9HQV | pdb_00009hqv

Cryo-EM structure of the small subunit of the mitochondrial ribosome from Toxoplasma gondii


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.52 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

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This is version 1.0 of the entry. See complete history


Literature

Numerous rRNA molecules form the apicomplexan mitoribosome via repurposed protein and RNA elements.

Shikha, S.Tobiasson, V.Ferreira Silva, M.Ovciarikova, J.Beraldi, D.Muhleip, A.Sheiner, L.

(2025) Nat Commun 16: 817-817

  • DOI: https://doi.org/10.1038/s41467-025-56057-9
  • Primary Citation of Related Structures:  
    9HQV, 9I05

  • PubMed Abstract: 

    Mitochondrial ribosomes (mitoribosomes) are essential, and their function of synthesising mitochondrial proteins is universal. The core of almost all mitoribosomes is formed from a small number of long and self-folding rRNA molecules. In contrast, the mitoribosome of the apicomplexan parasite Toxoplasma gondii assembles from over 50 extremely short rRNA molecules. Here, we use cryo-EM to discover the features that enable this unusual mitoribosome to perform its function. We reveal that poly-A tails added to rRNA molecules are integrated into the ribosome, and we demonstrate their essentiality for mitoribosome formation and for parasite survival. This is a distinct function for poly-A tails, which are otherwise known primarily as stabilisers of messenger RNAs. Furthermore, while ribosomes typically consist of unique rRNA sequences, here nine sequences are used twice, each copy integrated in a different mitoribosome domain, revealing one of the mechanisms enabling the extreme mitochondrial genome reduction characteristic to Apicomplexa and to a large group of related microbial eukaryotes. Finally, several transcription factor-like proteins are repurposed to compensate for reduced or lost critical ribosomal domains, including members of the ApiAP2 family thus far considered to be DNA-binding transcription factors.


  • Organizational Affiliation
    • School of Infection and Immunity, University of Glasgow, Glasgow, Scotland, UK.

Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Enoyl-CoA hydratase/isomerase family proteinA [auth BA]716Toxoplasma gondiiMutation(s): 0 
EC: 3.1.2.4
UniProt
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
mS75B [auth BB]25Toxoplasma gondiiMutation(s): 0 
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Pentatricopeptide repeat domain-containing proteinC [auth BC]686Toxoplasma gondiiMutation(s): 0 
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
mS92D [auth BD]147Toxoplasma gondiiMutation(s): 0 
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein, uS2mE [auth Ba]160Toxoplasma gondiiMutation(s): 0 
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Putative 30S ribosomal protein S5F [auth Bb]1,140Toxoplasma gondiiMutation(s): 0 
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
Putative mitochondrial ribosomal protein s6-2G [auth Bc]163Toxoplasma gondiiMutation(s): 0 
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
Putative ribosomal protein S8H [auth Bd]129Toxoplasma gondiiMutation(s): 0 
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
Putative ribosomal protein S9I [auth Be]530Toxoplasma gondiiMutation(s): 0 
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
uS10mJ [auth Bf]239Toxoplasma gondiiMutation(s): 0 
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
Putative ribosomal protein S11K [auth Bg]393Toxoplasma gondiiMutation(s): 0 
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
Putative 30S ribosomal protein S12L [auth Bh]594Toxoplasma gondiiMutation(s): 0 
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
us13mM [auth Bi]110Toxoplasma gondiiMutation(s): 0 
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
Putative ribosomal protein S14N [auth Bj]112Toxoplasma gondiiMutation(s): 0 
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
Putative 30S ribosomal protein S15O [auth Bk]395Toxoplasma gondiiMutation(s): 0 
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
Putative 30S ribosomal protein S16P [auth Bl]167Toxoplasma gondiiMutation(s): 0 
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
Putative ribosomal protein S17Q [auth Bm]116Toxoplasma gondiiMutation(s): 0 
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
Putative ribosomal protein S18R [auth Bn]738Toxoplasma gondiiMutation(s): 0 
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein, bS21mS [auth Bo]243Toxoplasma gondiiMutation(s): 0 
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
mS23T [auth Bp]377Toxoplasma gondiiMutation(s): 0 
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
Mitochondrial ribosomal protein, mS26U [auth Bq]447Toxoplasma gondiiMutation(s): 0 
UniProt
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Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein mS29V [auth Br]545Toxoplasma gondiiMutation(s): 0 
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Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
DNA double-strand break repair rad50 ATPaseW [auth Bs]616Toxoplasma gondiiMutation(s): 0 
UniProt
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Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
mS34X [auth Bt]302Toxoplasma gondiiMutation(s): 0 
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Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein mS35 mitochondrial conserved domain-containing proteinY [auth Bu]584Toxoplasma gondiiMutation(s): 0 
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Entity ID: 26
MoleculeChains Sequence LengthOrganismDetailsImage
CHCH domain-containing proteinZ [auth Bv]138Toxoplasma gondiiMutation(s): 0 
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Entity ID: 27
MoleculeChains Sequence LengthOrganismDetailsImage
Mitochondrial mRNA-processing protein COX24 C-terminal domain-containing proteinAA [auth Bx]263Toxoplasma gondiiMutation(s): 0 
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Entity ID: 28
MoleculeChains Sequence LengthOrganismDetailsImage
Homeodomain-like containing proteinBA [auth By]597Toxoplasma gondiiMutation(s): 0 
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Entity ID: 29
MoleculeChains Sequence LengthOrganismDetailsImage
mS45CA [auth Bz]531Toxoplasma gondiiMutation(s): 0 
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Entity ID: 30
MoleculeChains Sequence LengthOrganismDetailsImage
UNK1DA [auth Ua]20Toxoplasma gondiiMutation(s): 0 
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Entity ID: 31
MoleculeChains Sequence LengthOrganismDetailsImage
UNK2EA [auth Ub]7Toxoplasma gondiiMutation(s): 0 
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Entity ID: 32
MoleculeChains Sequence LengthOrganismDetailsImage
UNK3FA [auth Uc]10Toxoplasma gondiiMutation(s): 0 
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Entity ID: 33
MoleculeChains Sequence LengthOrganismDetailsImage
UNK4GA [auth Ud]72Toxoplasma gondiiMutation(s): 0 
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Entity ID: 34
MoleculeChains Sequence LengthOrganismDetailsImage
Chain UhHA [auth Uh]56Toxoplasma gondiiMutation(s): 0 
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Entity ID: 35
