› 7aor

Electron Microscopy
3.5Å resolution

mt-SSU from Trypanosoma cruzi in complex with mt-IF-3.

Released:
DOI: 10.2210/pdb7aor/pdb
PDB entry 7aor coloured by chain, front view.
PDB entry 7aor coloured by chain, side view.
PDB entry 7aor coloured by chain, top view.
Source organisms:
Primary publication:
Structure of the mature kinetoplastids mitoribosome and insights into its large subunit biogenesis.
Soufari H, Waltz F, Parrot C, Durrieu-Gaillard S, Bochler A, Kuhn L, Sissler M, Hashem Y
Proc Natl Acad Sci U S A 117 29851-29861 (2020)
PMID: 33168716
Related structures: EMD-11846

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero 57-mer (preferred)
PDBe Complex ID:
PDB-CPX-104236 (preferred)
Entry contents:
55 distinct polypeptide molecules
1 distinct RNA molecule
Macromolecules (56 distinct):
Mitochondrial SSU ribosomal protein Chain: u
Molecule details ›
Chain: u
Length: 874 amino acids
Theoretical weight: 99.24 KDa
Source organism: Trypanosoma cruzi strain CL Brener
UniProt:
  • Canonical: Q4DIY1 (Residues: 1-874; Coverage: 100%)
Gene name: Tc00.1047053511445.130
mS33 Chain: s
Molecule details ›
Chain: s
Length: 180 amino acids
Theoretical weight: 20.96 KDa
Source organism: Trypanosoma cruzi strain CL Brener
UniProt:
  • Canonical: Q4CTU7 (Residues: 1-180; Coverage: 100%)
Gene name: Tc00.1047053507775.40
Small ribosomal subunit protein mS29 Chain: r
Molecule details ›
Chain: r
Length: 500 amino acids
Theoretical weight: 57.87 KDa
Source organism: Trypanosoma cruzi strain CL Brener
UniProt:
  • Canonical: Q4DW24 (Residues: 1-500; Coverage: 100%)
Gene name: Tc00.1047053507603.50
Sequence domains: Mitochondrial ribosomal death-associated protein 3
uS19 Chain: n
Molecule details ›
Chain: n
Length: 172 amino acids
Theoretical weight: 19.87 KDa
Source organism: Trypanosoma cruzi strain CL Brener
UniProt:
  • Canonical: Q4D583 (Residues: 1-172; Coverage: 100%)
Gene name: Tc00.1047053507927.90
uS14m Chain: h
Molecule details ›
Chain: h
Length: 166 amino acids
Theoretical weight: 19.81 KDa
Source organism: Trypanosoma cruzi strain CL Brener
UniProt:
  • Canonical: Q4DRG2 (Residues: 1-166; Coverage: 100%)
Gene name: Tc00.1047053508547.40
LysM domain-containing protein Chain: e
Molecule details ›
Chain: e
Length: 818 amino acids
Theoretical weight: 94.28 KDa
Source organism: Trypanosoma cruzi strain CL Brener
UniProt:
  • Canonical: Q4DEM5 (Residues: 1-818; Coverage: 100%)
Gene name: Tc00.1047053507941.10
Sequence domains: LysM domain
mS72 Chain: az
Molecule details ›
Chain: az
Length: 163 amino acids
Theoretical weight: 19.4 KDa
Source organism: Trypanosoma cruzi strain CL Brener
UniProt:
  • Canonical: Q4DX04 (Residues: 1-163; Coverage: 100%)
Gene name: Tc00.1047053510533.100
mS71 Chain: ay
Molecule details ›
Chain: ay
Length: 218 amino acids
Theoretical weight: 25.87 KDa
Source organism: Trypanosoma cruzi strain CL Brener
UniProt:
  • Canonical: Q4DX19 (Residues: 1-218; Coverage: 100%)
Gene name: Tc00.1047053508831.90
mS70 Chain: ax
Molecule details ›
Chain: ax
Length: 172 amino acids
Theoretical weight: 20.68 KDa
Source organism: Trypanosoma cruzi strain CL Brener
UniProt:
  • Canonical: Q4DLH4 (Residues: 1-172; Coverage: 100%)
Gene name: Tc00.1047053503823.70
mS69 Chain: aw
Molecule details ›
Chain: aw
Length: 186 amino acids
Theoretical weight: 21.67 KDa
