9G6K image
Entry Detail
PDB ID:
9G6K
EMDB ID:
Keywords:
Title:
LSU structure derived from the LSU sample of the mitoribosome from T. gondii.
Biological Source:
Source Organism:
PDB Version:
Deposition Date:
2024-07-18
Release Date:
2024-12-11
Method Details:
Experimental Method:
Resolution:
2.89 Å
Aggregation State:
PARTICLE
Reconstruction Method:
SINGLE PARTICLE
Macromolecular Entities
Polymer Type:polypeptide(L)
Description:RRM domain-containing protein
Chain IDs:A (auth: L0)
Chain Length:44
Number of Molecules:1
Biological Source:Toxoplasma gondii
Polymer Type:polypeptide(L)
Description:Large ribosomal subunit protein mL54
Chain IDs:B (auth: L1)
Chain Length:92
Number of Molecules:1
Biological Source:Toxoplasma gondii
Polymer Type:polypeptide(L)
Description:mL162
Chain IDs:C (auth: L2)
Chain Length:31
Number of Molecules:1
Biological Source:Toxoplasma gondii
Polymer Type:polypeptide(L)
Description:Ribosomal l25 family protein
Chain IDs:D (auth: L3)
Chain Length:331
Number of Molecules:1
Biological Source:Toxoplasma gondii
Polymer Type:polypeptide(L)
Description:RAP domain-containing protein
Chain IDs:E (auth: L4)
Chain Length:430
Number of Molecules:1
Biological Source:Toxoplasma gondii
Polymer Type:polypeptide(L)
Description:mL183
Chain IDs:F (auth: L5)
Chain Length:36
Number of Molecules:1
Biological Source:Toxoplasma gondii
Polymer Type:polypeptide(L)
Description:uL1m
Chain IDs:G (auth: L6)
Chain Length:50
Number of Molecules:1
Biological Source:Toxoplasma gondii
Polymer Type:polypeptide(L)
Description:uL14m
Chain IDs:H (auth: L7)
Chain Length:114
Number of Molecules:1
Biological Source:Toxoplasma gondii
Polymer Type:polypeptide(L)
Description:Putative 50S ribosomal protein L17
Chain IDs:I (auth: L8)
Chain Length:33
Number of Molecules:1
Biological Source:Toxoplasma gondii
Polymer Type:polypeptide(L)
Description:DUF6832 domain-containing protein
Chain IDs:J (auth: L9)
Chain Length:91
Number of Molecules:1
Biological Source:Toxoplasma gondii
Polymer Type:polypeptide(L)
Description:Putative 50S ribosomal protein L13
Chain IDs:K (auth: LA)
Chain Length:214
Number of Molecules:1
Biological Source:Toxoplasma gondii
Polymer Type:polypeptide(L)
Description:Putative ribosomal protein L20
Chain IDs:L (auth: LB)
Chain Length:45
Number of Molecules:1
Biological Source:Toxoplasma gondii
Polymer Type:polypeptide(L)
Description:Macro domain-containing protein
Chain IDs:M (auth: LC)
Chain Length:527
Number of Molecules:1
Biological Source:Toxoplasma gondii
Polymer Type:polypeptide(L)
Description:Ribosomal protein L46
Chain IDs:N (auth: LD)
Chain Length:282
Number of Molecules:1
Biological Source:Toxoplasma gondii
Polymer Type:polypeptide(L)
Description:FAS1 domain-containing protein
Chain IDs:O (auth: LE)
Chain Length:338
Number of Molecules:1
Biological Source:Toxoplasma gondii
Polymer Type:polypeptide(L)
Description:bL36m
Chain IDs:P (auth: LF)
Chain Length:88
Number of Molecules:1
Biological Source:Toxoplasma gondii
Polymer Type:polypeptide(L)
Description:Ribosomal protein RPL22
Chain IDs:Q (auth: LG)
Chain Length:26
Number of Molecules:1
Biological Source:Toxoplasma gondii
Polymer Type:polypeptide(L)
Description:Ribosomal protein L9, N-terminal domain-containing protein
Chain IDs:R (auth: LH)
Chain Length:27
Number of Molecules:1
Biological Source:Toxoplasma gondii
Polymer Type:polypeptide(L)
Description:Putative 60S ribosomal protein L27
