ISDA: 9FIA

Deposition Date 2024-05-28

Release Date 2024-12-11

Last Version Date 2025-01-01

Entry Detail

PDB ID:

9FIA

Keywords:

RIBOSOME

Title:

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

Biological Source:

Source Organism:

Toxoplasma gondii (Taxon ID: 5811)

Method Details:

Experimental Method:

ELECTRON MICROSCOPY

Resolution:

3.29 Å

Aggregation State:

PARTICLE

Reconstruction Method:

SINGLE PARTICLE

Download Validation Report

Macromolecular Entities

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Mitochondrial ribosomal protein, mS145
Gene (Uniprot):TGME49_220200
Chain IDs:A (auth: B0)
Chain Length:680
Number of Molecules:1
Biological Source:Toxoplasma gondii

UniProt ID:S8GGX8

Polymer Type:polypeptide(L)
Molecule:unidentified peptide
Chain IDs:B (auth: B1)
Chain Length:8
Number of Molecules:1
Biological Source:Toxoplasma gondii

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Ribosomal protein S18, putative
Gene (Uniprot):TGME49_222990
Chain IDs:C (auth: B2)
Chain Length:738
Number of Molecules:1
Biological Source:Toxoplasma gondii

UniProt ID:S8F879 Pfam ID:PF01084

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Mitochondrial ribosomal protein, mS23
Chain IDs:D (auth: B3)
Chain Length:5
Number of Molecules:1
Biological Source:Toxoplasma gondii

UniProt ID:S8G6C8

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:CHCH domain-containing protein
Chain IDs:E (auth: B4)
Chain Length:138
Number of Molecules:1
Biological Source:Toxoplasma gondii

UniProt ID:A0A125YXL8

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Ribosomal protein S11, putative
Gene (Uniprot):TGME49_231120
Chain IDs:F (auth: B5)
Chain Length:393
Number of Molecules:1
Biological Source:Toxoplasma gondii

UniProt ID:S8F665

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Putative mitochondrial ribosomal protein s6-2
Chain IDs:G (auth: B6)
Chain Length:163
Number of Molecules:1
Biological Source:Toxoplasma gondii

UniProt ID:A0A125YRD5

Polymer Type:polypeptide(L)
Molecule:unidentified peptide
Chain IDs:H (auth: B7)
Chain Length:12
Number of Molecules:1
Biological Source:Toxoplasma gondii

Polymer Type:polypeptide(L)
Molecule:unidentified peptide
Chain IDs:I (auth: B8), PA (auth: Bj)
Chain Length:21
Number of Molecules:2
Biological Source:Toxoplasma gondii

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:DnaJ domain-containing protein
Chain IDs:J (auth: B9)
Chain Length:233
Number of Molecules:1
Biological Source:Toxoplasma gondii

UniProt ID:A0A125YYG6

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Mitochondrial ribosomal protein, mS137
Gene (Uniprot):TGME49_263840
Chain IDs:K (auth: BA)
Chain Length:34
Number of Molecules:1
Biological Source:Toxoplasma gondii

UniProt ID:S8F8D3

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:RAP domain-containing protein
Gene (Uniprot):TGME49_297890
Chain IDs:L (auth: BB)
Chain Length:8
Number of Molecules:1
Biological Source:Toxoplasma gondii

UniProt ID:S8GUD6

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Mitochondrial ribosomal protein, mS47
Gene (Uniprot):TGME49_257650
Chain IDs:M (auth: BC)
Chain Length:421
Number of Molecules:1
Biological Source:Toxoplasma gondii

UniProt ID:S8GBT4

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Pentatricopeptide repeat domain-containing protein
Gene (Uniprot):TGME49_290650
Chain IDs:N (auth: BD)
Chain Length:686
Number of Molecules:1
Biological Source:Toxoplasma gondii

UniProt ID:S8F073

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Mitochondrial ribosomal protein, mS140
Chain IDs:O (auth: BE)
Chain Length:18
Number of Molecules:1
Biological Source:Toxoplasma gondii

UniProt ID:S8G6E6

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Mitochondrial ribosomal protein, mS147
Gene (Uniprot):TGME49_312390
Chain IDs:P (auth: BF)
Chain Length:304
Number of Molecules:1
Biological Source:Toxoplasma gondii

UniProt ID:A0A125YYT2

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Ribosomal protein, uS2m
Chain IDs:Q (auth: BG)
Chain Length:160
Number of Molecules:1
Biological Source:Toxoplasma gondii

UniProt ID:A0A125YPC1

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Putative ribosomal protein S8
Chain IDs:R (auth: BH)
Chain Length:129
Number of Molecules:1
Biological Source:Toxoplasma gondii

UniProt ID:A0A125YNF6

Polymer Type:polypeptide(L)
Molecule:unidentified peptide
Chain IDs:S (auth: BI), W (auth: BN), FA (auth: BX)
Chain Length:13
Number of Molecules:3
Biological Source:Toxoplasma gondii