Source organism: Trypanosoma cruzi strain CL Brener
UniProt:
  • Canonical: Q4D0Q8 (Residues: 1-186; Coverage: 100%)
Gene name: Tc00.1047053509571.10
Rhodanese domain-containing protein Chain: au
Molecule details ›
Chain: au
Length: 247 amino acids
Theoretical weight: 30.18 KDa
Source organism: Trypanosoma cruzi strain CL Brener
UniProt:
  • Canonical: Q4DX83 (Residues: 1-247; Coverage: 100%)
Gene name: Tc00.1047053506945.170
Sequence domains: Rhodanese-like domain
mS58 Chain: ak
Molecule details ›
Chain: ak
Length: 314 amino acids
Theoretical weight: 35.02 KDa
Source organism: Trypanosoma cruzi strain CL Brener
UniProt:
  • Canonical: Q4DTE7 (Residues: 1-314; Coverage: 100%)
Gene name: Tc00.1047053510311.160
mS57 Chain: aj
Molecule details ›
Chain: aj
Length: 396 amino acids
Theoretical weight: 46.27 KDa
Source organism: Trypanosoma cruzi strain CL Brener
UniProt:
  • Canonical: Q4DA51 (Residues: 1-396; Coverage: 100%)
Gene name: Tc00.1047053507019.60
mS55 Chain: ag
Molecule details ›
Chain: ag
Length: 581 amino acids
Theoretical weight: 67.01 KDa
Source organism: Trypanosoma cruzi strain CL Brener
UniProt:
  • Canonical: Q4DWR5 (Residues: 1-581; Coverage: 100%)
Gene name: Tc00.1047053508409.320
mS54 Chain: af
Molecule details ›
Chain: af
Length: 677 amino acids
Theoretical weight: 77.91 KDa
Source organism: Trypanosoma cruzi strain CL Brener
UniProt:
  • Canonical: Q4CVW1 (Residues: 1-677; Coverage: 100%)
Gene name: Tc00.1047053505555.30
mS53 Chain: ae
Molecule details ›
Chain: ae
Length: 678 amino acids
Theoretical weight: 76.25 KDa
Source organism: Trypanosoma cruzi strain CL Brener
UniProt:
  • Canonical: Q4D651 (Residues: 1-678; Coverage: 100%)
Gene name: Tc00.1047053504881.40
Mitochondrial SSU ribosomal protein Chain: l
Molecule details ›
Chain: l
Length: 714 amino acids
Theoretical weight: 81.42 KDa
Source organism: Trypanosoma cruzi strain CL Brener
UniProt:
  • Canonical: Q4E2R4 (Residues: 1-714; Coverage: 100%)
Gene name: Tc00.1047053504153.190
mS50 Chain: ac
Molecule details ›
Chain: ac
Length: 1152 amino acids
Theoretical weight: 129.01 KDa
Source organism: Trypanosoma cruzi strain CL Brener
UniProt:
  • Canonical: Q4CW80 (Residues: 1-1152; Coverage: 100%)
Gene name: Tc00.1047053510529.30
mS49 Chain: ab
Molecule details ›
Chain: ab
Length: 1175 amino acids
Theoretical weight: 136.2 KDa
Source organism: Trypanosoma cruzi strain CL Brener
UniProt:
  • Canonical: Q4DNX8 (Residues: 1-1175; Coverage: 100%)
Gene name: Tc00.1047053509099.80
Mitochondrial RNA binding protein 1 Chain: ad
Molecule details ›
Chain: ad
Length: 810 amino acids
Theoretical weight: 95.14 KDa
Source organism: Trypanosoma cruzi strain CL Brener
UniProt:
  • Canonical: Q4DV41 (Residues: 1-810; Coverage: 100%)
Gene name: Tc00.1047053508647.220
Mitochondrial ribosomal protein S18 Chain: m
Molecule details ›
Chain: m
Length: 319 amino acids
Theoretical weight: 37.2 KDa
Source organism: Trypanosoma cruzi strain CL Brener
UniProt:
  • Canonical: Q4E4E0 (Residues: 1-319; Coverage: 100%)
Gene name: Tc00.1047053510187.110
uS15m Chain: i
Molecule details ›
Chain: i
Length: 429 amino acids
Theoretical weight: 50.08 KDa
Source organism: Trypanosoma cruzi strain CL Brener
UniProt:
  • Canonical: Q4DS13 (Residues: 1-429; Coverage: 100%)
Gene name: Tc00.1047053507949.50
uS11m Chain: f
