9G6K | pdb_00009g6k

LSU structure derived from the LSU sample of the mitoribosome from T. gondii.


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.89 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Model: in silico
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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
RRM domain-containing proteinA [auth L0]405Toxoplasma gondiiMutation(s): 0 
UniProt
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein mL54B [auth L1]92Toxoplasma gondiiMutation(s): 0 
UniProt
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
mL162C [auth L2]270Toxoplasma gondiiMutation(s): 0 
UniProt
Find proteins for A0A0F7V439 (Toxoplasma gondii (strain ATCC 50861 / VEG))
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal l25 family proteinD [auth L3]331Toxoplasma gondiiMutation(s): 0 
UniProt
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
RAP domain-containing proteinE [auth L4]430Toxoplasma gondiiMutation(s): 0 
UniProt
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
mL183F [auth L5]30Toxoplasma gondiiMutation(s): 0 
UniProt
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
uL1mG [auth L6]57Toxoplasma gondiiMutation(s): 0 
UniProt
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
uL14mH [auth L7]114Toxoplasma gondiiMutation(s): 0 
UniProt
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
Putative 50S ribosomal protein L17I [auth L8]246Toxoplasma gondiiMutation(s): 0 
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
DUF6832 domain-containing proteinJ [auth L9]475Toxoplasma gondiiMutation(s): 0 
UniProt
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
Putative 50S ribosomal protein L13K [auth LA]217Toxoplasma gondiiMutation(s): 0 
UniProt
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
Putative ribosomal protein L20L [auth LB]121Toxoplasma gondiiMutation(s): 0 
UniProt
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
Macro domain-containing proteinM [auth LC]527Toxoplasma gondiiMutation(s): 0 
UniProt
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein L46N [auth LD]282Toxoplasma gondiiMutation(s): 0 
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
FAS1 domain-containing proteinO [auth LE]338Toxoplasma gondiiMutation(s): 0 
UniProt
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
bL36mP [auth LF]88Toxoplasma gondiiMutation(s): 0 
UniProt
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein RPL22Q [auth LG]148Toxoplasma gondiiMutation(s): 0 
UniProt
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein L9, N-terminal domain-containing proteinR [auth LH]87Toxoplasma gondiiMutation(s): 0 
UniProt
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
Putative 60S ribosomal protein L27S [auth LI]79Toxoplasma gondiiMutation(s): 0 
UniProt
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
RAP domain-containing proteinT [auth LJ]443Toxoplasma gondiiMutation(s): 0 
UniProt
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
BIR proteinU [auth LK]219Toxoplasma gondiiMutation(s): 0 
UniProt
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Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
AMP-dependent synthetase/ligase domain-containing proteinV [auth LL]855Toxoplasma gondiiMutation(s): 0 
UniProt
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Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL11mW [auth LM]177Toxoplasma gondiiMutation(s): 0 
UniProt
Find proteins for A0A125YTN1 (Toxoplasma gondii (strain ATCC 50611 / Me49))
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Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
bL35mX [auth LN]113Toxoplasma gondiiMutation(s): 0 
UniProt
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Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
LSU ribosomal protein L2P, putativeY [auth LO]344Toxoplasma gondiiMutation(s): 0 
UniProt
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Entity ID: 26
MoleculeChains Sequence LengthOrganismDetailsImage
Peptidyl-prolyl cis-trans isomeraseZ [auth LP]230Toxoplasma gondiiMutation(s): 0 
EC: 5.2.1.8
UniProt
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Entity ID: 27
MoleculeChains Sequence LengthOrganismDetailsImage
mL175AA [auth LQ]70Toxoplasma gondiiMutation(s): 0 
UniProt
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Entity ID: 28
MoleculeChains Sequence LengthOrganismDetailsImage
mL172BA [auth LR]132Toxoplasma gondiiMutation(s): 0 
UniProt
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Entity ID: 29
