- PDB-7ane: Leishmania Major mitochondrial ribosome -
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Basic information
Entry
Database: PDB / ID: 7ane
Title
Leishmania Major mitochondrial ribosome
Components
(Peptidyl-prolyl cis-trans ...) x 2
(Putative ribosomal protein ...) x 3
30S Ribosomal protein S17-like proteinRibosome
50S ribosomal protein L13-like proteinRibosome
AKAP7_NLS domain-containing protein
C2H2-type domain-containing protein
Excreted/secreted protein 15
L51_S25_CI-B8 domain-containing protein
LIM zinc-binding domain-containing protein
Large ribosomal RNA
MRP-L46 domain-containing protein
Protein FYV4, mitochondrial
Putative 50S ribosomal protein L17
Putative superoxide dismutase
RIBOSOMAL_L9 domain-containing protein
Rhodanese domain-containing protein
Ribosomal protein L3-like proteinRibosome
Ribosomal_L16 domain-containing protein
Ribosomal_L18e/L15P domain-containing protein
Ribosomal_S5_C domain-containing protein
UA
UB
UC
UD
Ubiquitin-like domain-containing protein
bL19m
bL20m
bL21m
bL27m
bL28m
bL31m
bL32m
bL33m
bL35m
bL36m
bS16m
bS18m
bS21m
bS6m
mL100
mL38
mL40
mL41
mL42
mL49
mL52
mL53
mL59/64
mL63
mL68
mL69
mL70
mL72
mL73
mL74
mL75
mL76
mL79
mL80
mL82
mL84
mL85
mL86
mL87
mL88
mL89
mL93
mL94
mL95
mL96
mL97
mL98
mL99
mS22
mS23
mS26
mS29
mS33
mS34
mS35
mS37
mS43
mS47
mS48
mS49
mS50
mS51
mS52
mS53
mS55
mS56
mS57
mS58
mS59
mS60
mS61
mS62
mS63
mS65
mS66
mS69
mS70
mS71
mS72
mS73
uL10m
uL22m
uL23m
uL24m
uL29m
uL30m
uL4m
uS10m
uS11m
uS14m
uS15m
uS19m
uS3m
uS8m
uS9m
Keywords
RIBOSOME / Mitochondria / Kinetoplastid
Function / homology
Function and homology information
: / 3-hydroxyisobutyryl-CoA hydrolase activity / kinetoplast / enoyl-CoA hydratase activity / regulation of protein kinase A signaling / nuclear lumen / mRNA stabilization / mitochondrial large ribosomal subunit / ciliary plasm / mitochondrial small ribosomal subunit ...: / 3-hydroxyisobutyryl-CoA hydrolase activity / kinetoplast / enoyl-CoA hydratase activity / regulation of protein kinase A signaling / nuclear lumen / mRNA stabilization / mitochondrial large ribosomal subunit / ciliary plasm / mitochondrial small ribosomal subunit / mitochondrial ribosome / cyclosporin A binding / mitochondrial translation / fatty acid beta-oxidation / superoxide dismutase / protein kinase A regulatory subunit binding / superoxide dismutase activity / peptidylprolyl isomerase / peptidyl-prolyl cis-trans isomerase activity / large ribosomal subunit / protein folding / large ribosomal subunit rRNA binding / negative regulation of translation / rRNA binding / ribosome / structural constituent of ribosome / ribonucleoprotein complex / translation / mRNA binding / mitochondrion / RNA binding / nucleoplasm / membrane / metal ion binding / nucleus / cytosol / cytoplasm Similarity search - Function
Nucleoid-associated protein YbaB-like domain superfamily / Protein kinase A anchor protein, nuclear localisation signal domain / AKAP7 2'5' RNA ligase-like domain / Probable Zinc-ribbon domain / Probable Zinc-ribbon domain / Enoyl-CoA hydratase/isomerase, HIBYL-CoA-H type / Enoyl-CoA hydratase/isomerase / Protein Fyv4 / IGR protein motif / IGR ...Nucleoid-associated protein YbaB-like domain superfamily / Protein kinase A anchor protein, nuclear localisation signal domain / AKAP7 2'5' RNA ligase-like domain / Probable Zinc-ribbon domain / Probable Zinc-ribbon domain / Enoyl-CoA hydratase/isomerase, HIBYL-CoA-H type / Enoyl-CoA hydratase/isomerase / Protein Fyv4 / IGR protein motif / IGR / Cyclic phosphodiesterase / PPR repeat family / Mitochondrial 28S ribosomal protein S34 / Mitochondrial 28S ribosomal protein S34 / Pentatricopeptide (PPR) repeat profile. / Ribosomal protein S23/S29, mitochondrial / Mitochondrial ribosomal death-associated protein 3 / Rhodanese Homology Domain / Pentatricopeptide repeat / Ribosomal protein L46, N-terminal / 39S mitochondrial ribosomal protein L46 / LIM domain / 39S ribosomal protein L46, mitochondrial / Zinc-binding domain present in Lin-11, Isl-1, Mec-3. / Zinc finger, LIM-type / LIM domain profile. / Manganese/iron superoxide