› 7ase

Electron Microscopy
3.33Å resolution

43S preinitiation complex from Trypanosoma cruzi with the kDDX60 helicase

Released:
DOI: 10.2210/pdb7ase/pdb
PDB entry 7ase coloured by chain, front view.
PDB entry 7ase coloured by chain, side view.
PDB entry 7ase coloured by chain, top view.
Source organism: Trypanosoma cruzi
Primary publication:
Structural Differences in Translation Initiation between Pathogenic Trypanosomatids and Their Mammalian Hosts.
Bochler A, Querido JB, Prilepskaja T, Soufari H, Simonetti A, Del Cistia ML, Kuhn L, Ribeiro AR, Valášek LS, Hashem Y
OpenAccess logo Cell Rep 33 108534 (2020)
PMID: 33357443
Related structures: EMD-11893

Function and Biology Details

Reaction catalysed: 
GTP + H(2)O = GDP + phosphate
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero 52-mer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-100336 (preferred)
Entry contents:
50 distinct polypeptide molecules
2 distinct RNA molecules
Macromolecules (52 distinct):
ATP-dependent DEAD/H RNA helicase Chain: f
Molecule details ›
Chain: f
Length: 2174 amino acids
Theoretical weight: 246.75 KDa
Source organism: Trypanosoma cruzi
UniProt:
  • Canonical: Q4E5Z1 (Residues: 1-2174; Coverage: 100%)
Gene name: Tc00.1047053508153.1050
Sequence domains:
40S ribosomal protein S24 Chain: y
Molecule details ›
Chain: y
Length: 137 amino acids
Theoretical weight: 15.71 KDa
Source organism: Trypanosoma cruzi
UniProt:
  • Canonical: Q4DW38 (Residues: 1-137; Coverage: 100%)
Gene names: Tc00.1047053507681.150, Tc00.1047053507681.160
Sequence domains: Ribosomal protein S24e
S1 motif domain-containing protein Chain: s
Molecule details ›
Chain: s
Length: 418 amino acids
Theoretical weight: 47.7 KDa
Source organism: Trypanosoma cruzi
UniProt:
  • Canonical: Q4E620 (Residues: 1-418; Coverage: 100%)
Gene name: Tc00.1047053508153.730
Sequence domains:
Ubiquitin-ribosomal protein eL40 fusion protein Chain: j
Molecule details ›
Chain: j
Length: 150 amino acids
Theoretical weight: 16.62 KDa
Source organism: Trypanosoma cruzi
UniProt:
  • Canonical: A0A2V2VP49 (Residues: 1-150; Coverage: 100%)
Gene names: C4B63_13g195, C4B63_52g151
Sequence domains:
Translation initiation factor IF2/IF5 domain-containing protein Chain: n
Molecule details ›
Chain: n
Length: 343 amino acids
Theoretical weight: 38.23 KDa
Source organism: Trypanosoma cruzi
UniProt:
  • Canonical: Q4DH88 (Residues: 1-343; Coverage: 100%)
Gene name: Tc00.1047053503955.70
Sequence domains: Domain found in IF2B/IF5
Activated protein kinase C receptor, putative Chain: p
Molecule details ›
Chain: p
Length: 318 amino acids
Theoretical weight: 35.07 KDa
Source organism: Trypanosoma cruzi
UniProt:
  • Canonical: Q4DTN2 (Residues: 1-318; Coverage: 100%)
Gene names: Tc00.1047053511211.120, Tc00.1047053511211.130
Sequence domains: WD domain, G-beta repeat
40S ribosomal protein S16, putative Chain: r
Molecule details ›
Chain: r
Length: 149 amino acids
Theoretical weight: 16.84 KDa
Source organism: Trypanosoma cruzi
UniProt:
  • Canonical: Q4DEK4 (Residues: 1-149; Coverage: 100%)
Gene names: Tc00.1047053503899.20, Tc00.1047053503899.30
Sequence domains: Ribosomal protein S9/S16
40S ribosomal protein S18, putative Chain: u
Molecule details ›
Chain: u
Length: 153 amino acids
Theoretical weight: 17.59 KDa
Source organism: Trypanosoma cruzi
UniProt:
  • Canonical: Q4E093 (Residues: 1-153; Coverage: 100%)
Gene names: Tc00.1047053506679.100, Tc00.1047053506679.94
Sequence domains: Ribosomal protein S13/S18
40S ribosomal protein S23, putative Chain: m
Molecule details ›
Chain: m
Length: 143 amino acids
Theoretical weight: 15.96 KDa
Source organism: Trypanosoma cruzi
UniProt:
  • Canonical: Q4DTQ1 (Residues: 1-143; Coverage: 100%)
Gene names: Tc00.1047053504181.20, Tc00.1047053504181.30, Tc00.1047053509695.180, Tc00.1047053509695.184
Sequence domains: Ribosomal protein S12/S23
40S ribosomal protein S8 Chain: Z
Molecule details ›
Chain: Z
Length: 221 amino acids
Theoretical weight: 25.25 KDa
Source organism: Trypanosoma cruzi
UniProt:
  • Canonical: Q4DU83 (Residues: 1-221; Coverage: 100%)
Gene name: Tc00.1047053511903.110
Sequence domains: Ribosomal protein S8e
Small ribosomal subunit protein uS7 domain-containing protein Chain: o
Molecule details ›
Chain: o
Length: 190 amino acids
Theoretical weight: 21.29 KDa
Source organism: Trypanosoma cruzi
UniProt:
  • Canonical: Q4E0Q3 (Residues: 1-190; Coverage: 100%)
Gene names: Tc00.1047053506297.150, Tc00.1047053506297.160
Sequence domains: Ribosomal protein S7p/S5e
40S ribosomal protein S7 Chain: q
Molecule details ›
Chain: q
Length: 211 amino acids
Theoretical weight: 24.9 KDa
Source organism: Trypanosoma cruzi
UniProt:
  • Canonical: Q4CUC7 (Residues: 1-211; Coverage: 100%)
Gene name: Tc00.1047053506593.30
Sequence domains: Ribosomal protein S7e
Small ribosomal subunit protein uS15 N-terminal domain-containing protein Chain: R
Molecule details ›
Chain: R
Length: 151 amino acids
Theoretical weight: 17.3 KDa
Source organism: Trypanosoma cruzi
UniProt:
  • Canonical: Q4DC38 (Residues: 1-151; Coverage: 100%)
Gene name: Tc00.1047053511291.90
Sequence domains:
40S ribosomal protein S27, putative Chain: S
Molecule details ›
Chain: S
Length: 86 amino acids
Theoretical weight: 9.58 KDa
Source organism: Trypanosoma cruzi
UniProt:
  • Canonical: Q4DN73 (Residues: 1-86; Coverage: 100%)
Gene names: Tc00.1047053506963.14, Tc00.1047053511233.14, Tc00.1047053511277.175
Sequence domains: Ribosomal protein S27
40S ribosomal protein S26 Chain: t
Molecule details ›
Chain: t
Length: 112 amino acids
Theoretical weight: 12.79 KDa
Source organism: Trypanosoma cruzi
UniProt:
  • Canonical: Q4CYE4 (Residues: 1-112; Coverage: 100%)
Gene names: Tc00.1047053503801.20, Tc00.1047053508817.60
Sequence domains: Ribosomal protein S26e
40S ribosomal protein S33 Chain: U
Molecule details ›
Chain: U
Length: 91 amino acids
Theoretical weight: 10.02 KDa
Source organism: Trypanosoma cruzi
UniProt:
  • Canonical: A0A061J677 (Residues: 1-91; Coverage: 100%)