Chain IDs:S (auth: LI)
Chain Length:48
Number of Molecules:1
Biological Source:Toxoplasma gondii
Polymer Type:polypeptide(L)
Description:RAP domain-containing protein
Chain IDs:T (auth: LJ)
Chain Length:443
Number of Molecules:1
Biological Source:Toxoplasma gondii
Polymer Type:polypeptide(L)
Description:BIR protein
Chain IDs:U (auth: LK)
Chain Length:184
Number of Molecules:1
Biological Source:Toxoplasma gondii
Polymer Type:polypeptide(L)
Description:AMP-dependent synthetase/ligase domain-containing protein
Chain IDs:V (auth: LL)
Chain Length:91
Number of Molecules:1
Biological Source:Toxoplasma gondii
Polymer Type:polypeptide(L)
Description:Large ribosomal subunit protein uL11m
Chain IDs:W (auth: LM)
Chain Length:189
Number of Molecules:1
Biological Source:Toxoplasma gondii
Polymer Type:polypeptide(L)
Description:bL35m
Chain IDs:X (auth: LN)
Chain Length:60
Number of Molecules:1
Biological Source:Toxoplasma gondii
Polymer Type:polypeptide(L)
Description:LSU ribosomal protein L2P, putative
Chain IDs:Y (auth: LO)
Chain Length:344
Number of Molecules:1
Biological Source:Toxoplasma gondii
Polymer Type:polypeptide(L)
Description:Peptidyl-prolyl cis-trans isomerase
Chain IDs:Z (auth: LP)
Chain Length:230
Number of Molecules:1
Biological Source:Toxoplasma gondii
Polymer Type:polypeptide(L)
Description:mL175
Chain IDs:AA (auth: LQ)
Chain Length:70
Number of Molecules:1
Biological Source:Toxoplasma gondii
Polymer Type:polypeptide(L)
Description:mL172
Chain IDs:BA (auth: LR)
Chain Length:28
Number of Molecules:1
Biological Source:Toxoplasma gondii
Polymer Type:polypeptide(L)
Description:Large ribosomal subunit protein uL24c
Chain IDs:CA (auth: LS)
Chain Length:7
Number of Molecules:1
Biological Source:Toxoplasma gondii
Polymer Type:polypeptide(L)
Description:Putative 50S ribosomal protein L33
Chain IDs:DA (auth: LT)
Chain Length:117
Number of Molecules:1
Biological Source:Toxoplasma gondii
Polymer Type:polypeptide(L)
Description:Large ribosomal subunit protein mL49
Chain IDs:EA (auth: LU)
Chain Length:232
Number of Molecules:1
Biological Source:Toxoplasma gondii
Polymer Type:polypeptide(L)
Description:mL148
Chain IDs:FA (auth: LV)
Chain Length:10
Number of Molecules:1
Biological Source:Toxoplasma gondii
Polymer Type:polypeptide(L)
Description:Putative 50S ribosomal protein L3
Chain IDs:GA (auth: LW)
Chain Length:306
Number of Molecules:1
Biological Source:Toxoplasma gondii
Polymer Type:polypeptide(L)
Description:mL176
Chain IDs:HA (auth: LX)
Chain Length:98
Number of Molecules:1
Biological Source:Toxoplasma gondii
Polymer Type:polypeptide(L)
Description:Ribosomal L22p/L17e protein
Chain IDs:IA (auth: LY)
Chain Length:10
Number of Molecules:1
Biological Source:Toxoplasma gondii
Polymer Type:polypeptide(L)
Description:mL174
Chain IDs:JA (auth: LZ)
Chain Length:120
Number of Molecules:1
Biological Source:Toxoplasma gondii
Polymer Type:polypeptide(L)
Description:Large ribosomal subunit protein uL23m
Chain IDs:KA (auth: La)
Chain Length:214
Number of Molecules:1
Biological Source:Toxoplasma gondii
Polymer Type:polypeptide(L)
Description:RAP domain-containing protein
Chain IDs:LA (auth: Lb)
Chain Length:45
Number of Molecules:1
Biological Source:Toxoplasma gondii
Polymer Type:polypeptide(L)
Description:RAP domain-containing protein
Chain IDs:MA (auth: Lc)
Chain Length:527
Number of Molecules:1
Biological Source:Toxoplasma gondii
