9HQV image
Deposition Date 2024-12-17
Release Date 2025-06-11
Last Version Date 2025-06-11
Entry Detail
PDB ID:
9HQV
Keywords:
Title:
Cryo-EM structure of the small subunit of the mitochondrial ribosome from Toxoplasma gondii
Biological Source:
Source Organism:
Method Details:
Experimental Method:
Resolution:
2.52 Å
Aggregation State:
PARTICLE
Reconstruction Method:
SINGLE PARTICLE
Macromolecular Entities
Polymer Type:polypeptide(L)
Molecule:Enoyl-CoA hydratase/isomerase family protein
Gene (Uniprot):TGRH88_019270
Chain IDs:A (auth: BA)
Chain Length:160
Number of Molecules:1
Biological Source:Toxoplasma gondii
Polymer Type:polypeptide(L)
Molecule:mS75
Chain IDs:B (auth: BB)
Chain Length:25
Number of Molecules:1
Biological Source:Toxoplasma gondii
Polymer Type:polypeptide(L)
Molecule:Pentatricopeptide repeat domain-containing protein
Gene (Uniprot):TGRH88_015100
Chain IDs:C (auth: BC)
Chain Length:686
Number of Molecules:1
Biological Source:Toxoplasma gondii
Polymer Type:polypeptide(L)
Molecule:mS92
Gene (Uniprot):TGRH88_012710
Chain IDs:D (auth: BD)
Chain Length:129
Number of Molecules:1
Biological Source:Toxoplasma gondii
Polymer Type:polypeptide(L)
Molecule:Ribosomal protein, uS2m
Gene (Uniprot):TGRH88_077160
Chain IDs:E (auth: Ba)
Chain Length:160
Number of Molecules:1
Biological Source:Toxoplasma gondii
Polymer Type:polypeptide(L)
Molecule:Putative 30S ribosomal protein S5
Gene (Uniprot):TGRH88_026070
Chain IDs:F (auth: Bb)
Chain Length:25
Number of Molecules:1
Biological Source:Toxoplasma gondii
Polymer Type:polypeptide(L)
Molecule:Putative mitochondrial ribosomal protein s6-2
Gene (Uniprot):TGRH88_026740
Chain IDs:G (auth: Bc)
Chain Length:686
Number of Molecules:1
Biological Source:Toxoplasma gondii
Polymer Type:polypeptide(L)
Molecule:Putative ribosomal protein S8
Gene (Uniprot):TGRH88_069320
Chain IDs:H (auth: Bd)
Chain Length:129
Number of Molecules:1
Biological Source:Toxoplasma gondii
Polymer Type:polypeptide(L)
Molecule:Putative ribosomal protein S9
Gene (Uniprot):TGRH88_022730
Chain IDs:I (auth: Be)
Chain Length:530
Number of Molecules:1
Biological Source:Toxoplasma gondii
Polymer Type:polypeptide(L)
Molecule:uS10m
Gene (Uniprot):TGRH88_069230
Chain IDs:J (auth: Bf)
Chain Length:239
Number of Molecules:1
Biological Source:Toxoplasma gondii
Polymer Type:polypeptide(L)
Molecule:Putative ribosomal protein S11
Gene (Uniprot):TGRH88_075440
Chain IDs:K (auth: Bg)
Chain Length:393
Number of Molecules:1
Biological Source:Toxoplasma gondii
Polymer Type:polypeptide(L)
Molecule:Putative 30S ribosomal protein S12
Gene (Uniprot):TGRH88_057870
Chain IDs:L (auth: Bh)
Chain Length:594
Number of Molecules:1
Biological Source:Toxoplasma gondii
Polymer Type:polypeptide(L)
Molecule:us13m
Gene (Uniprot):TGRH88_010790
Chain IDs:M (auth: Bi)
Chain Length:110
Number of Molecules:1
Biological Source:Toxoplasma gondii
Polymer Type:polypeptide(L)
Molecule:Putative ribosomal protein S14
Gene (Uniprot):TGRH88_066030
Chain IDs:N (auth: Bj)
Chain Length:112
Number of Molecules:1
Biological Source:Toxoplasma gondii
Polymer Type:polypeptide(L)
Molecule:Putative 30S ribosomal protein S15
Gene (Uniprot):TGRH88_056540