Gene name: TRSC58_02430
Sequence domains: Ribosomal protein S28e
40S ribosomal protein S14, putative Chain: v
Molecule details ›
Chain: v
Length: 144 amino acids
Theoretical weight: 15.6 KDa
Source organism: Trypanosoma cruzi
UniProt:
  • Canonical: Q4D6I5 (Residues: 1-144; Coverage: 100%)
Gene names: Tc00.1047053409117.20, Tc00.1047053506945.230, Tc00.1047053508823.50
Sequence domains: Ribosomal protein S11
Small ribosomal subunit protein uS17 N-terminal domain-containing protein Chain: X
Molecule details ›
Chain: X
Length: 173 amino acids
Theoretical weight: 20.02 KDa
Source organism: Trypanosoma cruzi
UniProt:
  • Canonical: Q4D0U7 (Residues: 1-173; Coverage: 100%)
Gene names: Tc00.1047053508319.70, Tc00.1047053508405.40
Sequence domains:
Putative 40S ribosomal protein S9 Chain: B
Molecule details ›
Chain: B
Length: 190 amino acids
Theoretical weight: 22.18 KDa
Source organism: Trypanosoma cruzi
UniProt:
  • Canonical: A0A2V2WBN2 (Residues: 1-190; Coverage: 100%)
Gene name: C3747_139g48
Sequence domains:
Small ribosomal subunit protein uS2 Chain: F
Molecule details ›
Chain: F
Length: 245 amino acids
Theoretical weight: 27.91 KDa
Source organism: Trypanosoma cruzi
UniProt:
  • Canonical: Q4CQU0 (Residues: 1-245; Coverage: 100%)
Gene names: Tc00.1047053503719.20, Tc00.1047053509825.14
Sequence domains: Ribosomal protein S2
S5 DRBM domain-containing protein Chain: d
Molecule details ›
Chain: d
Length: 263 amino acids
Theoretical weight: 28.57 KDa
Source organism: Trypanosoma cruzi
UniProt:
  • Canonical: Q4DIZ9 (Residues: 1-263; Coverage: 100%)
Gene names: Tc00.1047053503833.40, Tc00.1047053506213.60, Tc00.1047053511287.120, Tc00.1047053511287.40
Sequence domains:
Putative 40S ribosomal protein S21 Chain: g
Molecule details ›
Chain: g
Length: 247 amino acids
Theoretical weight: 27.63 KDa
Source organism: Trypanosoma cruzi
UniProt:
  • Canonical: A0A2V2UKQ3 (Residues: 1-247; Coverage: 100%)
Gene name: C4B63_212g18
Sequence domains: Ribosomal protein S21e
40S ribosomal protein S25 Chain: a
Molecule details ›
Chain: a
Length: 110 amino acids
Theoretical weight: 12.38 KDa
Source organism: Trypanosoma cruzi
UniProt:
  • Canonical: Q4DTX6 (Residues: 1-110; Coverage: 100%)
Gene names: Tc00.1047053504105.94, Tc00.1047053509233.190
Sequence domains: S25 ribosomal protein
RRM domain-containing protein Chain: J
Molecule details ›
Chain: J
Length: 257 amino acids
Theoretical weight: 27.68 KDa
Source organism: Trypanosoma cruzi
UniProt:
  • Canonical: Q4DY32 (Residues: 1-257; Coverage: 100%)
Gene name: Tc00.1047053511727.270
Sequence domains: RNA recognition motif
40S ribosomal protein S12 Chain: h
Molecule details ›
Chain: h
Length: 141 amino acids
Theoretical weight: 15.79 KDa
Source organism: Trypanosoma cruzi
UniProt:
  • Canonical: Q4CSL1 (Residues: 1-141; Coverage: 100%)
Gene names: Tc00.1047053503395.50, Tc00.1047053506181.59
Sequence domains: Ribosomal protein L7Ae/L30e/S12e/Gadd45 family
protein-synthesizing GTPase Chain: 5
Molecule details ›
Chain: 5