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL24cCA [auth LS]228Toxoplasma gondiiMutation(s): 0 
UniProt
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Entity ID: 30
MoleculeChains Sequence LengthOrganismDetailsImage
Putative 50S ribosomal protein L33DA [auth LT]117Toxoplasma gondiiMutation(s): 0 
UniProt
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Entity ID: 31
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein mL49EA [auth LU]79Toxoplasma gondiiMutation(s): 0 
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Entity ID: 32
MoleculeChains Sequence LengthOrganismDetailsImage
mL148FA [auth LV]880Toxoplasma gondiiMutation(s): 0 
UniProt
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Entity ID: 33
MoleculeChains Sequence LengthOrganismDetailsImage
Putative 50S ribosomal protein L3GA [auth LW]306Toxoplasma gondiiMutation(s): 0 
UniProt
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Entity ID: 34
MoleculeChains Sequence LengthOrganismDetailsImage
mL176HA [auth LX]92Toxoplasma gondiiMutation(s): 0 
UniProt
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Entity ID: 35
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal L22p/L17e proteinIA [auth LY]346Toxoplasma gondiiMutation(s): 0 
UniProt
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Entity ID: 36
MoleculeChains Sequence LengthOrganismDetailsImage
mL174JA [auth LZ]197Toxoplasma gondiiMutation(s): 0 
UniProt
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Entity ID: 37
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL23mKA [auth La]214Toxoplasma gondiiMutation(s): 0 
UniProt
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Entity ID: 38
MoleculeChains Sequence LengthOrganismDetailsImage
RAP domain-containing proteinLA [auth Lb]733Toxoplasma gondiiMutation(s): 0 
UniProt
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Entity ID: 39
MoleculeChains Sequence LengthOrganismDetailsImage
RAP domain-containing proteinMA [auth Lc]512Toxoplasma gondiiMutation(s): 0 
UniProt
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Entity ID: 40
MoleculeChains Sequence LengthOrganismDetailsImage
RAP domain-containing proteinNA [auth Ld]437Toxoplasma gondiiMutation(s): 0 
UniProt
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Entity ID: 41
MoleculeChains Sequence LengthOrganismDetailsImage
RAP domain-containing proteinOA [auth Le]376Toxoplasma gondiiMutation(s): 0 
UniProt
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Entity ID: 42
MoleculeChains Sequence LengthOrganismDetailsImage
HECT-domain (Ubiquitin-transferase) domain-containing proteinPA [auth Lf]226Toxoplasma gondiiMutation(s): 0 
UniProt
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Entity ID: 43
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL29mQA [auth Lg]214Toxoplasma gondiiMutation(s): 0 
UniProt
Find proteins for A0A125YVS8 (Toxoplasma gondii (strain ATCC 50611 / Me49))
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Entity ID: 44
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL4mRA [auth Lh]464Toxoplasma gondiiMutation(s): 0 
UniProt
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Entity ID: 45
MoleculeChains Sequence LengthOrganismDetailsImage
RAP domain-containing proteinSA [auth Li]602Toxoplasma gondiiMutation(s): 0 
UniProt
Find proteins for S8FC14 (Toxoplasma gondii (strain ATCC 50611 / Me49))
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Entity ID: 46
MoleculeChains Sequence LengthOrganismDetailsImage
mL177TA [auth Lj]122Toxoplasma gondiiMutation(s): 0 
UniProt
Find proteins for A0A125YYH1 (Toxoplasma gondii (strain ATCC 50611 / Me49))
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Entity ID: 47
MoleculeChains Sequence LengthOrganismDetailsImage
AP2 domain transcription factor AP2VIIb-2UA [auth Lk]184Toxoplasma gondiiMutation(s): 0 
UniProt
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Entity ID: 48
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein mL43VA [auth Ll]190Toxoplasma gondiiMutation(s): 0 
UniProt
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Entity ID: 49
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL24cWA [auth Lm]189Toxoplasma gondiiMutation(s): 0 
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Entity ID: 50
MoleculeChains Sequence LengthOrganismDetailsImage
mL185XA [auth Ln]60Toxoplasma gondiiMutation(s): 0 
UniProt
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Entity ID: 51
MoleculeChains Sequence LengthOrganismDetailsImage
