- PDB-7aih: The Large subunit of the Kinetoplastid mitochondrial ribosome -
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Basic information
Entry
Database: PDB / ID: 7aih
Title
The Large subunit of the Kinetoplastid mitochondrial ribosome
Components
(Peptidyl-prolyl cis-trans ...) x 2
(Putative ribosomal protein ...) x 3
50S ribosomal protein L13-like protein
C2H2-type domain-containing protein
L51_S25_CI-B8 domain-containing protein
LIM zinc-binding domain-containing protein
MRP-L46 domain-containing protein
Putative 50S ribosomal protein L17
RIBOSOMAL_L9 domain-containing protein
Ribosomal RNA
Ribosomal protein L3-like protein
Ribosomal_L16 domain-containing protein
Ribosomal_L18e/L15P domain-containing protein
UA
UB
UC
UD
bL19m
bL20
bL21m
bL27m
bL28m
bL31m
bL32m
bL33m
bL35m
bL36m
mL100
mL38
mL40
mL41
mL42
mL49
mL52,mL52
mL53
mL54/69
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
uL10m
uL22m
uL23m
uL24m
uL29m
uL30m
uL4m
Keywords
RIBOSOME / Mitochondria / Kinetoplastid
Function / homology
Function and homology information
kinetoplast / nuclear lumen / mitochondrial large ribosomal subunit / ciliary plasm / mitochondrial ribosome / cyclosporin A binding / mitochondrial translation / peptidylprolyl isomerase / peptidyl-prolyl cis-trans isomerase activity / large ribosomal subunit ...kinetoplast / nuclear lumen / mitochondrial large ribosomal subunit / ciliary plasm / mitochondrial ribosome / cyclosporin A binding / mitochondrial translation / peptidylprolyl isomerase / peptidyl-prolyl cis-trans isomerase activity / large ribosomal subunit / protein folding / large ribosomal subunit rRNA binding / rRNA binding / negative regulation of translation / ribosome / structural constituent of ribosome / ribonucleoprotein complex / translation / mRNA binding / mitochondrion / RNA binding / membrane / nucleus / metal ion binding / cytosol / cytoplasm Similarity search - Function
PPR repeat family / LIM domain / Pentatricopeptide (PPR) repeat profile. / Zinc-binding domain present in Lin-11, Isl-1, Mec-3. / Zinc finger, LIM-type / LIM domain profile. / Pentatricopeptide repeat / Ribosomal protein L46, N-terminal / 39S mitochondrial ribosomal protein L46 / 39S ribosomal protein L46, mitochondrial ...PPR repeat family / LIM domain / Pentatricopeptide (PPR) repeat profile. / Zinc-binding domain present in Lin-11, Isl-1, Mec-3. / Zinc finger, LIM-type / LIM domain profile. / Pentatricopeptide repeat / Ribosomal protein L46, N-terminal / 39S mitochondrial ribosomal protein L46 / 39S ribosomal protein L46, mitochondrial / 39S ribosomal protein L43/54S ribosomal protein L51 / Ribosomal protein L47, mitochondrial / MRP-L47 superfamily, mitochondrial / Mitochondrial 39-S ribosomal protein L47 (MRP-L47) / Phosphatidylethanolamine-binding protein, eukaryotic / PEBP-like superfamily / 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 / 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 L24 / Ribosomal protein L3, bacterial/organelle-type / Ribosomal protein L15, bacterial-type / 50S ribosomal protein uL4 / Ribosomal protein L10e/L16 / Ribosomal protein L10e/L16 superfamily / Ribosomal protein L16p/L10e / Tetratricopeptide-like helical domain superfamily / Ribosomal Proteins L2, C-terminal domain / Ribosomal protein L2, C-terminal / Ribosomal Proteins L2, C-terminal domain / Ribosomal protein L24 signature. / Ribosomal protein L24/L26, conserved site / Ribosomal protein L2 / Ribosomal protein L13 / Ribosomal protein L13 / Ribosomal protein L13 superfamily / Ribosomal protein L25/L23 / Ribosomal protein L30, ferredoxin-like fold domain superfamily / Ribosomal proteins 50S-L15, 50S-L18e, 60S-L27A / Ribosomal protein L14P / Ribosomal protein L14 superfamily / Ribosomal protein L14p/L23e / Ribosomal protein L26/L24, KOW domain / Ribosomal protein L22/L17 / Ribosomal protein L22/L17 superfamily / Ribosomal protein L22p/L17e / Ribosomal protein L3 / Ribosomal protein L3 / Ribosomal protein L4/L1e / Ribosomal protein L4 domain superfamily / Ribosomal protein L4/L1 family / Ribosomal protein L18e/L15P / Ribosomal L18e/L15P superfamily / Alpha/Beta hydrolase fold / Ribosomal protein L23/L15e core domain superfamily / Translation protein SH3-like domain superfamily / Thioredoxin-like superfamily / Translation protein, beta-barrel domain superfamily / Ribosomal protein L2, domain 2 / Nucleotide-binding alpha-beta plait domain superfamily Similarity search - Domain/homology
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Flagellar attachment zone protein 1 / Uncharacterized protein / Ribosomal protein L9 domain-containing protein / Rhodanese domain-containing protein / Large ribosomal subunit protein uL11m ...NICOTINAMIDE-ADENINE-DINUCLEOTIDE / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Flagellar attachment zone protein 1 / Uncharacterized protein / Ribosomal protein L9 domain-containing protein / Rhodanese domain-containing protein / Large ribosomal subunit protein uL11m / Uncharacterized protein / Ribosomal protein L3-like protein / C2H2-type domain-containing protein / Uncharacterized protein / Uncharacterized protein / Uncharacterized protein / Uncharacterized protein / Large ribosomal subunit protein bL20c / Peptidyl-prolyl cis-trans isomerase / Uncharacterized 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 / Phosphatidylethanolamine-binding protein / Uncharacterized protein / 39S ribosomal protein L42, mitochondrial / Large ribosomal subunit protein mL43 / Uncharacterized protein / Uncharacterized protein / 39S ribosomal protein L28, mitochondrial / Uncharacterized protein / AMP-binding domain-containing protein / LIM zinc-binding domain-containing protein / Uncharacterized protein / Uncharacterized protein / Uncharacterized protein / KOW domain-containing protein / Large ribosomal subunit protein uL23m / Peptidyl-prolyl cis-trans isomerase / Large ribosomal subunit protein uL22c / Mitochondrial RNA binding complex 1 subunit / Uncharacterized protein / Uncharacterized protein / Uncharacterized protein / Uncharacterized protein / Prophage protein / Uncharacterized protein / AB hydrolase-1 domain-containing protein / Putative 50S ribosomal protein L17 / Large ribosomal subunit protein uL15/eL18 domain-containing protein / Ribosomal_L16 domain-containing protein / Large ribosomal subunit protein bL21m / 39S ribosomal protein L16, mitochondrial / Uncharacterized protein / Large ribosomal subunit protein uL4m / Uncharacterized protein / Uncharacterized protein / Putative ribosomal protein L2 / Ribosomal protein L9 domain-containing protein / Uncharacterized protein / Uncharacterized protein / MRP-L46 domain-containing protein / Uncharacterized protein / Ribosomal protein L30 ferredoxin-like fold domain-containing protein / Large ribosomal subunit protein uL29m Similarity search - Component
Biological species
Leishmania major (eukaryote)
Method
ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.6 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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