MoleculeChains Sequence LengthOrganismDetailsImage
Unknown peptideIA [auth Ui],
KA [auth Uk]
13Toxoplasma gondiiMutation(s): 0 
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Entity ID: 36
MoleculeChains Sequence LengthOrganismDetailsImage
Chain UjJA [auth Uj]60Toxoplasma gondiiMutation(s): 0 
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Entity ID: 37
MoleculeChains Sequence LengthOrganismDetailsImage
GLY-ARG-SER-LYS-VAL-LEU-ILE-ARG-ARG-LEU-LYS-GLU-ARG-ALA-LYS-LYS-GLU-ALA-GLU-LYS-LYS-ALALA [auth Ul]22Toxoplasma gondiiMutation(s): 0 
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Entity ID: 38
MoleculeChains Sequence LengthOrganismDetailsImage
ARG-ALA-GLU-LEU-VAL-ALA-ALA-GLN-VAL-ARG-GLU-LYS-LEU-ALA-ILE-LYS-MET-ALA-ASN-ALA-LEU-ALAMA [auth Um]22Toxoplasma gondiiMutation(s): 0 
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Entity ID: 39
MoleculeChains Sequence LengthOrganismDetailsImage
Chain UnNA [auth Un]24Toxoplasma gondiiMutation(s): 0 
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Entity ID: 40
MoleculeChains Sequence LengthOrganismDetailsImage
chain UoOA [auth Uo]26Toxoplasma gondiiMutation(s): 0 
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Entity ID: 41
MoleculeChains Sequence LengthOrganismDetailsImage
chain UpPA [auth Up]24Toxoplasma gondiiMutation(s): 0 
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Entity ID: 42
MoleculeChains Sequence LengthOrganismDetailsImage
chain UqQA [auth Uq]32Toxoplasma gondiiMutation(s): 0 
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Entity ID: 43
MoleculeChains Sequence LengthOrganismDetailsImage
mS117RA [auth Ya]551Toxoplasma gondiiMutation(s): 0 
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Entity ID: 44
MoleculeChains Sequence LengthOrganismDetailsImage
ATP-dependent Clp protease proteolytic subunit,related proteinSA [auth Yb]1,048Toxoplasma gondiiMutation(s): 0 
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Entity ID: 45
MoleculeChains Sequence LengthOrganismDetailsImage
mS119TA [auth Yc]268Toxoplasma gondiiMutation(s): 0 
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Entity ID: 46
MoleculeChains Sequence LengthOrganismDetailsImage
mS120UA [auth Yd]680Toxoplasma gondiiMutation(s): 0 
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Entity ID: 47
MoleculeChains Sequence LengthOrganismDetailsImage
mS121VA [auth Ye]304Toxoplasma gondiiMutation(s): 0 
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Entity ID: 48
MoleculeChains Sequence LengthOrganismDetailsImage
Macro domain-containing proteinWA [auth Yf]698Toxoplasma gondiiMutation(s): 0 
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Entity ID: 49
MoleculeChains Sequence LengthOrganismDetailsImage
Thioredoxin domain-containing proteinXA [auth Yg]940Toxoplasma gondiiMutation(s): 0 
UniProt
Find proteins for S8F8D3 (Toxoplasma gondii (strain ATCC 50611 / Me49))
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Entity ID: 50
MoleculeChains Sequence LengthOrganismDetailsImage
mS124YA [auth Yh]280Toxoplasma gondiiMutation(s): 0 
UniProt
Find proteins for A0A0F7VBJ0 (Toxoplasma gondii (strain ATCC 50861 / VEG))
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Entity ID: 51
MoleculeChains Sequence LengthOrganismDetailsImage
mS125ZA [auth Yi]930Toxoplasma gondiiMutation(s): 0 
UniProt
Find proteins for S8G3J1 (Toxoplasma gondii (strain ATCC 50611 / Me49))
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Entity ID: 52
MoleculeChains Sequence LengthOrganismDetailsImage
DnaJ domain-containing proteinAB [auth Yj]233Toxoplasma gondiiMutation(s): 0 
UniProt
Find proteins for A0A125YYG6 (Toxoplasma gondii (strain ATCC 50611 / Me49))
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Entity ID: 53
MoleculeChains Sequence LengthOrganismDetailsImage
RAP domain-containing proteinBB [auth Yk]1,547Toxoplasma gondiiMutation(s): 0 
UniProt
Find proteins for S8GUD6 (Toxoplasma gondii (strain ATCC 50611 / Me49))
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Entity ID: 54
MoleculeChains Sequence LengthOrganismDetailsImage
mS128CB [auth Yl]316Toxoplasma gondiiMutation(s): 0 
UniProt
Find proteins for S8GU15 (Toxoplasma gondii (strain ATCC 50611 / Me49))
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Entity ID: 55
MoleculeChains Sequence LengthOrganismDetailsImage
RAP domain-containing proteinDB [auth Ym]801Toxoplasma gondiiMutation(s): 0 
UniProt
Find proteins for S8F0U0 (Toxoplasma gondii (strain ATCC 50611 / Me49))
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Entity ID: 56
MoleculeChains Sequence LengthOrganismDetailsImage
AP2 domain transcription factor AP2IX-6EB [auth Yn]432Toxoplasma gondiiMutation(s): 0 
UniProt
Find proteins for S8G8E7 (Toxoplasma gondii (strain ATCC 50611 / Me49))
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Entity ID: 57
MoleculeChains Sequence LengthOrganismDetailsImage
mS131FB [auth Yo]421Toxoplasma gondiiMutation(s): 0 
UniProt
Find proteins for A0A125YG13 (Toxoplasma gondii (strain ATCC 50611 / Me49))
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Entity ID: 58
MoleculeChains Sequence LengthOrganismDetailsImage
mS132GB [auth Yp]181Toxoplasma gondiiMutation(s): 0 
