9FIA | pdb_00009fia

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


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.29 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


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
Mitochondrial ribosomal protein, mS145A [auth B0]680Toxoplasma gondiiMutation(s): 0 
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
unidentified peptideB [auth B1]17Toxoplasma gondiiMutation(s): 0 
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein S18, putativeC [auth B2]738Toxoplasma gondiiMutation(s): 0 
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Mitochondrial ribosomal protein, mS23D [auth B3]377Toxoplasma gondiiMutation(s): 0 
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
CHCH domain-containing proteinE [auth B4]138Toxoplasma gondiiMutation(s): 0 
UniProt
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein S11, putativeF [auth B5]393Toxoplasma gondiiMutation(s): 0 
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
Putative mitochondrial ribosomal protein s6-2G [auth B6]163Toxoplasma gondiiMutation(s): 0 
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
unidentified peptideH [auth B7]12Toxoplasma gondiiMutation(s): 0 
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
unidentified peptideI [auth B8],
PA [auth Bj]
21Toxoplasma gondiiMutation(s): 0 
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
DnaJ domain-containing proteinJ [auth B9]233Toxoplasma gondiiMutation(s): 0 
UniProt
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
Mitochondrial ribosomal protein, mS137K [auth BA]939Toxoplasma gondiiMutation(s): 0 
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
RAP domain-containing proteinL [auth BB]1,547Toxoplasma gondiiMutation(s): 0 
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
Mitochondrial ribosomal protein, mS47M [auth BC]421Toxoplasma gondiiMutation(s): 0 
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
Pentatricopeptide repeat domain-containing proteinN [auth BD]686Toxoplasma gondiiMutation(s): 0 
UniProt
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
Mitochondrial ribosomal protein, mS140O [auth BE]1,053Toxoplasma gondiiMutation(s): 0 
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
Mitochondrial ribosomal protein, mS147P [auth BF]304Toxoplasma gondiiMutation(s): 0 
UniProt
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein, uS2mQ [auth BG]160Toxoplasma gondiiMutation(s): 0 
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
Putative ribosomal protein S8R [auth BH]129Toxoplasma gondiiMutation(s): 0 
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
unidentified peptideFA [auth BX],
S [auth BI],
W [auth BN]
13Toxoplasma gondiiMutation(s): 0 
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
unidentified peptideT [auth BJ]26Toxoplasma gondiiMutation(s): 0 
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
Mitochondrial ribosomal protein, mS26U [auth BK]530Toxoplasma gondiiMutation(s): 0 
UniProt
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Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
Putative ribosomal protein S17V [auth BL]116Toxoplasma gondiiMutation(s): 0 
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Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
Putative 30S ribosomal protein S15X [auth BO]395Toxoplasma gondiiMutation(s): 0 
UniProt
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Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
unidentified peptideY [auth BP]47Toxoplasma gondiiMutation(s): 0 
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Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
Macro domain-containing proteinZ [auth BQ]698Toxoplasma gondiiMutation(s): 0 
UniProt
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Entity ID: 26
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein, bS21mAA [auth BS]243Toxoplasma gondiiMutation(s): 0 
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Entity ID: 27
MoleculeChains Sequence LengthOrganismDetailsImage
Mitochondrial ribosomal protein, mS156BA [auth BT]280Toxoplasma gondiiMutation(s): 0 
UniProt
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Entity ID: 28
MoleculeChains Sequence LengthOrganismDetailsImage
unidentified peptideCA [auth BU]14Toxoplasma gondiiMutation(s): 0 
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Entity ID: 29
MoleculeChains Sequence LengthOrganismDetailsImage
Putative homeodomain containing proteinDA [auth BV]597Toxoplasma gondiiMutation(s): 0 
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Entity ID: 30
MoleculeChains Sequence LengthOrganismDetailsImage
Mitochondrial ribosomal protein, mS144EA [auth BW]547Toxoplasma gondiiMutation(s): 0 
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Entity ID: 31
MoleculeChains Sequence LengthOrganismDetailsImage
unidentified peptideGA [auth BY]11Toxoplasma gondiiMutation(s): 0 
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Entity ID: 32
MoleculeChains Sequence LengthOrganismDetailsImage
unidentified peptideHA [auth Ba]10Toxoplasma gondiiMutation(s): 0 
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Entity ID: 33
MoleculeChains Sequence LengthOrganismDetailsImage
unidentified peptideIA [auth Bb]8Toxoplasma gondiiMutation(s): 0 
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Entity ID: 34
