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 9I05 | pdb_00009i05

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


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.20 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

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This is version 1.1 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 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.

Macromolecule Content 

  • Total Structure Weight: 3,935.33 kDa 
  • Atom Count: 171,368 
  • Modeled Residue Count: 17,927 
  • Deposited Residue Count: 31,577 
  • Unique protein chains: 75
  • Unique nucleic acid chains: 32

Macromolecules


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Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Putative LSU ribosomal protein L2PA [auth Aa]578Toxoplasma gondiiMutation(s): 0 
UniProt
Find proteins for A0A7J6KET1 (Toxoplasma gondii)
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Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL3mB [auth Ab]514Toxoplasma gondiiMutation(s): 0 
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Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL4mC [auth Ac]802Toxoplasma gondiiMutation(s): 0 
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Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
HECT-domain (Ubiquitin-transferase) domain-containing proteinD [auth Ad]392Toxoplasma gondiiMutation(s): 0 
UniProt
Find proteins for A0A7J6K7T4 (Toxoplasma gondii)
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Entity ID: 5
MoleculeChains  Sequence LengthOrganismDetailsImage
Ribosomal protein L9, N-terminal domain-containing proteinE [auth Ae]492Toxoplasma gondiiMutation(s): 0 
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Entity ID: 6
MoleculeChains  Sequence LengthOrganismDetailsImage
Putative ribosomal protein L11F [auth Af]180Toxoplasma gondiiMutation(s): 0 
UniProt
Find proteins for A0A7J6KEF6 (Toxoplasma gondii)
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Entity ID: 7
MoleculeChains  Sequence LengthOrganismDetailsImage
Putative 50S ribosomal protein L13G [auth Ag]231Toxoplasma gondiiMutation(s): 0 
UniProt
Find proteins for A0A7J6K0U2 (Toxoplasma gondii)
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Entity ID: 8
MoleculeChains  Sequence LengthOrganismDetailsImage
Putative LSU ribosomal protein L14PH [auth Ah]122Toxoplasma gondiiMutation(s): 0 
UniProt
Find proteins for A0A7J6K196 (Toxoplasma gondii)
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Entity ID: 9
MoleculeChains  Sequence LengthOrganismDetailsImage
Ribosomal protein L15, putativeI [auth Ai]638Toxoplasma gondiiMutation(s): 0 
UniProt
Find proteins for S8GIU7 (Toxoplasma gondii (strain ATCC 50611 / Me49))
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Entity ID: 10
MoleculeChains  Sequence LengthOrganismDetailsImage
Putative 50S ribosomal protein L16J [auth Aj]187Toxoplasma gondiiMutation(s): 0 
UniProt
Find proteins for A0A7J6K7Z7 (Toxoplasma gondii)
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Entity ID: 11
MoleculeChains  Sequence LengthOrganismDetailsImage
Putative 50S ribosomal protein L17K [auth Ak]247Toxoplasma gondiiMutation(s): 0 
UniProt
Find proteins for A0A7J6KEY9 (Toxoplasma gondii)
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Entity ID: 12
MoleculeChains  Sequence LengthOrganismDetailsImage
50S ribosomal protein L19, chloroplasticL [auth Al]744Toxoplasma gondiiMutation(s): 0 
UniProt
Find proteins for A0A7J6JZ22 (Toxoplasma gondii)
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Entity ID: 13
MoleculeChains  Sequence LengthOrganismDetailsImage
Putative ribosomal protein L20M [auth Am]121Toxoplasma gondiiMutation(s): 0 
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Find proteins for B9PY19 (Toxoplasma gondii)
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Entity ID: 14
MoleculeChains  Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein bL21mN [auth An]681Toxoplasma gondiiMutation(s): 0 
UniProt
Find proteins for A0A7J6K7U7 (Toxoplasma gondii)
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Entity ID: 15
MoleculeChains  Sequence LengthOrganismDetailsImage
Ribosomal L22p/L17e proteinO [auth Ao]573Toxoplasma gondiiMutation(s): 0 
UniProt
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Entity ID: 16