Molecule details ›
Chain: f
Length: 325 amino acids
Theoretical weight: 37.72 KDa
Source organism: Trypanosoma cruzi strain CL Brener
UniProt:
  • Canonical: Q4CT44 (Residues: 1-325; Coverage: 100%)
Gene name: Tc00.1047053503555.20
30S ribosomal protein S8 Chain: c
Molecule details ›
Chain: c
Length: 285 amino acids
Theoretical weight: 33.22 KDa
Source organism: Trypanosoma cruzi strain CL Brener
UniProt:
  • Canonical: Q4DY17 (Residues: 1-285; Coverage: 100%)
Gene name: Tc00.1047053506357.110
Sequence domains: Ribosomal protein S8
Ribosomal protein S9 Chain: d
Molecule details ›
Chain: d
Length: 445 amino acids
Theoretical weight: 50.34 KDa
Source organism: Trypanosoma cruzi strain CL Brener
UniProt:
  • Canonical: Q4DEW9 (Residues: 1-445; Coverage: 100%)
Gene name: Tc00.1047053510515.110
Sequence domains: Ribosomal protein S9/S16
mS73 Chain: ba
Molecule details ›
Chain: ba
Length: 217 amino acids
Theoretical weight: 24.78 KDa
Source organism: Trypanosoma cruzi strain CL Brener
UniProt:
  • Canonical: Q4D7F8 (Residues: 1-217; Coverage: 100%)
Gene name: Tc00.1047053511731.70
Ubiquitin-like domain-containing protein Chain: av
Molecule details ›
Chain: av
Length: 237 amino acids
Theoretical weight: 27.69 KDa
Source organism: Trypanosoma cruzi strain CL Brener
UniProt:
  • Canonical: Q4E2I9 (Residues: 1-237; Coverage: 100%)
Gene name: Tc00.1047053508479.310
Probable Zinc-ribbon domain-containing protein Chain: at
Molecule details ›
Chain: at
Length: 259 amino acids
Theoretical weight: 29.83 KDa
Source organism: Trypanosoma cruzi strain CL Brener
UniProt:
  • Canonical: Q4E1X5 (Residues: 1-259; Coverage: 100%)
Gene name: Tc00.1047053507993.33
Sequence domains: Probable Zinc-ribbon domain
A-kinase anchor protein 7-like phosphoesterase domain-containing protein Chain: ar
Molecule details ›
Chain: ar
Length: 268 amino acids
Theoretical weight: 30.78 KDa
Source organism: Trypanosoma cruzi strain CL Brener
UniProt:
  • Canonical: Q4DBB7 (Residues: 1-268; Coverage: 100%)
Gene name: Tc00.1047053509161.50
Sequence domains: AKAP7 2'5' RNA ligase-like domain
Opioid growth factor receptor (OGFr) conserved domain-containing protein Chain: aq
Molecule details ›
Chain: aq
Length: 299 amino acids
Theoretical weight: 34.34 KDa
Source organism: Trypanosoma cruzi strain CL Brener
UniProt:
  • Canonical: Q4E0X6 (Residues: 1-299; Coverage: 100%)
Gene name: Tc00.1047053508277.200
mS62 Chain: ap
Molecule details ›
Chain: ap
Length: 277 amino acids
Theoretical weight: 31.62 KDa
Source organism: Trypanosoma cruzi strain CL Brener
UniProt:
  • Canonical: Q4D014 (Residues: 1-277; Coverage: 100%)
Gene name: Tc00.1047053511803.50
Trans-sialidase Chain: ao
Molecule details ›
Chain: ao
Length: 283 amino acids
Theoretical weight: 32.92 KDa
Source organism: Trypanosoma cruzi strain CL Brener
UniProt:
  • Canonical: Q4D7Y5 (Residues: 1-283; Coverage: 100%)
Gene name: Tc00.1047053510755.80
mS56 Chain: ai
Molecule details ›
Chain: ai
Length: 410 amino acids
Theoretical weight: 47.86 KDa
Source organism: Trypanosoma cruzi strain CL Brener
UniProt:
  • Canonical: Q4D4C7 (Residues: 1-410; Coverage: 100%)
Gene name: Tc00.1047053506831.60
mS60 Chain: an
Molecule details ›
Chain: an
Length: 293 amino acids
Theoretical weight: 34.41 KDa
Source organism: Trypanosoma cruzi strain CL Brener
UniProt:
  • Canonical: Q4DJ95 (Residues: 1-293; Coverage: 100%)
Gene name: Tc00.1047053511815.100
3-hydroxyisobutyryl-CoA hydrolase Chain: z
Molecule details ›
Chain: z
Length: 1181 amino acids
Theoretical weight: 134.73 KDa
Source organism: Trypanosoma cruzi strain CL Brener
UniProt:
  • Canonical: Q4DD80 (Residues: 1-1181; Coverage: 100%)
Gene name: Tc00.1047053509747.30
Sequence domains: Enoyl-CoA hydratase/isomerase
Manganese/iron superoxide dismutase C-terminal domain-containing protein Chain: y
Molecule details ›
Chain: y
Length: 449 amino acids
Theoretical weight: 49.03 KDa
Source organism: Trypanosoma cruzi strain CL Brener
UniProt:
  • Canonical: Q4CSF0 (Residues: 1-449; Coverage: 100%)
Gene name: Tc00.1047053504129.30
Sequence domains: Iron/manganese superoxide dismutases, C-terminal domain
Manganese/iron superoxide dismutase C-terminal domain-containing protein Chain: x
Molecule details ›
Chain: x
Length: 345 amino acids
Theoretical weight: 39 KDa
Source organism: Trypanosoma cruzi strain CL Brener
UniProt:
  • Canonical: Q4CPX3 (Residues: 1-345; Coverage: 100%)
Gene name: Tc00.1047053511521.30
Sequence domains: Iron/manganese superoxide dismutases, C-terminal domain
Small ribosomal subunit protein mS41 Chain: w
Molecule details ›
Chain: w
Length: 186 amino acids
Theoretical weight: 22.39 KDa
Source organism: Trypanosoma cruzi strain CL Brener
UniProt:
  • Canonical: Q4DZS3 (Residues: 1-186; Coverage: 100%)
Gene name: Tc00.1047053507711.50
mS37 Chain: v
Molecule details ›
Chain: v
Length: 215 amino acids
Theoretical weight: 24.57 KDa
Source organism: Trypanosoma cruzi strain CL Brener
UniProt:
  • Canonical: Q4DRC8 (Residues: 1-215; Coverage: 100%)
Gene name: Tc00.1047053509693.30
mS38 Chain: bb
Molecule details ›
Chain: bb
Length: 238 amino acids
Theoretical weight: 26.5 KDa
Source organism: Trypanosoma cruzi strain CL Brener
UniProt:
  • Canonical: Q4DMI0 (Residues: 1-238; Coverage: 100%)
Gene name: Tc00.1047053508881.54
Trafficking protein particle complex subunit Chain: t
Molecule details ›
Chain: t
Length: 256 amino acids
Theoretical weight: 28.87 KDa
Source organism: Trypanosoma cruzi strain CL Brener
UniProt:
  • Canonical: Q4E2D1 (Residues: 1-256; Coverage: 100%)
Gene name: Tc00.1047053509979.230
mS59 Chain: al
Molecule details ›
Chain: al
Length: 308 amino acids
Theoretical weight: 35.61 KDa
Source organism: Trypanosoma cruzi strain CL Brener
UniProt:
  • Canonical: Q4DRU1 (Residues: 1-308; Coverage: 100%)
Gene name: Tc00.1047053510943.36
mS26 Chain: q
Molecule details ›
Chain: q
Length: 442 amino acids
Theoretical weight: 51.72 KDa
Source organism: Trypanosoma cruzi strain CL Brener
UniProt:
  • Canonical: Q4DUA8 (Residues: 1-442; Coverage: 100%)
Gene name: Tc00.1047053507011.90
mS23 Chain: p
Molecule details ›
Chain: p
Length: 308 amino acids
Theoretical weight: 34.87 KDa
Source organism: Trypanosoma cruzi strain CL Brener
UniProt:
  • Canonical: Q4DRR8 (Residues: 1-308; Coverage: 100%)
Gene name: Tc00.1047053506739.40
Chromosome passenger complex (CPC) protein INCENP N terminal Chain: Ca
Molecule details ›
Chain: Ca
Length: 603 amino acids
Theoretical weight: 73.12 KDa
Source organism: Trypanosoma cruzi strain CL Brener
UniProt:
  • Canonical: Q4E4S6 (Residues: 1-603; Coverage: 100%)
Gene name: Tc00.1047053508461.340