Polymer Type:polypeptide(L)
Description:RAP domain-containing protein
Chain IDs:NA (auth: Ld)
Chain Length:282
Number of Molecules:1
Biological Source:Toxoplasma gondii
Polymer Type:polypeptide(L)
Description:RAP domain-containing protein
Chain IDs:OA (auth: Le)
Chain Length:338
Number of Molecules:1
Biological Source:Toxoplasma gondii
Polymer Type:polypeptide(L)
Description:HECT-domain (Ubiquitin-transferase) domain-containing protein
Chain IDs:PA (auth: Lf)
Chain Length:88
Number of Molecules:1
Biological Source:Toxoplasma gondii
Polymer Type:polypeptide(L)
Description:Large ribosomal subunit protein uL29m
Chain IDs:QA (auth: Lg)
Chain Length:26
Number of Molecules:1
Biological Source:Toxoplasma gondii
Polymer Type:polypeptide(L)
Description:Large ribosomal subunit protein uL4m
Chain IDs:RA (auth: Lh)
Chain Length:27
Number of Molecules:1
Biological Source:Toxoplasma gondii
Polymer Type:polypeptide(L)
Description:RAP domain-containing protein
Chain IDs:SA (auth: Li)
Chain Length:48
Number of Molecules:1
Biological Source:Toxoplasma gondii
Polymer Type:polypeptide(L)
Description:mL177
Chain IDs:TA (auth: Lj)
Chain Length:443
Number of Molecules:1
Biological Source:Toxoplasma gondii
Polymer Type:polypeptide(L)
Description:AP2 domain transcription factor AP2VIIb-2
Chain IDs:UA (auth: Lk)
Chain Length:184
Number of Molecules:1
Biological Source:Toxoplasma gondii
Polymer Type:polypeptide(L)
Description:Large ribosomal subunit protein mL43
Chain IDs:VA (auth: Ll)
Chain Length:91
Number of Molecules:1
Biological Source:Toxoplasma gondii
Polymer Type:polypeptide(L)
Description:Large ribosomal subunit protein uL24c
Chain IDs:WA (auth: Lm)
Chain Length:189
Number of Molecules:1
Biological Source:Toxoplasma gondii
Polymer Type:polypeptide(L)
Description:mL185
Chain IDs:XA (auth: Ln)
Chain Length:60
Number of Molecules:1
Biological Source:Toxoplasma gondii
Polymer Type:polypeptide(L)
Description:Transmembrane protein
Chain IDs:YA (auth: Lo)
Chain Length:344
Number of Molecules:1
Biological Source:Toxoplasma gondii
Polymer Type:polypeptide(L)
Description:bL19m
Chain IDs:ZA (auth: Lp)
Chain Length:230
Number of Molecules:1
Biological Source:Toxoplasma gondii
Polymer Type:polypeptide(L)
Description:RAP domain-containing protein
Chain IDs:AB (auth: Lq)
Chain Length:70
Number of Molecules:1
Biological Source:Toxoplasma gondii
Polymer Type:polypeptide(L)
Description:Putative ribosomal protein L28
Chain IDs:BB (auth: Lr)
Chain Length:28
Number of Molecules:1
Biological Source:Toxoplasma gondii
Polymer Type:polypeptide(L)
Description:Ribosomal protein L15, putative
Chain IDs:CB (auth: Ls)
Chain Length:7
Number of Molecules:1
Biological Source:Toxoplasma gondii
Polymer Type:polypeptide(L)
Description:mL40
Chain IDs:DB (auth: Lt)
Chain Length:117
Number of Molecules:1
Biological Source:Toxoplasma gondii
Polymer Type:polypeptide(L)
Description:mL164
Chain IDs:EB (auth: Lu)
Chain Length:232
Number of Molecules:1
Biological Source:Toxoplasma gondii
Polymer Type:polypeptide(L)
Description:mL180
Chain IDs:FB (auth: Lv)
Chain Length:10
Number of Molecules:1
Biological Source:Toxoplasma gondii
Polymer Type:polypeptide(L)
Description:Putative 50S ribosomal protein L16
Chain IDs:GB (auth: Lw)
Chain Length:306
Number of Molecules:1
Biological Source:Toxoplasma gondii
Polymer Type:polypeptide(L)
Description:mL173
Chain IDs:HB (auth: Lx)