MoleculeChains Sequence LengthOrganismDetailsImage
Enoyl-CoA hydratase/isomerase family proteinJA [auth Bc]716Toxoplasma gondiiMutation(s): 0 
EC: 3.1.2.4
UniProt
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Entity ID: 35
MoleculeChains Sequence LengthOrganismDetailsImage
unidentified peptideKA [auth Bd]33Toxoplasma gondiiMutation(s): 0 
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Entity ID: 36
MoleculeChains Sequence LengthOrganismDetailsImage
unidentified peptideLA [auth Be]18Toxoplasma gondiiMutation(s): 0 
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Entity ID: 37
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein, uS2mMA [auth Bg]302Toxoplasma gondiiMutation(s): 0 
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Entity ID: 38
MoleculeChains Sequence LengthOrganismDetailsImage
Putative 30S ribosomal protein S16NA [auth Bh]167Toxoplasma gondiiMutation(s): 0 
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Entity ID: 39
MoleculeChains Sequence LengthOrganismDetailsImage
Mitochondrial ribosomal protein, mS153OA [auth Bi]268Toxoplasma gondiiMutation(s): 0 
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Entity ID: 40
MoleculeChains Sequence LengthOrganismDetailsImage
Mitochondrial ribosomal protein, mS26QA [auth Bk]447Toxoplasma gondiiMutation(s): 0 
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Entity ID: 41
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S12, putativeRA [auth Bl]593Toxoplasma gondiiMutation(s): 0 
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Entity ID: 42
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S5, putativeSA [auth HJ]1,140Toxoplasma gondiiMutation(s): 0 
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Entity ID: 43
MoleculeChains Sequence LengthOrganismDetailsImage
Acylphosphatase-like domain-containing proteinTA [auth HS]235Toxoplasma gondiiMutation(s): 0 
UniProt
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Entity ID: 44
MoleculeChains LengthOrganismImage
ulr11UA [auth b1]8Toxoplasma gondii
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Entity ID: 45
MoleculeChains LengthOrganismImage
SSUEVA [auth b2]48Toxoplasma gondii
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Entity ID: 46
MoleculeChains LengthOrganismImage
ulr12WA [auth b3]5Toxoplasma gondii
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Entity ID: 47
MoleculeChains LengthOrganismImage
RNA13XA [auth b4]34Toxoplasma gondii
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Entity ID: 48
MoleculeChains LengthOrganismImage
RNA19YA [auth bA]34Toxoplasma gondii
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Entity ID: 49
MoleculeChains LengthOrganismImage
RNA15ZA [auth bD]27Toxoplasma gondii
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Entity ID: 50
MoleculeChains LengthOrganismImage
RNA8AB [auth bE]107Toxoplasma gondii
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Entity ID: 51
MoleculeChains LengthOrganismImage
ulr13BB [auth bG]4Toxoplasma gondii
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Entity ID: 52
MoleculeChains LengthOrganismImage
ulr14CB [auth bH]2Toxoplasma gondii
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Entity ID: 53
MoleculeChains LengthOrganismImage
ulr15DB [auth bI]3Toxoplasma gondii
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Entity ID: 54
MoleculeChains LengthOrganismImage
RNA33EB [auth bJ]71Toxoplasma gondii
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Entity ID: 55
MoleculeChains LengthOrganismImage
RNA5FB [auth bK]83Toxoplasma gondii
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Entity ID: 56
MoleculeChains LengthOrganismImage
RNA17GB [auth bL]48Toxoplasma gondii
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Entity ID: 57
MoleculeChains LengthOrganismImage
SSUBHB [auth bN]122Toxoplasma gondii
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Entity ID: 58
MoleculeChains LengthOrganismImage
SSUAIB [auth bO]115Toxoplasma gondii
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Entity ID: 59
MoleculeChains LengthOrganismImage
ulr16JB [auth bP]15Toxoplasma gondii
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Entity ID: 60
MoleculeChains LengthOrganismImage
ulr17KB [auth bQ]14Toxoplasma gondii
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Entity ID: 61
MoleculeChains LengthOrganismImage
RNA30LB [auth bR]31Toxoplasma gondii
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Entity ID: 62
MoleculeChains LengthOrganismImage
url18MB [auth bS]31Toxoplasma gondii
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Entity ID: 63
MoleculeChains LengthOrganismImage
SSUFNB [auth bT]60Toxoplasma gondii
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Entity ID: 64
MoleculeChains LengthOrganismImage
ulr19OB [auth bU]25Toxoplasma gondii
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Entity ID: 65
MoleculeChains LengthOrganismImage
ulr20PB [auth bV]6Toxoplasma gondii
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Entity ID: 66
MoleculeChains LengthOrganismImage
ulr21QB [auth bY]11Toxoplasma gondii
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Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.29 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.20.1-4487

Structure Validation

View Full Validation Report



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