HMG box domain-containing protein Chain: g
Molecule details ›
Chain: g
Length: 193 amino acids
Theoretical weight: 23.03 KDa
Source organism: Trypanosoma cruzi strain CL Brener
UniProt:
  • Canonical: Q4DET1 (Residues: 1-193; Coverage: 100%)
Gene name: Tc00.1047053506175.80
bS16m Chain: j
Molecule details ›
Chain: j
Length: 189 amino acids
Theoretical weight: 22.42 KDa
Source organism: Trypanosoma cruzi strain CL Brener
UniProt:
  • Canonical: Q4D6Y0 (Residues: 1-189; Coverage: 100%)
Gene name: Tc00.1047053508813.70
bS6m Chain: b
Molecule details ›
Chain: b
Length: 160 amino acids
Theoretical weight: 19.19 KDa
Source organism: Trypanosoma cruzi strain CL Brener
UniProt:
  • Canonical: Q4DZA7 (Residues: 1-160; Coverage: 100%)
Gene name: Tc00.1047053504105.60
MURF5 Chain: bd
Molecule details ›
Chain: bd
Length: 90 amino acids
Theoretical weight: 10.81 KDa
Source organism: Trypanosoma cruzi strain CL Brener
Small ribosomal subunit protein uS5 C-terminal domain-containing protein Chain: a
Molecule details ›
Chain: a
Length: 434 amino acids
Theoretical weight: 49.82 KDa
Source organism: Trypanosoma cruzi strain CL Brener
UniProt:
  • Canonical: Q4DYR0 (Residues: 1-434; Coverage: 100%)
Gene name: Tc00.1047053507641.150
Sequence domains: Ribosomal protein S5, C-terminal domain
mt-iF3 Chain: bc
Molecule details ›
Chain: bc
Length: 376 amino acids
Theoretical weight: 42.91 KDa
Source organism: Trypanosoma cruzi strain CL Brener
UniProt:
  • Canonical: Q4D913 (Residues: 1-376; Coverage: 100%)
Gene name: Tc00.1047053507513.100
mS48 Chain: aa
Molecule details ›
Chain: aa
Length: 1827 amino acids
Theoretical weight: 206.53 KDa
Source organism: Trypanosoma cruzi strain CL Brener
UniProt:
  • Canonical: Q4DVD2 (Residues: 1-1827; Coverage: 100%)
Gene name: Tc00.1047053511217.90
30S Ribosomal protein S17-like protein Chain: k
Molecule details ›
Chain: k
Length: 309 amino acids
Theoretical weight: 35.84 KDa
Source organism: Trypanosoma cruzi
UniProt:
  • Canonical: A0A2V2XQ88 (Residues: 1-309; Coverage: 100%)
Gene name: C3747_1g649
Sequence domains: Ribosomal protein S17
Ribosome protein S12 Chain: be
Molecule details ›
Chain: be
Length: 82 amino acids
Theoretical weight: 9.81 KDa
Source organism: Trypanosoma cruzi
UniProt:
  • Canonical: A0A2H4T2H0 (Residues: 1-82; Coverage: 100%)
Sequence domains: Ribosomal protein S12
mS65 Chain: as
Molecule details ›
Chain: as
Length: 261 amino acids
Theoretical weight: 29.68 KDa
Source organism: Trypanosoma cruzi strain CL Brener
UniProt:
  • Canonical: Q4D4G1 (Residues: 1-261; Coverage: 100%)
Gene name: Tc00.1047053511653.40
RNA (478-MER) Chains: 2, A
Molecule details ›
Chains: 2, A
Length: 8129 nucleotides
Theoretical weight: 2616.41 KDa
Sequence domains:
  • Trypanosomatid mitochondrial large subunit ribosomal RNA
  • Trypanosomatid mitochondrial small subunit ribosomal RNA

    • Ligands and Environments

    4 bound ligands:
    Ligand GTP 1 x GTP
    Ligand MG 1 x MG
    Ligand UTP 1 x UTP
    Ligand ZN 4 x ZN
    No modified residues

    Experiments and Validation Details

    Entry percentile scores
    Resolution: 3.5Å
    Relevant EMDB volumes: EMD-11846

    Quick links

    Citations

    5 review citations

    A Comparative Perspective on Ribosome Biogenesis: Unity and Diversity Across the Tree of Life.
    Jüttner et al. (2022)
    4 more