Chain IDs:O (auth: Bk)
Chain Length:395
Number of Molecules:1
Biological Source:Toxoplasma gondii
Polymer Type:polypeptide(L)
Molecule:Putative 30S ribosomal protein S16
Gene (Uniprot):TGRH88_008140
Chain IDs:P (auth: Bl)
Chain Length:167
Number of Molecules:1
Biological Source:Toxoplasma gondii
Polymer Type:polypeptide(L)
Molecule:Putative ribosomal protein S17
Gene (Uniprot):TGGT1_273060
Chain IDs:Q (auth: Bm)
Chain Length:116
Number of Molecules:1
Biological Source:Toxoplasma gondii
Polymer Type:polypeptide(L)
Molecule:Putative ribosomal protein S18
Gene (Uniprot):TGGT1_222990
Chain IDs:R (auth: Bn)
Chain Length:738
Number of Molecules:1
Biological Source:Toxoplasma gondii
Polymer Type:polypeptide(L)
Molecule:Ribosomal protein, bS21m
Gene (Uniprot):TGME49_248790
Chain IDs:S (auth: Bo)
Chain Length:243
Number of Molecules:1
Biological Source:Toxoplasma gondii
Polymer Type:polypeptide(L)
Molecule:mS23
Gene (Uniprot):TGRH88_047170
Chain IDs:T (auth: Bp)
Chain Length:377
Number of Molecules:1
Biological Source:Toxoplasma gondii
Polymer Type:polypeptide(L)
Molecule:Mitochondrial ribosomal protein, mS26
Gene (Uniprot):TGDOM2_225380
Chain IDs:U (auth: Bq)
Chain Length:447
Number of Molecules:1
Biological Source:Toxoplasma gondii
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit protein mS29
Gene (Uniprot):TGRH88_049610
Chain IDs:V (auth: Br)
Chain Length:545
Number of Molecules:1
Biological Source:Toxoplasma gondii
Polymer Type:polypeptide(L)
Molecule:DNA double-strand break repair rad50 ATPase
Gene (Uniprot):TGRH88_042050
Chain IDs:W (auth: Bs)
Chain Length:616
Number of Molecules:1
Biological Source:Toxoplasma gondii
Polymer Type:polypeptide(L)
Molecule:mS34
Gene (Uniprot):TGRH88_041300
Chain IDs:X (auth: Bt)
Chain Length:302
Number of Molecules:1
Biological Source:Toxoplasma gondii
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit protein mS35 mitochondrial conserved domain-containing protein
Gene (Uniprot):TGRH88_035400
Chain IDs:Y (auth: Bu)
Chain Length:584
Number of Molecules:1
Biological Source:Toxoplasma gondii
Polymer Type:polypeptide(L)
Molecule:CHCH domain-containing protein
Gene (Uniprot):TGRH88_052300
Chain IDs:Z (auth: Bv)
Chain Length:138
Number of Molecules:1
Biological Source:Toxoplasma gondii
Polymer Type:polypeptide(L)
Molecule:Mitochondrial mRNA-processing protein COX24 C-terminal domain-containing protein
Gene (Uniprot):BN1205_040235
Chain IDs:AA (auth: Bx)
Chain Length:263
Number of Molecules:1
Biological Source:Toxoplasma gondii
Polymer Type:polypeptide(L)
Molecule:Homeodomain-like containing protein
Gene (Uniprot):TGRH88_013790
Chain IDs:BA (auth: By)
Chain Length:597
Number of Molecules:1
Biological Source:Toxoplasma gondii
Polymer Type:polypeptide(L)
Molecule:mS45
Gene (Uniprot):TGRH88_039590
Chain IDs:CA (auth: Bz)
Chain Length:531
Number of Molecules:1
Biological Source:Toxoplasma gondii
Polymer Type:polyribonucleotide
Molecule:SSU-1
Chain IDs:MB (auth: SA)
Chain Length:91
Number of Molecules:1
Biological Source:Toxoplasma gondii
Polymer Type:polyribonucleotide
Molecule:SSU-2
Chain IDs:NB (auth: SB)
Chain Length:28
Number of Molecules:1
