9FI8 | pdb_00009fi8

SSU(head) structure derived from the SSU sample of the mitoribosome from T. gondii.


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.60 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Model: in silico
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This is version 1.1 of the entry. See complete history


Literature

Apicomplexan mitoribosome from highly fragmented rRNAs to a functional machine.

Wang, C.Kassem, S.Rocha, R.E.O.Sun, P.Nguyen, T.T.Kloehn, J.Liu, X.Brusini, L.Bonavoglia, A.Barua, S.Boissier, F.Lucia Del Cistia, M.Peng, H.Tang, X.Xie, F.Wang, Z.Vadas, O.Suo, X.Hashem, Y.Soldati-Favre, D.Jia, Y.

(2024) Nat Commun 15: 10689-10689

  • DOI: https://doi.org/10.1038/s41467-024-55033-z
  • Primary Citation of Related Structures:  
    9FI8, 9FIA, 9G6K

  • PubMed Abstract: 

    The phylum Apicomplexa comprises eukaryotic parasites that cause fatal diseases affecting millions of people and animals worldwide. Their mitochondrial genomes have been significantly reduced, leaving only three protein-coding genes and highly fragmented mitoribosomal rRNAs, raising challenging questions about mitoribosome composition, assembly and structure. Our study reveals how Toxoplasma gondii assembles over 40 mt-rRNA fragments using exclusively nuclear-encoded mitoribosomal proteins and three lineage-specific families of RNA-binding proteins. Among these are four proteins from the Apetala2/Ethylene Response Factor (AP2/ERF) family, originally known as transcription factors in plants and Apicomplexa, now repurposed as essential mitoribosome components. Cryo-EM analysis of the mitoribosome structure demonstrates how these AP2 proteins function as RNA binders to maintain mitoribosome integrity. The mitoribosome is also decorated with members of lineage-specific RNA-binding proteins belonging to RAP (RNA-binding domain abundant in Apicomplexa) proteins and HPR (heptatricopeptide repeat) families, highlighting the unique adaptations of these parasites. Solving the molecular puzzle of apicomplexan mitoribosome could inform the development of therapeutic strategies targeting organellar translation.


  • Organizational Affiliation
    • National Key Laboratory of Veterinary Public Health Security, Key Laboratory of Animal Epidemiology of the Ministry of Agriculture and Rural Affairs, National Animal Protozoa Laboratory & College of Veterinary Medicine, China Agricultural University, Beijing, 100193, China.

Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein mS29,mS29(DAP3)A [auth HA]493Toxoplasma gondiiMutation(s): 0 
UniProt
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein S9, putativeB [auth HB]156Toxoplasma gondiiMutation(s): 0 
UniProt
Find proteins for S8F943 (Toxoplasma gondii (strain ATCC 50611 / Me49))
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
uS10mC [auth HC]238Toxoplasma gondiiMutation(s): 0 
UniProt
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein S14, putativeD [auth HD]102Toxoplasma gondiiMutation(s): 0 
UniProt
Find proteins for A0A125YWE1 (Toxoplasma gondii (strain ATCC 50611 / Me49))
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
mS157E [auth HE]177Toxoplasma gondiiMutation(s): 0 
UniProt
Find proteins for S8G684 (Toxoplasma gondii (strain ATCC 50611 / Me49))
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
DNA double-strand break repair rad50 ATPaseF [auth HF]354Toxoplasma gondiiMutation(s): 0 
UniProt
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
mS149G [auth HG]97Toxoplasma gondiiMutation(s): 0 
UniProt
Find proteins for A0A125YMK3 (Toxoplasma gondii (strain ATCC 50611 / Me49))
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
ms158H [auth HH]90Toxoplasma gondiiMutation(s): 0 
UniProt
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
mS151I [auth HI]144Toxoplasma gondiiMutation(s): 0 
UniProt
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S5, putativeJ [auth HJ]441Toxoplasma gondiiMutation(s): 0 
UniProt
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
mS155K [auth HK]127Toxoplasma gondiiMutation(s): 0 
UniProt
Find proteins for S8EW95 (Toxoplasma gondii (strain ATCC 50611 / Me49))
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
mS159L [auth HL]83Toxoplasma gondiiMutation(s): 0 
UniProt
Find proteins for A0A125YYH5 (Toxoplasma gondii (strain ATCC 50611 / Me49))
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
RAP domain-containing proteinM [auth HM]610Toxoplasma gondiiMutation(s): 0 
UniProt
Find proteins for S8F0U0 (Toxoplasma gondii (strain ATCC 50611 / Me49))
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
mS161N [auth HN]26Toxoplasma gondiiMutation(s): 0 
UniProt
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
mS152O [auth HO]168Toxoplasma gondiiMutation(s): 0 
UniProt
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein mS35 mitochondrial conserved domain-containing proteinP [auth HP]246Toxoplasma gondiiMutation(s): 0 
UniProt
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
mS141Q [auth HQ]757Toxoplasma gondiiMutation(s): 0 
UniProt
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
AP2 domain transcription factor AP2IX-6R [auth HR]170Toxoplasma gondiiMutation(s): 0 
UniProt
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
Acylphosphatase-like domain-containing proteinS [auth HS]121Toxoplasma gondiiMutation(s): 0 
UniProt
Find proteins for A0A125YXT1 (Toxoplasma gondii (strain ATCC 50611 / Me49))
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
mS33/mS27T [auth HT]405Toxoplasma gondiiMutation(s): 0 
UniProt
Find proteins for A0A125YG13 (Toxoplasma gondii (strain ATCC 50611 / Me49))
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Entity ID: 21
MoleculeChains LengthOrganismImage
SSUB-SSUU [auth bN]58Toxoplasma gondii
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Entity ID: 22
MoleculeChains LengthOrganismImage
SSUDV [auth hB]56Toxoplasma gondii
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Entity ID: 23
MoleculeChains LengthOrganismImage
ulr22W [auth hD]15Toxoplasma gondii
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Entity ID: 24
MoleculeChains LengthOrganismImage
RNA9-SSUX [auth hG]68Toxoplasma gondii
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Entity ID: 25
MoleculeChains LengthOrganismImage
RNA5-SSUY [auth hL]33Toxoplasma gondii
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Entity ID: 26
MoleculeChains LengthOrganismImage
ulr23Z [auth hM]10Toxoplasma gondii
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Entity ID: 27
MoleculeChains LengthOrganismImage
RNA19-SSUAA [auth hR]27Toxoplasma gondii
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Entity ID: 28
MoleculeChains LengthOrganismImage
ulr24BA [auth hS]17Toxoplasma gondii
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Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.60 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.20.1-4487

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
European CommissionEuropean Union101088541

Revision History  (Full details and data files)

  • Version 1.0: 2024-12-11
    Type: Initial release
  • Version 1.1: 2025-01-01
    Changes: Data collection, Database references