) / References: UniProt: Q4DN73
#17: Protein 40S ribosomal protein S26


Mass: 12793.177 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma cruzi (eukaryote) / References: UniProt: Q4CYE4
#18: Protein 40S ribosomal protein S33


Mass: 10023.522 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma cruzi (eukaryote) / References: UniProt: A0A061J677
#19: Protein 40S ribosomal protein S14, putative


Mass: 15596.004 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma cruzi (eukaryote) / References: UniProt: Q4D6I5
#20: Protein 40S ribosomal protein S11, putative


Mass: 20018.307 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma cruzi (eukaryote) / References: UniProt: Q4D0U7
#22: Protein 40S ribosomal protein SA


Mass: 27913.182 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma cruzi (eukaryote) / References: UniProt: Q4CQU0
#23: Protein 40S ribosomal protein S2, putative


Mass: 28574.951 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma cruzi (eukaryote) / References: UniProt: Q4DIZ9
#25: Protein 40S ribosomal protein S25


Mass: 12379.955 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma cruzi (eukaryote) / References: UniProt: Q4DTX6
#27: Protein 40S ribosomal protein S12


Mass: 15792.110 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma cruzi (eukaryote) / References: UniProt: Q4CSL1
#29: Protein 40S ribosomal protein S6


Mass: 28344.391 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma cruzi (eukaryote) / References: UniProt: Q4DSU0
#30: Protein 40S ribosomal protein S17, putative


Mass: 16255.222 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma cruzi (eukaryote) / References: UniProt: Q4DK39
#32: Protein 40S ribosomal protein S3, putative


Mass: 24188.436 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma cruzi (eukaryote) / References: UniProt: Q4DMK9
#33: Protein 40S ribosomal protein S10, putative


Mass: 18284.725 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma cruzi (eukaryote) / References: UniProt: Q4E088
#35: Protein 40S ribosomal protein S15a, putative


Mass: 16255.128 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma cruzi (eukaryote) / References: UniProt: Q4CXX2
#36: Protein 40S ribosomal protein S30


Mass: 7445.938 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma cruzi (eukaryote) / References: UniProt: Q4DA48
#45: Protein 40S ribosomal protein S15, putative


Mass: 17554.453 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma cruzi (eukaryote) / References: UniProt: Q4DGZ5
#48: Protein 40S ribosomal protein S3a-2


Mass: 29134.721 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma cruzi (eukaryote) / References: UniProt: Q4DZ41
#52: Protein 40S ribosomal protein S4


Mass: 30936.521 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma cruzi (eukaryote) / References: UniProt: O62594

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Putative 40S ribosomal protein ... , 2 types, 2 molecules Bg

#21: Protein Putative 40S ribosomal protein S9


Mass: 22180.945 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma cruzi (eukaryote) / References: UniProt: A0A2V2WBN2
#24: Protein Putative 40S ribosomal protein S21


Mass: 27634.291 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma cruzi (eukaryote) / References: UniProt: A0A2V2UKQ3

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Eukaryotic translation initiation factor ... , 6 types, 6 molecules 5EYCIA

#28: Protein Eukaryotic translation initiation factor 2 subunit, putative


Mass: 52642.418 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma cruzi (eukaryote) / References: UniProt: Q4CPV7
#39: Protein Eukaryotic translation initiation factor 3 subunit E / eIF3e / Eukaryotic translation initiation factor 3 subunit 6


Mass: 46320.785 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma cruzi (eukaryote) / References: UniProt: Q4D7F2
#40: Protein Eukaryotic translation initiation factor 5, putative


Mass: 42887.738 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma cruzi (eukaryote) / References: UniProt: Q4DZB0
#46: Protein Eukaryotic translation initiation factor 3 subunit 8, putative


Mass: 82331.086 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma cruzi (eukaryote) / References: UniProt: Q4E3G1
#49: Protein Eukaryotic translation initiation factor 3 (EIF-3) interacting protein, putative


Mass: 56331.250 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma cruzi (eukaryote) / References: UniProt: Q4D5W3
#51: Protein Eukaryotic translation initiation factor 3 subunit 7-like protein, putative


Mass: 57492.965 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma cruzi (eukaryote) / References: UniProt: Q4DCN0

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Ribosomal protein ... , 3 types, 3 molecules LOQ

#31: Protein Ribosomal protein S20, putative


Mass: 13248.478 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma cruzi (eukaryote) / References: UniProt: Q4D6H7
#34: Protein Ribosomal protein S19, putative


Mass: 18861.287 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma cruzi (eukaryote) / References: UniProt: Q4DJY1
#41: Protein Ribosomal protein S29, putative


Mass: 6651.826 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma cruzi (eukaryote) / References: UniProt: Q4CXR4

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Protein/peptide , 1 types, 1 molecules D

#42: Protein/peptide eL41


Mass: 4348.417 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma cruzi (eukaryote) / References: UniProt: G0U1J3

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Non-polymers , 3 types, 3 molecules

#53: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#54: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#55: Chemical ChemComp-GNP / PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER


Mass: 522.196 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H17N6O13P3
Comment: GppNHp, GMPPNP, energy-carrying molecule analogue*YM

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Details

Has ligand of interestN
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

ComponentName: 43S preinitiation complex from Trypanosoma cruzi with the helicase kDDX60
Type: COMPLEX / Entity ID: #1-#52 / Source: NATURAL
Source (natural)Organism: Trypanosoma cruzi (eukaryote)
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid mesh size: 300 divisions/in. / Grid type: Quantifoil R2/2
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277.15 K

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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: OTHER
Image recordingElectron dose: 30 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

CTF correctionType: NONE
3D reconstructionResolution: 3.33 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 33775 / Symmetry type: POINT

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