Chain Length:98
Number of Molecules:1
Biological Source:Toxoplasma gondii
Polymer Type:polypeptide(L)
Description:Large ribosomal subunit protein bL21m
Chain IDs:IB (auth: Ly)
Chain Length:10
Number of Molecules:1
Biological Source:Toxoplasma gondii
Polymer Type:polypeptide(L)
Description:mL182
Chain IDs:JB (auth: Lz)
Chain Length:120
Number of Molecules:1
Biological Source:Toxoplasma gondii
Polymer Type:polypeptide(L)
Description:mL178
Chain IDs:KB (auth: UA)
Chain Length:85
Number of Molecules:1
Biological Source:Toxoplasma gondii
Polymer Type:polypeptide(L)
Description:bL27m
Chain IDs:LB (auth: UB)
Chain Length:174
Number of Molecules:1
Biological Source:Toxoplasma gondii
Polymer Type:polypeptide(L)
Description:mL179
Chain IDs:MB (auth: UC)
Chain Length:105
Number of Molecules:1
Biological Source:Toxoplasma gondii
Polymer Type:polypeptide(L)
Description:Transmembrane protein
Chain IDs:NB (auth: UD)
Chain Length:35
Number of Molecules:1
Biological Source:Toxoplasma gondii
Polymer Type:polypeptide(L)
Description:mL53
Chain IDs:OB (auth: UE)
Chain Length:113
Number of Molecules:1
Biological Source:Toxoplasma gondii
Polymer Type:polypeptide(L)
Description:bL32m
Chain IDs:PB (auth: UF)
Chain Length:78
Number of Molecules:1
Biological Source:Toxoplasma gondii
Polymer Type:polypeptide(L)
Description:AP2 domain transcription factor AP2IV-1
Chain IDs:QB (auth: UG)
Chain Length:158
Number of Molecules:1
Biological Source:Toxoplasma gondii
Polymer Type:polypeptide(L)
Description:mL181
Chain IDs:RB (auth: UH)
Chain Length:47
Number of Molecules:1
Biological Source:Toxoplasma gondii
Polymer Type:polypeptide(L)
Description:mL184
Chain IDs:SB (auth: UI)
Chain Length:35
Number of Molecules:1
Biological Source:Toxoplasma gondii
Polymer Type:polyribonucleotide
Description:RNA23t
Chain IDs:TB (auth: l0)
Chain Length:44
Number of Molecules:1
Biological Source:Toxoplasma gondii
Polymer Type:polyribonucleotide
Description:RNA29
Chain IDs:UB (auth: l1)
Chain Length:92
Number of Molecules:1
Biological Source:Toxoplasma gondii
Polymer Type:polyribonucleotide
Description:LSUB
Chain IDs:VB (auth: l2)
Chain Length:31
Number of Molecules:1
Biological Source:Toxoplasma gondii
Polymer Type:polyribonucleotide
Description:RNA6
Chain IDs:WB (auth: l3)
Chain Length:331
Number of Molecules:1
Biological Source:Toxoplasma gondii
Polymer Type:polyribonucleotide
Description:RNA1
Chain IDs:XB (auth: l4)
Chain Length:430
Number of Molecules:1
Biological Source:Toxoplasma gondii
Polymer Type:polyribonucleotide
Description:RNA31
Chain IDs:YB (auth: l5)
Chain Length:36
Number of Molecules:1
Biological Source:Toxoplasma gondii
Polymer Type:polyribonucleotide
Description:RNA14
Chain IDs:ZB (auth: l6)
Chain Length:50
Number of Molecules:1
Biological Source:Toxoplasma gondii
Polymer Type:polyribonucleotide
Description:RNA11
Chain IDs:AC (auth: l7)
Chain Length:114
Number of Molecules:1
Biological Source:Toxoplasma gondii
Polymer Type:polyribonucleotide
Description:RNA36
Chain IDs:BC (auth: l8)
Chain Length:33
Number of Molecules:1
Biological Source:Toxoplasma gondii
Polymer Type:polyribonucleotide
Description:RNA3
Chain IDs:CC (auth: l9)
Chain Length:91
Number of Molecules:1
Biological Source:Toxoplasma gondii
Polymer Type:polyribonucleotide
Description:RNA2
Chain IDs:DC (auth: lA)
Chain Length:214
Number of Molecules:1
Biological Source:Toxoplasma gondii