Transmembrane proteinYA [auth Lo]283Toxoplasma gondiiMutation(s): 0 
UniProt
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Entity ID: 52
MoleculeChains Sequence LengthOrganismDetailsImage
bL19mZA [auth Lp]368Toxoplasma gondiiMutation(s): 0 
UniProt
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Entity ID: 53
MoleculeChains Sequence LengthOrganismDetailsImage
RAP domain-containing proteinAB [auth Lq]787Toxoplasma gondiiMutation(s): 0 
UniProt
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Entity ID: 54
MoleculeChains Sequence LengthOrganismDetailsImage
Putative ribosomal protein L28BB [auth Lr]281Toxoplasma gondiiMutation(s): 0 
UniProt
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Entity ID: 55
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein L15, putativeCB [auth Ls]311Toxoplasma gondiiMutation(s): 0 
UniProt
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Entity ID: 56
MoleculeChains Sequence LengthOrganismDetailsImage
mL40DB [auth Lt]240Toxoplasma gondiiMutation(s): 0 
UniProt
Find proteins for S8F2D4 (Toxoplasma gondii (strain ATCC 50611 / Me49))
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Entity ID: 57
MoleculeChains Sequence LengthOrganismDetailsImage
mL164EB [auth Lu]232Toxoplasma gondiiMutation(s): 0 
UniProt
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Entity ID: 58
MoleculeChains Sequence LengthOrganismDetailsImage
mL180FB [auth Lv]112Toxoplasma gondiiMutation(s): 0 
UniProt
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Entity ID: 59
MoleculeChains Sequence LengthOrganismDetailsImage
Putative 50S ribosomal protein L16GB [auth Lw]179Toxoplasma gondiiMutation(s): 0 
UniProt
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Entity ID: 60
MoleculeChains Sequence LengthOrganismDetailsImage
mL173HB [auth Lx]98Toxoplasma gondiiMutation(s): 0 
UniProt
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Entity ID: 61
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein bL21mIB [auth Ly]404Toxoplasma gondiiMutation(s): 0 
UniProt
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Entity ID: 62
MoleculeChains Sequence LengthOrganismDetailsImage
mL182JB [auth Lz]120Toxoplasma gondiiMutation(s): 0 
UniProt
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Entity ID: 63
MoleculeChains Sequence LengthOrganismDetailsImage
mL178KB [auth UA]85Toxoplasma gondiiMutation(s): 0 
UniProt
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Entity ID: 64
MoleculeChains Sequence LengthOrganismDetailsImage
bL27mLB [auth UB]174Toxoplasma gondiiMutation(s): 0 
UniProt
Find proteins for S8GME4 (Toxoplasma gondii (strain ATCC 50611 / Me49))
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Entity ID: 65
MoleculeChains Sequence LengthOrganismDetailsImage
mL179MB [auth UC]105Toxoplasma gondiiMutation(s): 0 
UniProt
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Entity ID: 66
MoleculeChains Sequence LengthOrganismDetailsImage
Transmembrane proteinNB [auth UD]35Toxoplasma gondiiMutation(s): 0 
UniProt
Find proteins for A0A125YKV7 (Toxoplasma gondii (strain ATCC 50611 / Me49))
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Entity ID: 67
MoleculeChains Sequence LengthOrganismDetailsImage
mL53OB [auth UE]113Toxoplasma gondiiMutation(s): 0 
UniProt
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Entity ID: 68
MoleculeChains Sequence LengthOrganismDetailsImage
bL32mPB [auth UF]78Toxoplasma gondiiMutation(s): 0 
UniProt
Find proteins for A0A125YQ85 (Toxoplasma gondii (strain ATCC 50611 / Me49))
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Entity ID: 69
MoleculeChains Sequence LengthOrganismDetailsImage
AP2 domain transcription factor AP2IV-1QB [auth UG]158Toxoplasma gondiiMutation(s): 0 
UniProt
Find proteins for S8GSN6 (Toxoplasma gondii (strain ATCC 50611 / Me49))
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Entity ID: 70
MoleculeChains Sequence LengthOrganismDetailsImage
mL181RB [auth UH]47Toxoplasma gondiiMutation(s): 0 
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Entity ID: 71
MoleculeChains Sequence LengthOrganismDetailsImage
mL184SB [auth UI]35Toxoplasma gondiiMutation(s): 0 
UniProt
Find proteins for A0A0F7V869 (Toxoplasma gondii (strain ATCC 50861 / VEG))
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Entity ID: 72
MoleculeChains LengthOrganismImage
RNA23tTB [auth l0]44Toxoplasma gondii
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Entity ID: 73
MoleculeChains LengthOrganismImage
RNA29UB [auth l1]50Toxoplasma gondii
