ISDA

Deposition Date 2020-10-27

Release Date 2021-04-14

Last Version Date 2024-10-16

Entry Detail

PDB ID:

7ASE

Keywords:

TRANSLATION

Title:

43S preinitiation complex from Trypanosoma cruzi with the kDDX60 helicase

Biological Source:

Source Organism:

Trypanosoma cruzi (Taxon ID: 5693)

Method Details:

Experimental Method:

ELECTRON MICROSCOPY

Resolution:

3.33 Å

Aggregation State:

PARTICLE

Reconstruction Method:

SINGLE PARTICLE

Download Validation Report

Macromolecular Entities

Polymer Type:polyribonucleotide
Molecule:18S
Chain IDs:C (auth: 0)
Chain Length:2319
Number of Molecules:1
Biological Source:Trypanosoma cruzi

Polymer Type:polyribonucleotide
Molecule:initiator tRNA-Met
Chain IDs:B (auth: 1)
Chain Length:75
Number of Molecules:1
Biological Source:Trypanosoma cruzi

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Eukaryotic translation initiation factor 2 subunit, putative
Gene (Uniprot):Tc00.1047053503819.30, Tc00.1047053510359.310
Chain IDs:BA (auth: 5)
Chain Length:477
Number of Molecules:1
Biological Source:Trypanosoma cruzi

UniProt ID:Q4CPV7 Pfam ID:PF00009, PF09173

Protein Blast

Polymer Type:polypeptide(L)
Molecule:eIF3A
Gene (Uniprot):Tc00.1047053508919.140
Chain IDs:UA (auth: 8)
Chain Length:762
Number of Molecules:1
Biological Source:Trypanosoma cruzi

UniProt ID:Q4DL69

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Eukaryotic translation initiation factor 3 subunit 7-like protein, putative
Gene (Uniprot):Tc00.1047053506943.160
Chain IDs:YA (auth: A)
Chain Length:502
Number of Molecules:1
Biological Source:Trypanosoma cruzi

UniProt ID:Q4DCN0 Pfam ID:PF05091

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Putative 40S ribosomal protein S9
Gene (Uniprot):C3747_139g48
Chain IDs:U (auth: B)
Chain Length:190
Number of Molecules:1
Biological Source:Trypanosoma cruzi

UniProt ID:A0A2V2WBN2 Pfam ID:PF00163, PF01479

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Eukaryotic translation initiation factor 3 subunit 8, putative
Gene (Uniprot):Tc00.1047053507611.310
Chain IDs:TA (auth: C)
Chain Length:66
Number of Molecules:1
Biological Source:Trypanosoma cruzi

UniProt ID:Q4E3G1 Pfam ID:PF05470

Protein Blast

Polymer Type:polypeptide(L)
Molecule:eL41
Gene (Uniprot):TVY486_0805550, TVY486_0805560, TVY486_0805570
Chain IDs:PA (auth: D)
Chain Length:263
Number of Molecules:1
Biological Source:Trypanosoma cruzi

UniProt ID:G0U1J3 Pfam ID:PF05162

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Eukaryotic translation initiation factor 3 subunit E
Gene (Uniprot):Tc00.1047053509205.30
Chain IDs:MA (auth: E)
Chain Length:407
Number of Molecules:1
Biological Source:Trypanosoma cruzi

UniProt ID:Q4D7F2 Pfam ID:PF01399

Protein Blast

Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein SA
Gene (Uniprot):Tc00.1047053503719.20, Tc00.1047053509825.14
Chain IDs:V (auth: F)
Chain Length:245
Number of Molecules:1
Biological Source:Trypanosoma cruzi

UniProt ID:Q4CQU0 Pfam ID:PF00318

Protein Blast

Polymer Type:polypeptide(L)
Molecule:JAB_MPN domain-containing protein
Gene (Uniprot):Tc00.1047053510089.200
Chain IDs:QA (auth: G)
Chain Length:247
Number of Molecules:1
Biological Source:Trypanosoma cruzi

UniProt ID:Q4DQZ2 Pfam ID:PF01398

Protein Blast

Polymer Type:polypeptide(L)
Molecule:eIF3H
Gene (Uniprot):Tc00.1047053508543.100
Chain IDs:XA (auth: H)
Chain Length:141
Number of Molecules:1
Biological Source:Trypanosoma cruzi

UniProt ID:Q4DSJ1

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Eukaryotic translation initiation factor 3 (EIF-3) interacting protein, putative
Gene (Uniprot):Tc00.1047053508169.90
Chain IDs:WA (auth: I)
Chain Length:141
Number of Molecules:1
Biological Source:Trypanosoma cruzi