Length: 477 amino acids
Theoretical weight: 52.64 KDa
Source organism: Trypanosoma cruzi
UniProt:
  • Canonical: Q4CPV7 (Residues: 1-477; Coverage: 100%)
Gene names: Tc00.1047053503819.30, Tc00.1047053510359.310
Sequence domains:
40S ribosomal protein S6 Chain: P
Molecule details ›
Chain: P
Length: 250 amino acids
Theoretical weight: 28.34 KDa
Source organism: Trypanosoma cruzi
UniProt:
  • Canonical: Q4DSU0 (Residues: 1-250; Coverage: 100%)
Gene name: Tc00.1047053510769.49
Sequence domains: Ribosomal protein S6e
40S ribosomal protein S17, putative Chain: i
Molecule details ›
Chain: i
Length: 141 amino acids
Theoretical weight: 16.26 KDa
Source organism: Trypanosoma cruzi
UniProt:
  • Canonical: Q4DK39 (Residues: 1-141; Coverage: 100%)
Gene name: Tc00.1047053508827.79
Sequence domains: Ribosomal S17
Small ribosomal subunit protein uS10 domain-containing protein Chain: L
Molecule details ›
Chain: L
Length: 117 amino acids
Theoretical weight: 13.25 KDa
Source organism: Trypanosoma cruzi
UniProt:
  • Canonical: Q4D6H7 (Residues: 1-117; Coverage: 100%)
Gene names: Tc00.1047053508475.10, Tc00.1047053508823.120, Tc00.1047053508823.140
Sequence domains: Ribosomal protein S10p/S20e
40S ribosomal protein S3 Chain: M
Molecule details ›
Chain: M
Length: 214 amino acids
Theoretical weight: 24.19 KDa
Source organism: Trypanosoma cruzi
UniProt:
  • Canonical: Q4DMK9 (Residues: 1-214; Coverage: 100%)
Gene names: Tc00.1047053504021.109, Tc00.1047053507677.39, Tc00.1047053509353.30
Sequence domains:
Plectin/eS10 N-terminal domain-containing protein Chain: N
Molecule details ›
Chain: N
Length: 161 amino acids
Theoretical weight: 18.28 KDa
Source organism: Trypanosoma cruzi
UniProt:
  • Canonical: Q4E088 (Residues: 1-161; Coverage: 100%)
Gene names: Tc00.1047053506679.140, Tc00.1047053506679.150
Sequence domains: Plectin/S10 domain
Ribosomal protein S19, putative Chain: O
Molecule details ›
Chain: O
Length: 167 amino acids
Theoretical weight: 18.86 KDa
Source organism: Trypanosoma cruzi
UniProt:
  • Canonical: Q4DJY1 (Residues: 1-167; Coverage: 100%)
Gene name: Tc00.1047053510879.20
Sequence domains: Ribosomal protein S19e
40S ribosomal protein S15a, putative Chain: b
Molecule details ›
Chain: b
Length: 145 amino acids
Theoretical weight: 16.26 KDa
Source organism: Trypanosoma cruzi
UniProt:
  • Canonical: Q4CXX2 (Residues: 1-145; Coverage: 100%)
Gene name: Tc00.1047053508041.30
Sequence domains: Ribosomal protein S8
40S ribosomal protein S30 Chain: c
Molecule details ›
Chain: c
Length: 66 amino acids
Theoretical weight: 7.45 KDa
Source organism: Trypanosoma cruzi
UniProt:
  • Canonical: Q4DA48 (Residues: 1-66; Coverage: 100%)
Gene names: Tc00.1047053507019.83, Tc00.1047053507019.86
Sequence domains: Ribosomal protein S30
SUI1 domain-containing protein Chain: V
Molecule details ›
Chain: V
Length: 109 amino acids
Theoretical weight: 12.58 KDa
Source organism: Trypanosoma cruzi
UniProt:
  • Canonical: Q4DM75 (Residues: 1-109; Coverage: 100%)