dismutase, N-terminal / Iron/manganese superoxide dismutases, alpha-hairpin domain / Rhodanese-like domain / LysM domain / Ribosomal protein L47, mitochondrial / MRP-L47 superfamily, mitochondrial / 39S ribosomal protein L43/54S ribosomal protein L51 / Mitochondrial 39-S ribosomal protein L47 (MRP-L47) / Phosphatidylethanolamine-binding protein, eukaryotic / Rhodanese domain profile. / Rhodanese-like domain superfamily / PEBP-like superfamily / LysM domain / Manganese/iron superoxide dismutase, C-terminal / Manganese/iron superoxide dismutase, C-terminal domain superfamily / Iron/manganese superoxide dismutases, C-terminal domain / Manganese/iron superoxide dismutase, N-terminal domain superfamily / Rhodanese-like domain / Cyclophilin-type peptidyl-prolyl cis-trans isomerase, conserved site / Cyclophilin-type peptidyl-prolyl cis-trans isomerase signature. / Cyclophilin-type peptidyl-prolyl cis-trans isomerase domain profile. / Cyclophilin-type peptidyl-prolyl cis-trans isomerase domain / Cyclophilin type peptidyl-prolyl cis-trans isomerase/CLD / AMP-dependent synthetase/ligase / AMP-binding enzyme / Cyclophilin-like domain superfamily / Ribosomal protein/NADH dehydrogenase domain / Mitochondrial ribosomal protein L51 / S25 / CI-B8 domain / Mitochondrial ribosomal protein L51 / S25 / CI-B8 domain / ClpP/crotonase-like domain superfamily / Zinc finger C2H2 superfamily / Zinc finger C2H2 type domain signature. / Zinc finger C2H2-type / Ribosomal protein L11, N-terminal / Ribosomal protein L11, N-terminal domain / Ribosomal protein L11/L12 / Ribosomal protein L11, C-terminal / Ribosomal protein L11, C-terminal domain superfamily / Ribosomal protein L11/L12, N-terminal domain superfamily / Ribosomal protein L11, RNA binding domain / Ribosomal protein L11/L12 / Ribosomal protein L9, N-terminal / Ribosomal protein L9, N-terminal domain / Ribosomal protein L28/L24 / Ribosomal protein L33 superfamily / : / Ribosomal protein L16 / Ribosomal protein L20 / Ribosomal protein L20, C-terminal / Ribosomal protein L21 / Ribosomal protein L17 / Ribosomal protein L17 superfamily / Ribosomal protein L17 / Ribosomal protein L21-like / L21-like superfamily / Ribosomal prokaryotic L21 protein / Ribosomal protein S6 superfamily / Ribosomal protein L24 / Translation elongation factor EF1B/ribosomal protein S6 / Ribosomal protein L3, bacterial/organelle-type / Ribosomal protein L15, bacterial-type / 50S ribosomal protein uL4 / Ribosomal protein S18 superfamily / Ribosomal protein S5, C-terminal / Ribosomal protein S5, C-terminal domain / Ribosomal protein L10e/L16 / Ribosomal protein L10e/L16 superfamily / Ribosomal protein L16p/L10e / Ribosomal protein S8 / Ribosomal protein S8 superfamily / Ribosomal protein S8 / Ribosomal protein L25/L23 / Ribosomal protein L30, ferredoxin-like fold domain superfamily / Tetratricopeptide-like helical domain superfamily Similarity search - Domain/homology
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Uncharacterized protein / Ribosomal protein L9 domain-containing protein / Uncharacterized protein / Rhodanese domain-containing protein ...NICOTINAMIDE-ADENINE-DINUCLEOTIDE / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Uncharacterized protein / Ribosomal protein L9 domain-containing protein / Uncharacterized protein / Rhodanese domain-containing protein / Large ribosomal subunit protein uL11m / Uncharacterized protein / Uncharacterized protein / Uncharacterized protein / Uncharacterized protein / Ribosomal protein L3-like protein / C2H2-type domain-containing protein / Uncharacterized protein / Uncharacterized protein / Uncharacterized protein / Uncharacterized protein / 30S Ribosomal protein S17-like protein / Uncharacterized protein / Excreted/secreted protein 15 / Uncharacterized protein / Uncharacterized protein / Uncharacterized protein / Uncharacterized protein / Uncharacterized protein / Uncharacterized protein / Large ribosomal subunit protein bL20c / Peptidyl-prolyl cis-trans isomerase / Uncharacterized protein / Uncharacterized protein / Ribosomal_S5_C domain-containing protein / Putative