UniProt ID:Q4D5W3 Pfam ID:PF10255

Protein Blast

Polymer Type:polypeptide(L)
Molecule:RNA-binding protein, putative
Gene (Uniprot):Tc00.1047053511727.270
Chain IDs:Z (auth: J)
Chain Length:257
Number of Molecules:1
Biological Source:Trypanosoma cruzi

UniProt ID:Q4DY32 Pfam ID:PF00076

Protein Blast

Polymer Type:polypeptide(L)
Molecule:CSN8_PSD8_EIF3K domain-containing protein
Gene (Uniprot):Tc00.1047053509267.40
Chain IDs:RA (auth: K)
Chain Length:203
Number of Molecules:1
Biological Source:Trypanosoma cruzi

UniProt ID:Q4DDK1 Pfam ID:PF10075

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Ribosomal protein S20, putative
Gene (Uniprot):Tc00.1047053508475.10, Tc00.1047053508823.120, Tc00.1047053508823.140
Chain IDs:EA (auth: L)
Chain Length:117
Number of Molecules:1
Biological Source:Trypanosoma cruzi

UniProt ID:Q4D6H7 Pfam ID:PF00338

Protein Blast

Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S3, putative
Gene (Uniprot):Tc00.1047053504021.109, Tc00.1047053507677.39, Tc00.1047053509353.30
Chain IDs:FA (auth: M)
Chain Length:143
Number of Molecules:1
Biological Source:Trypanosoma cruzi

UniProt ID:Q4DMK9 Pfam ID:PF07650, PF00189

Protein Blast

Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S10, putative
Gene (Uniprot):Tc00.1047053506679.140, Tc00.1047053506679.150
Chain IDs:GA (auth: N)
Chain Length:343
Number of Molecules:1
Biological Source:Trypanosoma cruzi

UniProt ID:Q4E088 Pfam ID:PF03501

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Ribosomal protein S19, putative
Gene (Uniprot):Tc00.1047053510879.20
Chain IDs:HA (auth: O)
Chain Length:190
Number of Molecules:1
Biological Source:Trypanosoma cruzi

UniProt ID:Q4DJY1 Pfam ID:PF01090

Protein Blast

Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S6
Gene (Uniprot):Tc00.1047053510769.49
Chain IDs:CA (auth: P)
Chain Length:250
Number of Molecules:1
Biological Source:Trypanosoma cruzi

UniProt ID:Q4DSU0 Pfam ID:PF01092

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Ribosomal protein S29, putative
Gene (Uniprot):Tc00.1047053506025.14, Tc00.1047053511209.54, Tc00.1047053511805.15
Chain IDs:OA (auth: Q)
Chain Length:211
Number of Molecules:1
Biological Source:Trypanosoma cruzi

UniProt ID:Q4CXR4 Pfam ID:PF00253

Protein Blast

Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S13, putative
Gene (Uniprot):Tc00.1047053511291.90
Chain IDs:O (auth: R)
Chain Length:151
Number of Molecules:1
Biological Source:Trypanosoma cruzi

UniProt ID:Q4DC38 Pfam ID:PF08069, PF00312

Protein Blast

Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S27, putative
Gene (Uniprot):Tc00.1047053506963.14, Tc00.1047053511233.14, Tc00.1047053511277.175
Chain IDs:P (auth: S)
Chain Length:418
Number of Molecules:1
Biological Source:Trypanosoma cruzi

UniProt ID:Q4DN73 Pfam ID:PF01667

Protein Blast

Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S15, putative
Gene (Uniprot):Tc00.1047053511809.130, Tc00.1047053511809.99, Tc00.1047053511811.10
Chain IDs:SA (auth: T)
Chain Length:112
Number of Molecules:1
Biological Source:Trypanosoma cruzi

UniProt ID:Q4DGZ5 Pfam ID:PF00203

Protein Blast

Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S33
Gene (Uniprot):TRSC58_02430
Chain IDs:R (auth: U)
Chain Length:153
Number of Molecules:1
Biological Source:Trypanosoma cruzi

UniProt ID:A0A061J677 Pfam ID:PF01200

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Protein translation factor SUI1 homolog, putative
Gene (Uniprot):Tc00.1047053508515.20, Tc00.1047053508641.184
Chain IDs:KA (auth: V)
Chain Length:144
Number of Molecules:1
Biological Source:Trypanosoma cruzi