Polymer Type:polypeptide(L)
Molecule:unidentified peptide
Chain IDs:T (auth: BJ)
Chain Length:21
Number of Molecules:1
Biological Source:Toxoplasma gondii

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Mitochondrial ribosomal protein, mS26
Chain IDs:U (auth: BK)
Chain Length:447
Number of Molecules:1
Biological Source:Toxoplasma gondii

UniProt ID:S8EVV8

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Putative ribosomal protein S17
Chain IDs:V (auth: BL)
Chain Length:593
Number of Molecules:1
Biological Source:Toxoplasma gondii

UniProt ID:A0A125YU95

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Putative 30S ribosomal protein S15
Chain IDs:X (auth: BO)
Chain Length:115
Number of Molecules:1
Biological Source:Toxoplasma gondii

UniProt ID:A0A125YGX6

Polymer Type:polypeptide(L)
Molecule:unidentified peptide
Chain IDs:Y (auth: BP)
Chain Length:47
Number of Molecules:1
Biological Source:Toxoplasma gondii

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Macro domain-containing protein
Gene (Uniprot):TGME49_229900
Chain IDs:Z (auth: BQ)
Chain Length:698
Number of Molecules:1
Biological Source:Toxoplasma gondii

UniProt ID:S8GKJ3 Pfam ID:PF01661

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Ribosomal protein, bS21m
Gene (Uniprot):TGME49_248790
Chain IDs:AA (auth: BS)
Chain Length:243
Number of Molecules:1
Biological Source:Toxoplasma gondii

UniProt ID:S8G0I7

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Mitochondrial ribosomal protein, mS156
Chain IDs:BA (auth: BT)
Chain Length:280
Number of Molecules:1
Biological Source:Toxoplasma gondii

UniProt ID:A0A0F7VBJ0

Polymer Type:polypeptide(L)
Molecule:unidentified peptide
Chain IDs:CA (auth: BU)
Chain Length:14
Number of Molecules:1
Biological Source:Toxoplasma gondii

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Putative homeodomain containing protein
Chain IDs:DA (auth: BV)
Chain Length:6
Number of Molecules:1
Biological Source:Toxoplasma gondii

UniProt ID:S8F351

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Mitochondrial ribosomal protein, mS144
Gene (Uniprot):TGME49_229740
Chain IDs:EA (auth: BW)
Chain Length:547
Number of Molecules:1
Biological Source:Toxoplasma gondii

UniProt ID:S8F063

Polymer Type:polypeptide(L)
Molecule:unidentified peptide
Chain IDs:GA (auth: BY)
Chain Length:11
Number of Molecules:1
Biological Source:Toxoplasma gondii

Polymer Type:polypeptide(L)
Molecule:unidentified peptide
Chain IDs:HA (auth: Ba)
Chain Length:34
Number of Molecules:1
Biological Source:Toxoplasma gondii

Polymer Type:polypeptide(L)
Molecule:unidentified peptide
Chain IDs:IA (auth: Bb)
Chain Length:8
Number of Molecules:1
Biological Source:Toxoplasma gondii

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Enoyl-CoA hydratase/isomerase family protein
Chain IDs:JA (auth: Bc)
Chain Length:421
Number of Molecules:1
Biological Source:Toxoplasma gondii

UniProt ID:A0A125YR83

Polymer Type:polypeptide(L)
Molecule:unidentified peptide
Chain IDs:KA (auth: Bd)
Chain Length:686
Number of Molecules:1
Biological Source:Toxoplasma gondii

Polymer Type:polypeptide(L)
Molecule:unidentified peptide
Chain IDs:LA (auth: Be)
Chain Length:18
Number of Molecules:1
Biological Source:Toxoplasma gondii

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Ribosomal protein, uS2m
Chain IDs:MA (auth: Bg)
Chain Length:160
Number of Molecules:1
Biological Source:Toxoplasma gondii

UniProt ID:S8ETC4

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Putative 30S ribosomal protein S16
Chain IDs:NA (auth: Bh)
Chain Length:129
Number of Molecules:1
Biological Source:Toxoplasma gondii

UniProt ID:A0A125YN27

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Mitochondrial ribosomal protein, mS153
Chain IDs:OA (auth: Bi)
Chain Length:13
Number of Molecules:1
Biological Source:Toxoplasma gondii

UniProt ID:S8GJU2

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Mitochondrial ribosomal protein, mS26
Chain IDs:QA (auth: Bk)
Chain Length:447
Number of Molecules:1
Biological Source:Toxoplasma gondii

UniProt ID:S8G5S9

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S12, putative
Gene (Uniprot):TGME49_219770
Chain IDs:RA (auth: Bl)
Chain Length:593
Number of Molecules:1
Biological Source:Toxoplasma gondii

UniProt ID:S8EUD1 Pfam ID:PF00164

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S5, putative
Gene (Uniprot):TGME49_285970
Chain IDs:SA (auth: HJ)
Chain Length:1140
Number of Molecules:1
Biological Source:Toxoplasma gondii