ribosomal protein L14 / 50S ribosomal protein L13-like protein / Uncharacterized protein / Uncharacterized protein / Uncharacterized protein / Uncharacterized protein / Uncharacterized protein / Uncharacterized protein / Uncharacterized protein / Uncharacterized protein / Protein FYV4, mitochondrial / Uncharacterized protein / Uncharacterized protein / Uncharacterized protein / Phosphatidylethanolamine-binding protein / Uncharacterized protein / AKAP7_NLS domain-containing protein / 39S ribosomal protein L42, mitochondrial / Large ribosomal subunit protein mL43 / Rhodanese domain-containing protein / Uncharacterized protein / Uncharacterized protein / Uncharacterized protein / Uncharacterized protein / Putative superoxide dismutase / 39S ribosomal protein L28, mitochondrial / Uncharacterized protein / Uncharacterized protein / AMP-binding domain-containing protein / Uncharacterized protein / LIM zinc-binding domain-containing protein / Uncharacterized protein / Uncharacterized protein / Uncharacterized protein / Uncharacterized protein / Uncharacterized protein / Uncharacterized protein / Uncharacterized protein / Ubiquitin-like domain-containing protein / KOW domain-containing protein / Large ribosomal subunit protein uL23m / Uncharacterized protein / Uncharacterized protein / Peptidyl-prolyl cis-trans isomerase / Uncharacterized protein / Uncharacterized protein / Large ribosomal subunit protein uL22c / Uncharacterized protein / Mitochondrial RNA binding complex 1 subunit / Uncharacterized protein / Uncharacterized protein / Uncharacterized protein / Uncharacterized protein / Uncharacterized protein / Uncharacterized protein / Uncharacterized protein / Uncharacterized protein / Prophage protein / Uncharacterized protein / AB hydrolase-1 domain-containing protein / Uncharacterized protein / Putative 50S ribosomal protein L17 / Large ribosomal subunit protein uL15/eL18 domain-containing protein / Uncharacterized protein / Uncharacterized protein Similarity search - Component
Biological species
Leishmania major (eukaryote)
Method
ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.9 Å
Journal: Proc Natl Acad Sci U S A / Year: 2020 Title: Structure of the mature kinetoplastids mitoribosome and insights into its large subunit biogenesis. Authors: Heddy Soufari / Florent Waltz / Camila Parrot / Stéphanie Durrieu-Gaillard / Anthony Bochler / Lauriane Kuhn / Marie Sissler / Yaser Hashem / Abstract: Kinetoplastids are unicellular eukaryotic parasites responsible for such human pathologies as Chagas disease, sleeping sickness, and leishmaniasis. They have a single large mitochondrion, essential ...Kinetoplastids are unicellular eukaryotic parasites responsible for such human pathologies as Chagas disease, sleeping sickness, and leishmaniasis. They have a single large mitochondrion, essential for the parasite survival. In kinetoplastid mitochondria, most of the molecular machineries and gene expression processes have significantly diverged and specialized, with an extreme example being their mitochondrial ribosomes. These large complexes are in charge of translating the few essential mRNAs encoded by mitochondrial genomes. Structural studies performed in already highlighted the numerous peculiarities of these mitoribosomes and the maturation of their small subunit. However, several important aspects mainly related to the large subunit (LSU) remain elusive, such as the structure and maturation of its ribosomal RNA. Here we present a cryo-electron microscopy study of the protozoans and mitoribosomes. For both species, we obtained the structure of their mature mitoribosomes, complete rRNA of the LSU, as well as previously unidentified ribosomal proteins. In addition, we introduce the structure of an LSU assembly intermediate in the presence of 16 identified maturation factors. These maturation factors act on both the intersubunit and the solvent sides of the LSU, where they refold and chemically modify the rRNA and prevent early translation before full maturation of the LSU.
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