UniProt ID:Q4DM75 Pfam ID:PF01253

Protein Blast

Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S3a-2
Gene (Uniprot):Tc00.1047053511001.9, Tc00.1047053511001.18
Chain IDs:VA (auth: W)
Chain Length:254
Number of Molecules:1
Biological Source:Trypanosoma cruzi

UniProt ID:Q4DZ41 Pfam ID:PF01015

Protein Blast

Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S11, putative
Gene (Uniprot):Tc00.1047053508319.70, Tc00.1047053508405.40
Chain IDs:T (auth: X)
Chain Length:173
Number of Molecules:1
Biological Source:Trypanosoma cruzi

UniProt ID:Q4D0U7 Pfam ID:PF16205, PF00366

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Eukaryotic translation initiation factor 5, putative
Gene (Uniprot):Tc00.1047053504105.20
Chain IDs:NA (auth: Y)
Chain Length:137
Number of Molecules:1
Biological Source:Trypanosoma cruzi

UniProt ID:Q4DZB0 Pfam ID:PF01873

Protein Blast

Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S8
Gene (Uniprot):Tc00.1047053511903.110
Chain IDs:L (auth: Z)
Chain Length:221
Number of Molecules:1
Biological Source:Trypanosoma cruzi

UniProt ID:Q4DU83 Pfam ID:PF01201

Protein Blast

Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S25
Gene (Uniprot):Tc00.1047053504105.94, Tc00.1047053509233.190
Chain IDs:Y (auth: a)
Chain Length:502
Number of Molecules:1
Biological Source:Trypanosoma cruzi

UniProt ID:Q4DTX6 Pfam ID:PF03297

Protein Blast

Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S15a, putative
Gene (Uniprot):Tc00.1047053508041.30
Chain IDs:IA (auth: b)
Chain Length:190
Number of Molecules:1
Biological Source:Trypanosoma cruzi

UniProt ID:Q4CXX2 Pfam ID:PF00410

Protein Blast

Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S30
Gene (Uniprot):Tc00.1047053507019.83, Tc00.1047053507019.86
Chain IDs:JA (auth: c)
Chain Length:66
Number of Molecules:1
Biological Source:Trypanosoma cruzi

UniProt ID:Q4DA48 Pfam ID:PF04758

Protein Blast

Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S2, putative
Gene (Uniprot):Tc00.1047053503833.40, Tc00.1047053506213.60, Tc00.1047053511287.120, Tc00.1047053511287.40
Chain IDs:W (auth: d)
Chain Length:263
Number of Molecules:1
Biological Source:Trypanosoma cruzi

UniProt ID:Q4DIZ9 Pfam ID:PF00333, PF03719

Protein Blast

Polymer Type:polypeptide(L)
Molecule:kDDX60
Gene (Uniprot):Tc00.1047053508153.1050
Chain IDs:A (auth: f)
Chain Length:245
Number of Molecules:1
Biological Source:Trypanosoma cruzi

UniProt ID:Q4E5Z1 Pfam ID:PF23002, PF00270, PF00271

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Putative 40S ribosomal protein S21
Gene (Uniprot):C4B63_212g18
Chain IDs:X (auth: g)
Chain Length:247
Number of Molecules:1
Biological Source:Trypanosoma cruzi

UniProt ID:A0A2V2UKQ3 Pfam ID:PF01249

Protein Blast

Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S12
Gene (Uniprot):Tc00.1047053503395.50, Tc00.1047053506181.59
Chain IDs:AA (auth: h)
Chain Length:141
Number of Molecules:1
Biological Source:Trypanosoma cruzi

UniProt ID:Q4CSL1 Pfam ID:PF01248

Protein Blast

Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S17, putative
Gene (Uniprot):Tc00.1047053508827.79
Chain IDs:DA (auth: i)
Chain Length:141
Number of Molecules:1
Biological Source:Trypanosoma cruzi

UniProt ID:Q4DK39 Pfam ID:PF00833

Protein Blast

Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L40
Gene (Uniprot):C4B63_13g195, C4B63_52g151
Chain IDs:F (auth: j)
Chain Length:257
Number of Molecules:1
Biological Source:Trypanosoma cruzi

UniProt ID:A0A2V2VP49 Pfam ID:PF00240, PF01599

Protein Blast

Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S4
Gene (Uniprot):RibpS4
Chain IDs:ZA (auth: l)
Chain Length:117
Number of Molecules:1
Biological Source:Trypanosoma cruzi

UniProt ID:O62594 Pfam ID:PF08071, PF01479, PF00900, PF00467, PF16121

Protein Blast

Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S23, putative
Gene (Uniprot):Tc00.1047053504181.20, Tc00.1047053504181.30, Tc00.1047053509695.180, Tc00.1047053509695.184
Chain IDs:K (auth: m)
Chain Length:143
Number of Molecules:1
Biological Source:Trypanosoma cruzi