MoleculeChains  Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL23mP [auth Ap]253Toxoplasma gondiiMutation(s): 0 
UniProt
Find proteins for A0A7J6K299 (Toxoplasma gondii)
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Entity ID: 17
MoleculeChains  Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL24cQ [auth Aq]438Toxoplasma gondiiMutation(s): 0 
UniProt
Find proteins for A0A7J6JXG2 (Toxoplasma gondii)
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Entity ID: 18
MoleculeChains  Sequence LengthOrganismDetailsImage
Ribosomal l25 family proteinR [auth Ar]739Toxoplasma gondiiMutation(s): 0 
UniProt
Find proteins for S8ER88 (Toxoplasma gondii (strain ATCC 50611 / Me49))
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Entity ID: 19
MoleculeChains  Sequence LengthOrganismDetailsImage
bL27mS [auth As]391Toxoplasma gondiiMutation(s): 0 
UniProt
Find proteins for S8GME4 (Toxoplasma gondii (strain ATCC 50611 / Me49))
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Entity ID: 20
MoleculeChains  Sequence LengthOrganismDetailsImage
Putative ribosomal protein L28T [auth At]282Toxoplasma gondiiMutation(s): 0 
UniProt
Find proteins for A0A7J6K129 (Toxoplasma gondii)
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Entity ID: 21
MoleculeChains  Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL29mU [auth Au]236Toxoplasma gondiiMutation(s): 0 
UniProt
Find proteins for A0A7J6K1F8 (Toxoplasma gondii)
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Entity ID: 22
MoleculeChains  Sequence LengthOrganismDetailsImage
bL32mV [auth Av]88Toxoplasma gondiiMutation(s): 0 
UniProt
Find proteins for A0A7J6K9L3 (Toxoplasma gondii)
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Entity ID: 23
MoleculeChains  Sequence LengthOrganismDetailsImage
Putative 50S ribosomal protein L33W [auth Aw]126Toxoplasma gondiiMutation(s): 0 
UniProt
Find proteins for A0A7J6JWI3 (Toxoplasma gondii)
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Entity ID: 24
MoleculeChains  Sequence LengthOrganismDetailsImage
bL35mX [auth Ax]352Toxoplasma gondiiMutation(s): 0 
UniProt
Find proteins for A0A7J6KEG8 (Toxoplasma gondii)
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Entity ID: 25
MoleculeChains  Sequence LengthOrganismDetailsImage
bL36mY [auth Ay]200Toxoplasma gondiiMutation(s): 0 
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Entity ID: 26
MoleculeChains  Sequence LengthOrganismDetailsImage
mL40Z [auth Az]293Toxoplasma gondiiMutation(s): 0 
UniProt
Find proteins for A0A7J6KCG7 (Toxoplasma gondii)
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Entity ID: 27
MoleculeChains  Sequence LengthOrganismDetailsImage
Putative 60S ribosomal protein L2797Toxoplasma gondiiMutation(s): 0 
UniProt
Find proteins for A0A7J6JYF7 (Toxoplasma gondii)
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Entity ID: 28
MoleculeChains  Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein mL43BA [auth AB]203Toxoplasma gondiiMutation(s): 0 
UniProt
Find proteins for A0A7J6KC95 (Toxoplasma gondii)
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Entity ID: 29
MoleculeChains  Sequence LengthOrganismDetailsImage
Ribosomal protein L46CA [auth AC]598Toxoplasma gondiiMutation(s): 0 
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Find proteins for A0A7J6JX23 (Toxoplasma gondii)
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Entity ID: 30
MoleculeChains  Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein mL49DA [auth AD]310Toxoplasma gondiiMutation(s): 0 
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Find proteins for A0A7J6JUD4 (Toxoplasma gondii)
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Entity ID: 31
MoleculeChains  Sequence LengthOrganismDetailsImage
mL53EA [auth AE]217Toxoplasma gondiiMutation(s): 0 
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Find proteins for A0A7J6JX69 (Toxoplasma gondii)
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Entity ID: 32
MoleculeChains  Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein mL54FA [auth AF]515Toxoplasma gondiiMutation(s): 0 
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Entity ID: 33
MoleculeChains  Sequence LengthOrganismDetailsImage
BIR proteinGA [auth AG]271Toxoplasma gondiiMutation(s): 0 
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Find proteins for A0A7J6K0B0 (Toxoplasma gondii)
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Entity ID: 34