UniProt
Find proteins for S8G684 (Toxoplasma gondii (strain ATCC 50611 / Me49))
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Entity ID: 59
MoleculeChains Sequence LengthOrganismDetailsImage
Acylphosphatase-like domain-containing proteinHB [auth Yr]235Toxoplasma gondiiMutation(s): 0 
UniProt
Find proteins for A0A125YXT1 (Toxoplasma gondii (strain ATCC 50611 / Me49))
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Entity ID: 60
MoleculeChains Sequence LengthOrganismDetailsImage
mS135IB [auth Ys]181Toxoplasma gondiiMutation(s): 0 
UniProt
Find proteins for S8GML4 (Toxoplasma gondii (strain ATCC 50611 / Me49))
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Entity ID: 61
MoleculeChains Sequence LengthOrganismDetailsImage
mS136JB [auth Yt]475Toxoplasma gondiiMutation(s): 0 
UniProt
Find proteins for S8EW95 (Toxoplasma gondii (strain ATCC 50611 / Me49))
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Entity ID: 62
MoleculeChains Sequence LengthOrganismDetailsImage
mS137KB [auth Yu]367Toxoplasma gondiiMutation(s): 0 
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Entity ID: 63
MoleculeChains Sequence LengthOrganismDetailsImage
mS133LB [auth Yq]302Toxoplasma gondiiMutation(s): 0 
UniProt
Find proteins for A0A125YMK3 (Toxoplasma gondii (strain ATCC 50611 / Me49))
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Entity ID: 87
MoleculeChains Sequence LengthOrganismDetailsImage
mS138JC [auth Yv]419Toxoplasma gondiiMutation(s): 0 
UniProt
Find proteins for S8GBT4 (Toxoplasma gondii (strain ATCC 50611 / Me49))
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Entity ID: 64
MoleculeChains LengthOrganismImage
SSU-1MB [auth SA]91Toxoplasma gondii
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Entity ID: 65
MoleculeChains LengthOrganismImage
SSU-2NB [auth SB]28Toxoplasma gondii
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Entity ID: 66
MoleculeChains LengthOrganismImage
SSU-3OB [auth SC]23Toxoplasma gondii
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Entity ID: 67
MoleculeChains LengthOrganismImage
SSU-4PB [auth SD]47Toxoplasma gondii
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Entity ID: 68
MoleculeChains LengthOrganismImage
SSU-5QB [auth SE]73Toxoplasma gondii
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Entity ID: 69
MoleculeChains LengthOrganismImage
SSU-6RB [auth SF]120Toxoplasma gondii
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Entity ID: 70
MoleculeChains LengthOrganismImage
SSU-7SB [auth SG]26Toxoplasma gondii
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Entity ID: 71
MoleculeChains LengthOrganismImage
SSU-8TB [auth SH]25Toxoplasma gondii
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Entity ID: 72
MoleculeChains LengthOrganismImage
SSU-9UB [auth SI]53Toxoplasma gondii
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Entity ID: 73
MoleculeChains LengthOrganismImage
SSU-10VB [auth SJ]93Toxoplasma gondii
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Entity ID: 74
MoleculeChains LengthOrganismImage
SSU-11WB [auth SK]114Toxoplasma gondii
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Entity ID: 75
MoleculeChains LengthOrganismImage
SSU-12XB [auth SL]28Toxoplasma gondii
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Entity ID: 76
MoleculeChains LengthOrganismImage
SSU-13YB [auth SM]75Toxoplasma gondii
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Entity ID: 77
MoleculeChains LengthOrganismImage
SSU-14ZB [auth SN]24Toxoplasma gondii
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Entity ID: 78
MoleculeChains LengthOrganismImage
SSU-15AC [auth SO]16Toxoplasma gondii
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Entity ID: 79
MoleculeChains LengthOrganismImage
SSU-16BC [auth SP]33Toxoplasma gondii
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Entity ID: 80
MoleculeChains LengthOrganismImage
SSU-17CC [auth SQ]56Toxoplasma gondii
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Entity ID: 81
MoleculeChains LengthOrganismImage
SSU-18DC [auth SR]34Toxoplasma gondii
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Entity ID: 82
MoleculeChains LengthOrganismImage
SSU-19EC [auth SS]12Toxoplasma gondii
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Entity ID: 83
MoleculeChains LengthOrganismImage
SSU-20FC [auth ST]24Toxoplasma gondii
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Entity ID: 84
MoleculeChains LengthOrganismImage
SSU-21GC [auth SU]54Toxoplasma gondii
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Entity ID: 85
MoleculeChains LengthOrganismImage
tRNA E-siteHC [auth TP]21Toxoplasma gondii
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Entity ID: 86
MoleculeChains LengthOrganismImage
Chain UCIC [auth UC]31Toxoplasma gondii
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Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.52 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.21rc1_5058:

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Wellcome TrustUnited Kingdom--

Revision History  (Full details and data files)

  • Version 1.0: 2025-06-11
    Type: Initial release