UniProt ID:S8F5G8 Pfam ID:PF00333

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Acylphosphatase-like domain-containing protein
Chain IDs:TA (auth: HS)
Chain Length:235
Number of Molecules:1
Biological Source:Toxoplasma gondii

UniProt ID:A0A125YXT1

Polymer Type:polyribonucleotide
Molecule:ulr11
Chain IDs:UA (auth: b1)
Chain Length:8
Number of Molecules:1
Biological Source:Toxoplasma gondii

Polymer Type:polyribonucleotide
Molecule:SSUE
Chain IDs:VA (auth: b2)
Chain Length:738
Number of Molecules:1
Biological Source:Toxoplasma gondii

Polymer Type:polyribonucleotide
Molecule:ulr12
Chain IDs:WA (auth: b3)
Chain Length:5
Number of Molecules:1
Biological Source:Toxoplasma gondii

Polymer Type:polyribonucleotide
Molecule:RNA13
Chain IDs:XA (auth: b4)
Chain Length:138
Number of Molecules:1
Biological Source:Toxoplasma gondii

Polymer Type:polyribonucleotide
Molecule:RNA19
Chain IDs:YA (auth: bA)
Chain Length:34
Number of Molecules:1
Biological Source:Toxoplasma gondii

Polymer Type:polyribonucleotide
Molecule:RNA15
Chain IDs:ZA (auth: bD)
Chain Length:686
Number of Molecules:1
Biological Source:Toxoplasma gondii

Polymer Type:polyribonucleotide
Molecule:RNA8
Chain IDs:AB (auth: bE)
Chain Length:18
Number of Molecules:1
Biological Source:Toxoplasma gondii

Polymer Type:polyribonucleotide
Molecule:ulr13
Chain IDs:BB (auth: bG)
Chain Length:160
Number of Molecules:1
Biological Source:Toxoplasma gondii

Polymer Type:polyribonucleotide
Molecule:ulr14
Chain IDs:CB (auth: bH)
Chain Length:129
Number of Molecules:1
Biological Source:Toxoplasma gondii

Polymer Type:polyribonucleotide
Molecule:ulr15
Chain IDs:DB (auth: bI)
Chain Length:13
Number of Molecules:1
Biological Source:Toxoplasma gondii

Polymer Type:polyribonucleotide
Molecule:RNA33
Chain IDs:EB (auth: bJ)
Chain Length:21
Number of Molecules:1
Biological Source:Toxoplasma gondii

Polymer Type:polyribonucleotide
Molecule:RNA5
Chain IDs:FB (auth: bK)
Chain Length:447
Number of Molecules:1
Biological Source:Toxoplasma gondii

Polymer Type:polyribonucleotide
Molecule:RNA17
Chain IDs:GB (auth: bL)
Chain Length:593
Number of Molecules:1
Biological Source:Toxoplasma gondii

Polymer Type:polyribonucleotide
Molecule:SSUB
Chain IDs:HB (auth: bN)
Chain Length:13
Number of Molecules:1
Biological Source:Toxoplasma gondii

Polymer Type:polyribonucleotide
Molecule:SSUA
Chain IDs:IB (auth: bO)
Chain Length:115
Number of Molecules:1
Biological Source:Toxoplasma gondii

Polymer Type:polyribonucleotide
Molecule:ulr16
Chain IDs:JB (auth: bP)
Chain Length:47
Number of Molecules:1
Biological Source:Toxoplasma gondii

Polymer Type:polyribonucleotide
Molecule:ulr17
Chain IDs:KB (auth: bQ)
Chain Length:698
Number of Molecules:1
Biological Source:Toxoplasma gondii

Polymer Type:polyribonucleotide
Molecule:RNA30
Chain IDs:LB (auth: bR)
Chain Length:31
Number of Molecules:1
Biological Source:Toxoplasma gondii

Polymer Type:polyribonucleotide
Molecule:url18
Chain IDs:MB (auth: bS)
Chain Length:243
Number of Molecules:1
Biological Source:Toxoplasma gondii

Polymer Type:polyribonucleotide
Molecule:SSUF
Chain IDs:NB (auth: bT)
Chain Length:280
Number of Molecules:1
Biological Source:Toxoplasma gondii

Polymer Type:polyribonucleotide
Molecule:ulr19
Chain IDs:OB (auth: bU)
Chain Length:14
Number of Molecules:1
Biological Source:Toxoplasma gondii

Polymer Type:polyribonucleotide
Molecule:ulr20
Chain IDs:PB (auth: bV)
Chain Length:6
Number of Molecules:1
Biological Source:Toxoplasma gondii

Polymer Type:polyribonucleotide
Molecule:ulr21
Chain IDs:QB (auth: bY)
Chain Length:11
Number of Molecules:1
Biological Source:Toxoplasma gondii

Ligand Molecules

Primary Citation

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.Show

Nat Commun 15 10689 10689 (2024)

PMID: 39690155 DOI: 10.1038/s41467-024-55033-z

Abstact

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.

Legend

Protein

Chemical

Disease

Primary Citation of related structures