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Entity ID: 74
MoleculeChains LengthOrganismImage
LSUBVB [auth l2]31Toxoplasma gondii
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Entity ID: 75
MoleculeChains LengthOrganismImage
RNA6WB [auth l3]59Toxoplasma gondii
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Entity ID: 76
MoleculeChains LengthOrganismImage
RNA1XB [auth l4]94Toxoplasma gondii
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Entity ID: 77
MoleculeChains LengthOrganismImage
RNA31YB [auth l5]36Toxoplasma gondii
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Entity ID: 78
MoleculeChains LengthOrganismImage
RNA14ZB [auth l6]50Toxoplasma gondii
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Entity ID: 79
MoleculeChains LengthOrganismImage
RNA11AC [auth l7]69Toxoplasma gondii
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Entity ID: 80
MoleculeChains LengthOrganismImage
RNA36BC [auth l8]33Toxoplasma gondii
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Entity ID: 81
MoleculeChains LengthOrganismImage
RNA3CC [auth l9]91Toxoplasma gondii
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Entity ID: 82
MoleculeChains LengthOrganismImage
RNA2DC [auth lA]65Toxoplasma gondii
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Entity ID: 83
MoleculeChains LengthOrganismImage
RNA38EC [auth lB]45Toxoplasma gondii
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Entity ID: 84
MoleculeChains LengthOrganismImage
RNA35FC [auth lC]27Toxoplasma gondii
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Entity ID: 85
MoleculeChains LengthOrganismImage
RNA32GC [auth lD]16Toxoplasma gondii
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Entity ID: 86
MoleculeChains LengthOrganismImage
RNA15HC [auth lE]29Toxoplasma gondii
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Entity ID: 87
MoleculeChains LengthOrganismImage
RNA10IC [auth lF]88Toxoplasma gondii
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Entity ID: 88
MoleculeChains LengthOrganismImage
LSUCJC [auth lG]26Toxoplasma gondii
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Entity ID: 89
MoleculeChains LengthOrganismImage
RNA16KC [auth lH]27Toxoplasma gondii
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Entity ID: 90
MoleculeChains LengthOrganismImage
RNA13LC [auth lI]48Toxoplasma gondii
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Entity ID: 91
MoleculeChains LengthOrganismImage
LSUD/EMC [auth lJ]279Toxoplasma gondii
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Entity ID: 92
MoleculeChains LengthOrganismImage
SSUFNC [auth lK]38Toxoplasma gondii
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Entity ID: 93
MoleculeChains LengthOrganismImage
RNA7OC [auth lL]91Toxoplasma gondii
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Entity ID: 94
MoleculeChains LengthOrganismImage
LSUF/GPC [auth lM]194Toxoplasma gondii
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Entity ID: 95
MoleculeChains LengthOrganismImage
RNA37QC [auth lN]62Toxoplasma gondii
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Entity ID: 96
MoleculeChains LengthOrganismImage
LSUARC [auth lO]180Toxoplasma gondii
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Entity ID: 97
MoleculeChains LengthOrganismImage
ulr1SC [auth lP]29Toxoplasma gondii
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Entity ID: 98
MoleculeChains LengthOrganismImage
ulr2TC [auth lQ]37Toxoplasma gondii
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Entity ID: 99
MoleculeChains LengthOrganismImage
ulr3UC [auth lR]28Toxoplasma gondii
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Entity ID: 100
MoleculeChains LengthOrganismImage
ulr4VC [auth lS]7Toxoplasma gondii
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Entity ID: 101
MoleculeChains LengthOrganismImage
ulr5WC [auth lT],
ZC [auth lW]
14Toxoplasma gondii
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Entity ID: 102
MoleculeChains LengthOrganismImage
ulr6XC [auth lU]15Toxoplasma gondii
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Entity ID: 103
MoleculeChains LengthOrganismImage
ulr7,ulr8BD [auth lY],
YC [auth lV]
10Toxoplasma gondii
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Entity ID: 104
MoleculeChains LengthOrganismImage
ulr9AD [auth lX]58Toxoplasma gondii
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Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.89 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