Biological Source:Toxoplasma gondii
Polymer Type:polyribonucleotide
Molecule:SSU-3
Chain IDs:OB (auth: SC)
Chain Length:23
Number of Molecules:1
Biological Source:Toxoplasma gondii
Polymer Type:polyribonucleotide
Molecule:SSU-4
Chain IDs:PB (auth: SD)
Chain Length:47
Number of Molecules:1
Biological Source:Toxoplasma gondii
Polymer Type:polyribonucleotide
Molecule:SSU-5
Chain IDs:QB (auth: SE)
Chain Length:73
Number of Molecules:1
Biological Source:Toxoplasma gondii
Polymer Type:polyribonucleotide
Molecule:SSU-6
Chain IDs:RB (auth: SF)
Chain Length:120
Number of Molecules:1
Biological Source:Toxoplasma gondii
Polymer Type:polyribonucleotide
Molecule:SSU-7
Chain IDs:SB (auth: SG)
Chain Length:26
Number of Molecules:1
Biological Source:Toxoplasma gondii
Polymer Type:polyribonucleotide
Molecule:SSU-8
Chain IDs:TB (auth: SH)
Chain Length:25
Number of Molecules:1
Biological Source:Toxoplasma gondii
Polymer Type:polyribonucleotide
Molecule:SSU-9
Chain IDs:UB (auth: SI)
Chain Length:53
Number of Molecules:1
Biological Source:Toxoplasma gondii
Polymer Type:polyribonucleotide
Molecule:SSU-10
Chain IDs:VB (auth: SJ)
Chain Length:93
Number of Molecules:1
Biological Source:Toxoplasma gondii
Polymer Type:polyribonucleotide
Molecule:SSU-11
Chain IDs:WB (auth: SK)
Chain Length:114
Number of Molecules:1
Biological Source:Toxoplasma gondii
Polymer Type:polyribonucleotide
Molecule:SSU-12
Chain IDs:XB (auth: SL)
Chain Length:28
Number of Molecules:1
Biological Source:Toxoplasma gondii
Polymer Type:polyribonucleotide
Molecule:SSU-13
Chain IDs:YB (auth: SM)
Chain Length:75
Number of Molecules:1
Biological Source:Toxoplasma gondii
Polymer Type:polyribonucleotide
Molecule:SSU-14
Chain IDs:ZB (auth: SN)
Chain Length:24
Number of Molecules:1
Biological Source:Toxoplasma gondii
Polymer Type:polyribonucleotide
Molecule:SSU-15
Chain IDs:AC (auth: SO)
Chain Length:16
Number of Molecules:1
Biological Source:Toxoplasma gondii
Polymer Type:polyribonucleotide
Molecule:SSU-16
Chain IDs:BC (auth: SP)
Chain Length:33
Number of Molecules:1
Biological Source:Toxoplasma gondii
Polymer Type:polyribonucleotide
Molecule:SSU-17
Chain IDs:CC (auth: SQ)
Chain Length:56
Number of Molecules:1
Biological Source:Toxoplasma gondii
Polymer Type:polyribonucleotide
Molecule:SSU-18
Chain IDs:DC (auth: SR)
Chain Length:34
Number of Molecules:1
Biological Source:Toxoplasma gondii
Polymer Type:polyribonucleotide
Molecule:SSU-19
Chain IDs:EC (auth: SS)
Chain Length:12
Number of Molecules:1
Biological Source:Toxoplasma gondii
Polymer Type:polyribonucleotide
Molecule:SSU-20
Chain IDs:FC (auth: ST)
Chain Length:24
Number of Molecules:1
Biological Source:Toxoplasma gondii
Polymer Type:polyribonucleotide
Molecule:SSU-21
Chain IDs:GC (auth: SU)
Chain Length:54
Number of Molecules:1
Biological Source:Toxoplasma gondii
Polymer Type:polyribonucleotide
Molecule:tRNA E-site
Chain IDs:HC (auth: TP)
Chain Length:21
Number of Molecules:1
Biological Source:Toxoplasma gondii
Polymer Type:polyribonucleotide
Molecule:Chain UC
Chain IDs:IC (auth: UC)
Chain Length:10
Number of Molecules:1
Biological Source:Toxoplasma gondii
Polymer Type:polypeptide(L)
Molecule:UNK1
Chain IDs:DA (auth: Ua)