MoleculeChains  Sequence LengthOrganismDetailsImage
mL102HA [auth AH]396Toxoplasma gondiiMutation(s): 0 
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Find proteins for A0A0F7V869 (Toxoplasma gondii (strain ATCC 50861 / VEG))
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Entity ID: 35
MoleculeChains  Sequence LengthOrganismDetailsImage
RAP domain-containing proteinIA [auth AI]656Toxoplasma gondiiMutation(s): 0 
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Find proteins for A0A7J6KFM0 (Toxoplasma gondii)
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Entity ID: 36
MoleculeChains  Sequence LengthOrganismDetailsImage
mL130JA [auth Xa]544Toxoplasma gondiiMutation(s): 0 
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Entity ID: 37
MoleculeChains  Sequence LengthOrganismDetailsImage
RRM domain-containing proteinKA [auth Xb]664Toxoplasma gondiiMutation(s): 0 
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Entity ID: 38
MoleculeChains  Sequence LengthOrganismDetailsImage
mL132LA [auth Xc]198Toxoplasma gondiiMutation(s): 0 
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Entity ID: 39
MoleculeChains  Sequence LengthOrganismDetailsImage
RAP domain-containing proteinMA [auth Xd]903Toxoplasma gondiiMutation(s): 0 
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Entity ID: 40
MoleculeChains  Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL24cNA [auth Xe]229Toxoplasma gondiiMutation(s): 0 
UniProt
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Entity ID: 41
MoleculeChains  Sequence LengthOrganismDetailsImage
FAS1 domain-containing proteinOA [auth Xf]706Toxoplasma gondiiMutation(s): 0 
UniProt
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Entity ID: 42
MoleculeChains  Sequence LengthOrganismDetailsImage
DUF6832 domain-containing proteinPA [auth Xg]486Toxoplasma gondiiMutation(s): 0 
Gene Names: TGRH88_010990
UniProt
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Entity ID: 43
MoleculeChains  Sequence LengthOrganismDetailsImage
RAP domain-containing proteinQA [auth Xh]632Toxoplasma gondiiMutation(s): 0 
UniProt
Find proteins for A0A7J6KAP7 (Toxoplasma gondii)
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Entity ID: 44
MoleculeChains  Sequence LengthOrganismDetailsImage
RAP domain-containing proteinRA [auth Xi]445Toxoplasma gondiiMutation(s): 0 
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Entity ID: 45
MoleculeChains  Sequence LengthOrganismDetailsImage
RAP domain-containing proteinSA [auth Xj]1,012Toxoplasma gondiiMutation(s): 0 
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Find proteins for A0A7J6K4L1 (Toxoplasma gondii)
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Entity ID: 46
MoleculeChains  Sequence LengthOrganismDetailsImage
RNA recognition motif-containing proteinTA [auth Xk]244Toxoplasma gondiiMutation(s): 0 
UniProt
Find proteins for A0A7J6KGH2 (Toxoplasma gondii)
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Entity ID: 47
MoleculeChains  Sequence LengthOrganismDetailsImage
RAP domain-containing proteinDB [auth Xv],
UA [auth Xl]
645Toxoplasma gondiiMutation(s): 0 
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Entity ID: 48
MoleculeChains  Sequence LengthOrganismDetailsImage
Macro domain-containing proteinVA [auth Xm]631Toxoplasma gondiiMutation(s): 0 
UniProt
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Entity ID: 49
MoleculeChains  Sequence LengthOrganismDetailsImage
AP2 domain transcription factor AP2VIIb-2WA [auth Xn]568Toxoplasma gondiiMutation(s): 0 
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Entity ID: 50
MoleculeChains  Sequence LengthOrganismDetailsImage
mL144XA [auth Xo]953Toxoplasma gondiiMutation(s): 0 
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Entity ID: 51
MoleculeChains  Sequence LengthOrganismDetailsImage
Peptidyl-prolyl cis-trans isomeraseYA [auth Xp]283Toxoplasma gondiiMutation(s): 0 
EC: 5.2.1.8
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Entity ID: 52
MoleculeChains  Sequence LengthOrganismDetailsImage
mL146ZA [auth Xq]1,112Toxoplasma gondiiMutation(s): 0 
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Entity ID: 53
MoleculeChains  Sequence LengthOrganismDetailsImage
RAP domain-containing proteinAB [auth Xr]713Toxoplasma gondiiMutation(s): 0 
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Entity ID: 54
MoleculeChains  Sequence LengthOrganismDetailsImage