Polymer Type:polyribonucleotide
Description:RNA38
Chain IDs:EC (auth: lB)
Chain Length:45
Number of Molecules:1
Biological Source:Toxoplasma gondii
Polymer Type:polyribonucleotide
Description:RNA35
Chain IDs:FC (auth: lC)
Chain Length:527
Number of Molecules:1
Biological Source:Toxoplasma gondii
Polymer Type:polyribonucleotide
Description:RNA32
Chain IDs:GC (auth: lD)
Chain Length:282
Number of Molecules:1
Biological Source:Toxoplasma gondii
Polymer Type:polyribonucleotide
Description:RNA15
Chain IDs:HC (auth: lE)
Chain Length:338
Number of Molecules:1
Biological Source:Toxoplasma gondii
Polymer Type:polyribonucleotide
Description:RNA10
Chain IDs:IC (auth: lF)
Chain Length:88
Number of Molecules:1
Biological Source:Toxoplasma gondii
Polymer Type:polyribonucleotide
Description:LSUC
Chain IDs:JC (auth: lG)
Chain Length:26
Number of Molecules:1
Biological Source:Toxoplasma gondii
Polymer Type:polyribonucleotide
Description:RNA16
Chain IDs:KC (auth: lH)
Chain Length:27
Number of Molecules:1
Biological Source:Toxoplasma gondii
Polymer Type:polyribonucleotide
Description:RNA13
Chain IDs:LC (auth: lI)
Chain Length:48
Number of Molecules:1
Biological Source:Toxoplasma gondii
Polymer Type:polyribonucleotide
Description:LSUD/E
Chain IDs:MC (auth: lJ)
Chain Length:443
Number of Molecules:1
Biological Source:Toxoplasma gondii
Polymer Type:polyribonucleotide
Description:SSUF
Chain IDs:NC (auth: lK)
Chain Length:184
Number of Molecules:1
Biological Source:Toxoplasma gondii
Polymer Type:polyribonucleotide
Description:RNA7
Chain IDs:OC (auth: lL)
Chain Length:91
Number of Molecules:1
Biological Source:Toxoplasma gondii
Polymer Type:polyribonucleotide
Description:LSUF/G
Chain IDs:PC (auth: lM)
Chain Length:189
Number of Molecules:1
Biological Source:Toxoplasma gondii
Polymer Type:polyribonucleotide
Description:RNA37
Chain IDs:QC (auth: lN)
Chain Length:60
Number of Molecules:1
Biological Source:Toxoplasma gondii
Polymer Type:polyribonucleotide
Description:LSUA
Chain IDs:RC (auth: lO)
Chain Length:344
Number of Molecules:1
Biological Source:Toxoplasma gondii
Polymer Type:polyribonucleotide
Description:ulr1
Chain IDs:SC (auth: lP)
Chain Length:230
Number of Molecules:1
Biological Source:Toxoplasma gondii
Polymer Type:polyribonucleotide
Description:ulr2
Chain IDs:TC (auth: lQ)
Chain Length:70
Number of Molecules:1
Biological Source:Toxoplasma gondii
Polymer Type:polyribonucleotide
Description:ulr3
Chain IDs:UC (auth: lR)
Chain Length:28
Number of Molecules:1
Biological Source:Toxoplasma gondii
Polymer Type:polyribonucleotide
Description:ulr4
Chain IDs:VC (auth: lS)
Chain Length:7
Number of Molecules:1
Biological Source:Toxoplasma gondii
Polymer Type:polyribonucleotide
Description:ulr5
Chain IDs:WC (auth: lT), ZC (auth: lW)
Chain Length:117
Number of Molecules:2
Biological Source:Toxoplasma gondii
Polymer Type:polyribonucleotide
Description:ulr6
Chain IDs:XC (auth: lU)
Chain Length:232
Number of Molecules:1
Biological Source:Toxoplasma gondii
Polymer Type:polyribonucleotide
Description:ulr7,ulr8
Chain IDs:YC (auth: lV), BD (auth: lY)
Chain Length:10
Number of Molecules:2
Biological Source:Toxoplasma gondii
Polymer Type:polyribonucleotide
Description:ulr9
Chain IDs:AD (auth: lX)
Chain Length:98
Number of Molecules:1
Biological Source:Toxoplasma gondii
Ligand Molecules
Primary Citation

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