Chain Length:20
Number of Molecules:1
Biological Source:Toxoplasma gondii
Polymer Type:polypeptide(L)
Molecule:UNK2
Chain IDs:EA (auth: Ub)
Chain Length:7
Number of Molecules:1
Biological Source:Toxoplasma gondii
Polymer Type:polypeptide(L)
Molecule:UNK3
Chain IDs:FA (auth: Uc)
Chain Length:10
Number of Molecules:1
Biological Source:Toxoplasma gondii
Polymer Type:polypeptide(L)
Molecule:UNK4
Chain IDs:GA (auth: Ud)
Chain Length:72
Number of Molecules:1
Biological Source:Toxoplasma gondii
Polymer Type:polypeptide(L)
Molecule:Chain Uh
Chain IDs:HA (auth: Uh)
Chain Length:56
Number of Molecules:1
Biological Source:Toxoplasma gondii
Polymer Type:polypeptide(L)
Molecule:Unknown peptide
Chain IDs:IA (auth: Ui), KA (auth: Uk)
Chain Length:13
Number of Molecules:2
Biological Source:Toxoplasma gondii
Polymer Type:polypeptide(L)
Molecule:Chain Uj
Chain IDs:JA (auth: Uj)
Chain Length:60
Number of Molecules:1
Biological Source:Toxoplasma gondii
Polymer Type:polypeptide(L)
Molecule:GLY-ARG-SER-LYS-VAL-LEU-ILE-ARG-ARG-LEU-LYS-GLU-ARG-ALA-LYS-LYS-GLU-ALA-GLU-LYS-LYS-ALA
Chain IDs:LA (auth: Ul)
Chain Length:22
Number of Molecules:1
Biological Source:Toxoplasma gondii
Polymer Type:polypeptide(L)
Molecule:ARG-ALA-GLU-LEU-VAL-ALA-ALA-GLN-VAL-ARG-GLU-LYS-LEU-ALA-ILE-LYS-MET-ALA-ASN-ALA-LEU-ALA
Chain IDs:MA (auth: Um)
Chain Length:22
Number of Molecules:1
Biological Source:Toxoplasma gondii
Polymer Type:polypeptide(L)
Molecule:Chain Un
Chain IDs:NA (auth: Un)
Chain Length:24
Number of Molecules:1
Biological Source:Toxoplasma gondii
Polymer Type:polypeptide(L)
Molecule:chain Uo
Chain IDs:OA (auth: Uo)
Chain Length:26
Number of Molecules:1
Biological Source:Toxoplasma gondii
Polymer Type:polypeptide(L)
Molecule:chain Up
Chain IDs:PA (auth: Up)
Chain Length:24
Number of Molecules:1
Biological Source:Toxoplasma gondii
Polymer Type:polypeptide(L)
Molecule:chain Uq
Chain IDs:QA (auth: Uq)
Chain Length:32
Number of Molecules:1
Biological Source:Toxoplasma gondii
Polymer Type:polypeptide(L)
Molecule:mS117
Gene (Uniprot):TGGT1_229740
Chain IDs:RA (auth: Ya)
Chain Length:551
Number of Molecules:1
Biological Source:Toxoplasma gondii
Polymer Type:polypeptide(L)
Molecule:ATP-dependent Clp protease proteolytic subunit,related protein
Gene (Uniprot):TGRH88_047300
Chain IDs:SA (auth: Yb)
Chain Length:1048
Number of Molecules:1
Biological Source:Toxoplasma gondii
Polymer Type:polypeptide(L)
Molecule:mS119
Gene (Uniprot):TGRH88_001960
Chain IDs:TA (auth: Yc)
Chain Length:268
Number of Molecules:1
Biological Source:Toxoplasma gondii
Polymer Type:polypeptide(L)
Molecule:mS120
Gene (Uniprot):TGRH88_023520
Chain IDs:UA (auth: Yd)
Chain Length:680
Number of Molecules:1
Biological Source:Toxoplasma gondii
Polymer Type:polypeptide(L)
Molecule:mS121
Gene (Uniprot):TGRH88_051630
Chain IDs:VA (auth: Ye)
Chain Length:304
Number of Molecules:1
Biological Source:Toxoplasma gondii
Polymer Type:polypeptide(L)
Molecule:Macro domain-containing protein
Gene (Uniprot):TGRH88_074400
Chain IDs:WA (auth: Yf)
Chain Length:698
Number of Molecules:1
Biological Source:Toxoplasma gondii
Polymer Type:polypeptide(L)
Molecule:Thioredoxin domain-containing protein