mL149BB [auth Xs]493Toxoplasma gondiiMutation(s): 0 
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Entity ID: 55
MoleculeChains  Sequence LengthOrganismDetailsImage
mL148CB [auth Xt]123Toxoplasma gondiiMutation(s): 0 
UniProt
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Entity ID: 56
MoleculeChains  Sequence LengthOrganismDetailsImage
Transmembrane proteinEB [auth Xw]329Toxoplasma gondiiMutation(s): 0 
UniProt
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Entity ID: 57
MoleculeChains  Sequence LengthOrganismDetailsImage
mL152FB [auth Xx]300Toxoplasma gondiiMutation(s): 0 
UniProt
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Entity ID: 58
MoleculeChains  Sequence LengthOrganismDetailsImage
mL153GB [auth Xy]424Toxoplasma gondiiMutation(s): 0 
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Entity ID: 59
MoleculeChains  Sequence LengthOrganismDetailsImage
AP2 domain transcription factor AP2IV-1HB [auth Xz]425Toxoplasma gondiiMutation(s): 0 
UniProt
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Entity ID: 60
MoleculeChains  Sequence LengthOrganismDetailsImage
mL155IB [auth XA]310Toxoplasma gondiiMutation(s): 0 
UniProt
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Entity ID: 61
MoleculeChains  Sequence LengthOrganismDetailsImage
mL156JB [auth XB]198Toxoplasma gondiiMutation(s): 0 
UniProt
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Entity ID: 62
MoleculeChains  Sequence LengthOrganismDetailsImage
mL157KB [auth XC]305Toxoplasma gondiiMutation(s): 0 
UniProt
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Entity ID: 63
MoleculeChains  Sequence LengthOrganismDetailsImage
mL158LB [auth XD]236Toxoplasma gondiiMutation(s): 0 
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Entity ID: 64
MoleculeChains  Sequence LengthOrganismDetailsImage
mL159MB [auth XE]150Toxoplasma gondiiMutation(s): 0 
UniProt
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Entity ID: 65
MoleculeChains  Sequence LengthOrganismDetailsImage
mL160NB [auth XF]141Toxoplasma gondiiMutation(s): 0 
UniProt
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Entity ID: 66
MoleculeChains  Sequence LengthOrganismDetailsImage
mL161OB [auth XG]476Toxoplasma gondiiMutation(s): 0 
UniProt
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Entity ID: 67
MoleculeChains  Sequence LengthOrganismDetailsImage
Ribosomal protein RPL22PB [auth XH]341Toxoplasma gondiiMutation(s): 0 
UniProt
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Entity ID: 68
MoleculeChains  Sequence LengthOrganismDetailsImage
Transmembrane proteinQB [auth XI]202Toxoplasma gondiiMutation(s): 0 
UniProt
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Entity ID: 69
MoleculeChains  Sequence LengthOrganismDetailsImage
Chain UaRB [auth XJ]280Toxoplasma gondiiMutation(s): 0 
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Entity ID: 70
MoleculeChains  Sequence LengthOrganismDetailsImage
Ribosomal l25 family proteinSB [auth Ua]26Toxoplasma gondiiMutation(s): 0 
UniProt
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Entity ID: 71
MoleculeChains  Sequence LengthOrganismDetailsImage
Chain UcTB [auth Ub]21Toxoplasma gondiiMutation(s): 0 
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Entity ID: 72
MoleculeChains  Sequence LengthOrganismDetailsImage
Chain UdUB [auth Uc]19Toxoplasma gondiiMutation(s): 0 
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Entity ID: 73
MoleculeChains  Sequence LengthOrganismDetailsImage
Chain UeVB [auth Ud]28Toxoplasma gondiiMutation(s): 0 
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Entity ID: 74
MoleculeChains  Sequence LengthOrganismDetailsImage
Chain UfWB [auth Ue]13Toxoplasma gondiiMutation(s): 0 
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Entity ID: 75
MoleculeChains  Sequence LengthOrganismDetailsImage
LSU-1XB [auth Uf]6Toxoplasma gondiiMutation(s): 0 
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Entity ID: 76
MoleculeChains LengthOrganismImage
LSU-2YB [auth RA]35Toxoplasma gondii
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Entity ID: 77
MoleculeChains LengthOrganismImage
LSU-3ZB [auth RB]27Toxoplasma gondii
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Entity ID: 78
MoleculeChains LengthOrganismImage
LSU-4AC [auth RC]33Toxoplasma gondii
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Entity ID: 79
MoleculeChains LengthOrganismImage