Gene names: Tc00.1047053508515.20, Tc00.1047053508641.184
Sequence domains: Translation initiation factor SUI1
S1-like domain-containing protein Chain: w
Molecule details ›
Chain: w
Length: 166 amino acids
Theoretical weight: 18.42 KDa
Source organism: Trypanosoma cruzi
UniProt:
  • Canonical: A0A2V2WGW5 (Residues: 5-170; Coverage: 98%)
Gene names: C3747_106g25, C3747_186g29
Sequence domains: Translation initiation factor 1A / IF-1
Eukaryotic translation initiation factor 3 subunit E Chain: E
Molecule details ›
Chain: E
Length: 407 amino acids
Theoretical weight: 46.32 KDa
Source organism: Trypanosoma cruzi
UniProt:
  • Canonical: Q4D7F2 (Residues: 1-407; Coverage: 100%)
Gene name: Tc00.1047053509205.30
Sequence domains: PCI domain
W2 domain-containing protein Chain: Y
Molecule details ›
Chain: Y
Length: 379 amino acids
Theoretical weight: 42.89 KDa
Source organism: Trypanosoma cruzi
UniProt:
  • Canonical: Q4DZB0 (Residues: 1-379; Coverage: 100%)
Gene name: Tc00.1047053504105.20
Sequence domains: Domain found in IF2B/IF5
Ribosomal protein S29, putative Chain: Q
Molecule details ›
Chain: Q
Length: 57 amino acids
Theoretical weight: 6.65 KDa
Source organism: Trypanosoma cruzi
UniProt:
  • Canonical: Q4CXR4 (Residues: 1-57; Coverage: 100%)
Gene names: Tc00.1047053506025.14, Tc00.1047053511209.54, Tc00.1047053511805.15
Sequence domains: Ribosomal protein S14p/S29e
60S ribosomal protein L41 Chain: D
Molecule details ›
Chain: D
Length: 34 amino acids
Theoretical weight: 4.35 KDa
Source organism: Trypanosoma cruzi
UniProt:
  • Canonical: G0U1J3 (Residues: 1-34; Coverage: 100%)
Gene names: TVY486_0805550, TVY486_0805560, TVY486_0805570
Sequence domains: Ribosomal protein L41
JAB1/MPN/MOV34 metalloenzyme domain-containing protein Chain: G
Molecule details ›
Chain: G
Length: 345 amino acids
Theoretical weight: 38.59 KDa
Source organism: Trypanosoma cruzi
UniProt:
  • Canonical: Q4DQZ2 (Residues: 1-345; Coverage: 100%)
Gene name: Tc00.1047053510089.200
Sequence domains: JAB1/Mov34/MPN/PAD-1 ubiquitin protease
CSN8/PSMD8/EIF3K domain-containing protein Chain: K
Molecule details ›
Chain: K
Length: 203 amino acids
Theoretical weight: 22.46 KDa
Source organism: Trypanosoma cruzi
UniProt:
  • Canonical: Q4DDK1 (Residues: 1-203; Coverage: 100%)
Gene name: Tc00.1047053509267.40
Sequence domains: CSN8/PSMD8/EIF3K family
40S ribosomal protein S15, putative Chain: T
Molecule details ›
Chain: T
Length: 152 amino acids
Theoretical weight: 17.55 KDa
Source organism: Trypanosoma cruzi
UniProt:
  • Canonical: Q4DGZ5 (Residues: 1-152; Coverage: 100%)
Gene names: Tc00.1047053511809.130, Tc00.1047053511809.99, Tc00.1047053511811.10
Sequence domains: Ribosomal protein S19
Eukaryotic translation initiation factor 3 subunit C N-terminal domain-containing protein Chain: C
Molecule details ›
Chain: C
Length: 716 amino acids
Theoretical weight: 82.33 KDa
Source organism: Trypanosoma cruzi
UniProt:
  • Canonical: Q4E3G1 (Residues: 1-716; Coverage: 100%)
Gene name: Tc00.1047053507611.310