Gene (Uniprot):TGRH88_067180
Chain IDs:XA (auth: Yg)
Chain Length:940
Number of Molecules:1
Biological Source:Toxoplasma gondii
Polymer Type:polypeptide(L)
Molecule:mS124
Chain IDs:YA (auth: Yh)
Chain Length:280
Number of Molecules:1
Biological Source:Toxoplasma gondii
Polymer Type:polypeptide(L)
Molecule:mS125
Gene (Uniprot):TGRH88_049830
Chain IDs:ZA (auth: Yi)
Chain Length:930
Number of Molecules:1
Biological Source:Toxoplasma gondii
Polymer Type:polypeptide(L)
Molecule:DnaJ domain-containing protein
Gene (Uniprot):TGRH88_008210
Chain IDs:AB (auth: Yj)
Chain Length:233
Number of Molecules:1
Biological Source:Toxoplasma gondii
Polymer Type:polypeptide(L)
Molecule:RAP domain-containing protein
Gene (Uniprot):TGRH88_002670
Chain IDs:BB (auth: Yk)
Chain Length:1547
Number of Molecules:1
Biological Source:Toxoplasma gondii
Polymer Type:polypeptide(L)
Molecule:mS128
Gene (Uniprot):TGRH88_001440
Chain IDs:CB (auth: Yl)
Chain Length:316
Number of Molecules:1
Biological Source:Toxoplasma gondii
Polymer Type:polypeptide(L)
Molecule:RAP domain-containing protein
Gene (Uniprot):TGRH88_082860
Chain IDs:DB (auth: Ym)
Chain Length:801
Number of Molecules:1
Biological Source:Toxoplasma gondii
Polymer Type:polypeptide(L)
Molecule:AP2 domain transcription factor AP2IX-6
Gene (Uniprot):TGRH88_014850
Chain IDs:EB (auth: Yn)
Chain Length:432
Number of Molecules:1
Biological Source:Toxoplasma gondii
Polymer Type:polypeptide(L)
Molecule:mS131
Gene (Uniprot):TGRH88_022840
Chain IDs:FB (auth: Yo)
Chain Length:421
Number of Molecules:1
Biological Source:Toxoplasma gondii
Polymer Type:polypeptide(L)
Molecule:mS132
Gene (Uniprot):TGRH88_046820
Chain IDs:GB (auth: Yp)
Chain Length:181
Number of Molecules:1
Biological Source:Toxoplasma gondii
Polymer Type:polypeptide(L)
Molecule:mS133
Gene (Uniprot):TGRH88_019760
Chain IDs:LB (auth: Yq)
Chain Length:302
Number of Molecules:1
Biological Source:Toxoplasma gondii
Polymer Type:polypeptide(L)
Molecule:Acylphosphatase-like domain-containing protein
Gene (Uniprot):TGGT1_249790
Chain IDs:HB (auth: Yr)
Chain Length:235
Number of Molecules:1
Biological Source:Toxoplasma gondii
Polymer Type:polypeptide(L)
Molecule:mS135
Gene (Uniprot):TGRH88_067310
Chain IDs:IB (auth: Ys)
Chain Length:181
Number of Molecules:1
Biological Source:Toxoplasma gondii
Polymer Type:polypeptide(L)
Molecule:mS136
Gene (Uniprot):TGRH88_041110
Chain IDs:JB (auth: Yt)
Chain Length:475
Number of Molecules:1
Biological Source:Toxoplasma gondii
Polymer Type:polypeptide(L)
Molecule:mS137
Chain IDs:KB (auth: Yu)
Chain Length:367
Number of Molecules:1
Biological Source:Toxoplasma gondii
Polymer Type:polypeptide(L)
Molecule:mS138
Gene (Uniprot):TGRH88_072270
Chain IDs:JC (auth: Yv)
Chain Length:419
Number of Molecules:1
Biological Source:Toxoplasma gondii
Primary Citation
Numerous rRNA molecules form the apicomplexan mitoribosome via repurposed protein and RNA elements.
Nat Commun 16 817 817 (2025)
PMID: 39827269 DOI: 10.1038/s41467-025-56057-9

Abstact

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.

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Primary Citation of related structures