LSU-5BC [auth RD]91Toxoplasma gondii
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Entity ID: 80
MoleculeChains LengthOrganismImage
LSU-6CC [auth RE]44Toxoplasma gondii
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Entity ID: 81
MoleculeChains LengthOrganismImage
LSU-7DC [auth RF]29Toxoplasma gondii
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Entity ID: 82
MoleculeChains LengthOrganismImage
LSU-8EC [auth RG]84Toxoplasma gondii
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Entity ID: 83
MoleculeChains LengthOrganismImage
LSU-9FC [auth RI]36Toxoplasma gondii
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Entity ID: 84
MoleculeChains LengthOrganismImage
LSU-10GC [auth RJ]59Toxoplasma gondii
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Entity ID: 85
MoleculeChains LengthOrganismImage
LSU-11HC [auth RK]10Toxoplasma gondii
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Entity ID: 86
MoleculeChains LengthOrganismImage
LSU-12IC [auth RL]178Toxoplasma gondii
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Entity ID: 87
MoleculeChains LengthOrganismImage
LSU-13JC [auth RM]71Toxoplasma gondii
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Entity ID: 88
MoleculeChains LengthOrganismImage
LSU-14KC [auth RN]26Toxoplasma gondii
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Entity ID: 89
MoleculeChains LengthOrganismImage
LSU-15LC [auth RO]26Toxoplasma gondii
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Entity ID: 90
MoleculeChains LengthOrganismImage
LSU-16MC [auth RP]11Toxoplasma gondii
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Entity ID: 91
MoleculeChains LengthOrganismImage
LSU-17NC [auth RQ]68Toxoplasma gondii
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Entity ID: 92
MoleculeChains LengthOrganismImage
LSU-18OC [auth RS]94Toxoplasma gondii
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Entity ID: 93
MoleculeChains LengthOrganismImage
LSU-19PC [auth RT]28Toxoplasma gondii
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Entity ID: 94
MoleculeChains LengthOrganismImage
LSU-20QC [auth RU]15Toxoplasma gondii
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Entity ID: 95
MoleculeChains LengthOrganismImage
LSU-21RC [auth RV]35Toxoplasma gondii
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Entity ID: 96
MoleculeChains LengthOrganismImage
LSU-22SC [auth RW]91Toxoplasma gondii
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Entity ID: 97
MoleculeChains LengthOrganismImage
LSU-23TC [auth RX]277Toxoplasma gondii
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Entity ID: 98
MoleculeChains LengthOrganismImage
LSU-24UC [auth RY]47Toxoplasma gondii
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Entity ID: 99
MoleculeChains LengthOrganismImage
LSU-25VC [auth RZ]45Toxoplasma gondii
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Entity ID: 100
MoleculeChains LengthOrganismImage
LSU-26WC [auth Ra]50Toxoplasma gondii
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Entity ID: 101
MoleculeChains LengthOrganismImage
LSU-27XC [auth Rb]28Toxoplasma gondii
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Entity ID: 102
MoleculeChains LengthOrganismImage
LSU-28YC [auth Rc]201Toxoplasma gondii
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Entity ID: 103
MoleculeChains LengthOrganismImage
LSU-29ZC [auth Rd]80Toxoplasma gondii
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Entity ID: 104
MoleculeChains LengthOrganismImage
LSU-30AD [auth Rf]29Toxoplasma gondii
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Entity ID: 105
MoleculeChains LengthOrganismImage
LSU-31BD [auth Rg]14Toxoplasma gondii
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Entity ID: 106
MoleculeChains LengthOrganismImage
LSU-32CD [auth Rh]49Toxoplasma gondii
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Entity ID: 107
MoleculeChains LengthOrganismImage
LSU-32DD [auth Ri]44Toxoplasma gondii
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Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.20 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.21rc1_5058:

Structure Validation

View Full Validation Report



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
  • Version 1.1: 2026-09-02
    Type: Remediation
    Reason: Metalloprotein remediation
    Changes: Data collection, Derived calculations, Structure summary