UniProt ID:Q4DTQ1 Pfam ID:PF00164

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Translation initiation factor, putative
Gene (Uniprot):Tc00.1047053503955.70
Chain IDs:G (auth: n)
Chain Length:343
Number of Molecules:1
Biological Source:Trypanosoma cruzi

UniProt ID:Q4DH88 Pfam ID:PF01873

Protein Blast

Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S5, putative
Gene (Uniprot):Tc00.1047053506297.150, Tc00.1047053506297.160
Chain IDs:M (auth: o)
Chain Length:190
Number of Molecules:1
Biological Source:Trypanosoma cruzi

UniProt ID:Q4E0Q3 Pfam ID:PF00177

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Guanine nucleotide-binding protein subunit beta-like protein
Gene (Uniprot):Tc00.1047053511211.120, Tc00.1047053511211.130
Chain IDs:H (auth: p)
Chain Length:250
Number of Molecules:1
Biological Source:Trypanosoma cruzi

UniProt ID:Q4DTN2 Pfam ID:PF00400

Protein Blast

Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S7
Gene (Uniprot):Tc00.1047053506593.30
Chain IDs:N (auth: q)
Chain Length:211
Number of Molecules:1
Biological Source:Trypanosoma cruzi

UniProt ID:Q4CUC7 Pfam ID:PF01251

Protein Blast

Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S16, putative
Gene (Uniprot):Tc00.1047053503899.20, Tc00.1047053503899.30
Chain IDs:I (auth: r)
Chain Length:151
Number of Molecules:1
Biological Source:Trypanosoma cruzi

UniProt ID:Q4DEK4 Pfam ID:PF00380

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Elongation initiation factor 2 alpha subunit, putative
Gene (Uniprot):Tc00.1047053508153.730
Chain IDs:E (auth: s)
Chain Length:418
Number of Molecules:1
Biological Source:Trypanosoma cruzi

UniProt ID:Q4E620 Pfam ID:PF00575, PF07541

Protein Blast

Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S26
Gene (Uniprot):Tc00.1047053503801.20, Tc00.1047053508817.60
Chain IDs:Q (auth: t)
Chain Length:112
Number of Molecules:1
Biological Source:Trypanosoma cruzi

UniProt ID:Q4CYE4 Pfam ID:PF01283

Protein Blast

Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S18, putative
Gene (Uniprot):Tc00.1047053506679.100, Tc00.1047053506679.94
Chain IDs:J (auth: u)
Chain Length:153
Number of Molecules:1
Biological Source:Trypanosoma cruzi

UniProt ID:Q4E093 Pfam ID:PF00416

Protein Blast

Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S14, putative
Gene (Uniprot):Tc00.1047053409117.20, Tc00.1047053506945.230, Tc00.1047053508823.50
Chain IDs:S (auth: v)
Chain Length:144
Number of Molecules:1
Biological Source:Trypanosoma cruzi

UniProt ID:Q4D6I5 Pfam ID:PF00411

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Putative eukaryotic translation initiation factor 1A
Gene (Uniprot):C3747_106g25, C3747_186g29
Chain IDs:LA (auth: w)
Chain Length:254
Number of Molecules:1
Biological Source:Trypanosoma cruzi

UniProt ID:A0A2V2WGW5 Pfam ID:PF01176

Protein Blast

Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S24
Gene (Uniprot):Tc00.1047053507681.150, Tc00.1047053507681.160
Chain IDs:D (auth: y)
Chain Length:137
Number of Molecules:1
Biological Source:Trypanosoma cruzi

UniProt ID:Q4DW38 Pfam ID:PF01282

Ligand Molecules

GNP

Primary Citation

Structural Differences in Translation Initiation between Pathogenic Trypanosomatids and Their Mammalian Hosts.

Bochler, A, Querido, J.B, Prilepskaja, T, Soufari, H, Simonetti, A, Del Cistia, M.L, Kuhn, L, Ribeiro, A.R, Valasek, L.S, Hashem, Y.Show

Cell Rep 33 108534 108534 (2020)

PMID: 33357443 DOI: 10.1016/j.celrep.2020.108534

Abstact

Canonical mRNA translation in eukaryotes begins with the formation of the 43S pre-initiation complex (PIC). Its assembly requires binding of initiator Met-tRNAiMet 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) 9S, 7S, and 6S, 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.

Legend

Protein

Chemical

Disease

Primary Citation of related structures