Sequence domains: Eukaryotic translation initiation factor 3 subunit 8 N-terminus
Eukaryotic translation initiation factor 3 subunit a Chain: 8
Molecule details ›
Chain: 8
Length: 762 amino acids
Theoretical weight: 87.44 KDa
Source organism: Trypanosoma cruzi
UniProt:
  • Canonical: Q4DL69 (Residues: 1-762; Coverage: 100%)
Gene name: Tc00.1047053508919.140
Small ribosomal subunit protein eS1B Chain: W
Molecule details ›
Chain: W
Length: 254 amino acids
Theoretical weight: 29.13 KDa
Source organism: Trypanosoma cruzi
UniProt:
  • Canonical: Q4DZ41 (Residues: 8-261; Coverage: 97%)
Gene names: Tc00.1047053511001.18, Tc00.1047053511001.9
Sequence domains: Ribosomal S3Ae family
Eukaryotic translation initiation factor 3 (eIF-3) interacting protein, putative Chain: I
Molecule details ›
Chain: I
Length: 489 amino acids
Theoretical weight: 56.33 KDa
Source organism: Trypanosoma cruzi
UniProt:
  • Canonical: Q4D5W3 (Residues: 1-489; Coverage: 100%)
Gene name: Tc00.1047053508169.90
Sequence domains: RNA polymerase I-associated factor PAF67
Eukaryotic translation initiation factor 3 subunit h Chain: H
Molecule details ›
Chain: H
Length: 334 amino acids
Theoretical weight: 38.41 KDa
Source organism: Trypanosoma cruzi
UniProt:
  • Canonical: Q4DSJ1 (Residues: 1-334; Coverage: 100%)
Gene name: Tc00.1047053508543.100
Eukaryotic translation initiation factor 3 subunit 7-like protein, putative Chain: A
Molecule details ›
Chain: A
Length: 502 amino acids
Theoretical weight: 57.49 KDa
Source organism: Trypanosoma cruzi
UniProt:
  • Canonical: Q4DCN0 (Residues: 1-502; Coverage: 100%)
Gene name: Tc00.1047053506943.160
Sequence domains: Eukaryotic translation initiation factor 3 subunit 7 (eIF-3)
40S ribosomal protein S4 Chain: l
Molecule details ›
Chain: l
Length: 273 amino acids
Theoretical weight: 30.94 KDa
Source organism: Trypanosoma cruzi
UniProt:
  • Canonical: O62594 (Residues: 1-273; Coverage: 100%)
Gene names: C3747_37g38, C3747_37g39, C3747_48g65, C3747_48g66, C4B63_170g17, C4B63_170g18, C4B63_170g19, C4B63_170g20, C4B63_170g21, C4B63_170g22, C4B63_46g76, C4B63_46g77, ECC02_009338, ECC02_009339, RibpS4, rpS4-1, rpS4-2, rpS4-3
Sequence domains:
initiator tRNA-Met Chain: 1
Molecule details ›
Chain: 1
Length: 75 nucleotides
Theoretical weight: 24.26 KDa
Sequence domains: tRNA
18S Chain: 0
Molecule details ›
Chain: 0
Length: 2319 nucleotides
Theoretical weight: 746.7 KDa
Sequence domains: Eukaryotic small subunit ribosomal RNA

Ligands and Environments

3 bound ligands:
Ligand ZN 1 x ZN
Ligand MG 1 x MG
Ligand GNP 1 x GNP
No modified residues

Experiments and Validation Details

Entry percentile scores
Resolution: 3.33Å
Relevant EMDB volumes: EMD-11893

Quick links

Citations

1 review citation

The molecular basis of translation initiation and its regulation in eukaryotes.
Brito Querido et al. (2023)
9 other articles

1 mention without citation

Structural Differences in Translation Initiation between Pathogenic Trypanosomatids and Their Mammalian Hosts.
Bochler et al. (2020)