- PDB-6hiv: Cryo-EM structure of the Trypanosoma brucei mitochondrial ribosom... -
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Basic information
Entry
Database: PDB / ID: 6hiv
Title
Cryo-EM structure of the Trypanosoma brucei mitochondrial ribosome - This entry contains the complete mitoribosome
Components
(50S ribosomal protein ...) x 3
(UNK) x 17
(bL12m) x 3
(mL68) x 2
12S rRNA
9s rRNA
bL19m
bL20m
bL21m
bL27m
bL28m
bL31m
bL32m
bL33m
bL35m
bL36m
bL9m
bS12m
bS16m
bS18m
bS6m
mL100
mL38
mL40
mL41
mL42
mL43
mL46
mL49
mL52
mL53
mL63
mL67
mL69
mL70
mL71
mL72
mL73
mL74
mL75
mL76
mL77
mL78
mL79
mL80
mL81
mL82
mL83
mL84
mL85
mL86
mL87
mL88
mL89
mL90
mL92
mL93
mL94
mL95
mL96
mL97
mL98
mL99
mS22
mS23
mS26
mS29
mS33
mS34
mS35
mS37
mS38
mS43
mS47
mS52
mS91
ms34
ms42
ms48
ms49
ms50
ms51
ms53
ms54
ms55
ms56
ms57
ms58
ms59
ms60
ms61
ms62
ms63
ms64
ms65
ms66
ms67
ms68
ms69
ms70
ms71
ms72
ms73
ms74
mt-IF-3
uL10m
uL11m
uL15m
uL22m
uL23m
uL24m
uL29m
uL30m
uL3m
uL4m
uS10m
uS11m
uS12
uS14m
uS15m
uS17m
uS19m
uS3m
uS55m
uS8m
uS9m
Keywords
RIBOSOME / mitoribosome / translation / Trypanosoma / large ribosomal subunit / small ribosomal subunit / 12S rRNA / 9S rRNA / ribosomal protein
Function / homology
Function and homology information
modulation of formation of structure involved in a symbiotic process / organellar small ribosomal subunit / organellar large ribosomal subunit / 3-hydroxyisobutyryl-CoA hydrolase / 3-hydroxyisobutyryl-CoA hydrolase activity / mitochondrial mRNA editing complex / mitochondrial RNA processing / kinetoplast / thiosulfate sulfurtransferase activity / regulation of protein kinase A signaling ...modulation of formation of structure involved in a symbiotic process / organellar small ribosomal subunit / organellar large ribosomal subunit / 3-hydroxyisobutyryl-CoA hydrolase / 3-hydroxyisobutyryl-CoA hydrolase activity / mitochondrial mRNA editing complex / mitochondrial RNA processing / kinetoplast / thiosulfate sulfurtransferase activity / regulation of protein kinase A signaling / quorum sensing / nuclear lumen / enoyl-CoA hydratase activity / mitochondrial large ribosomal subunit / ciliary plasm / mRNA stabilization / mitochondrial small ribosomal subunit / post-transcriptional regulation of gene expression / mitochondrial ribosome / cyclosporin A binding / fatty acid beta-oxidation / mitochondrial translation / superoxide dismutase / protein kinase A regulatory subunit binding / superoxide dismutase activity / RNA processing / ciliary basal body / mitochondrion organization / 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 / membrane / nucleus / metal ion binding / cytosol / cytoplasm Similarity search - Function
Ribosomal protein S12 / Ribosomal protein S12 / : / : / 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 ...Ribosomal protein S12 / Ribosomal protein S12 / : / : / 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 domain / Enoyl-CoA hydratase/isomerase, HIBYL-CoA-H type / Enoyl-CoA hydratase/isomerase / Protein Fyv4 / IGR protein motif / IGR / Cyclic phosphodiesterase / Pentatricopeptide (PPR) repeat profile. / LIM domain / Ribosomal protein S23/S29, mitochondrial / Mitochondrial ribosomal death-associated protein 3 / 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 / DnaJ domain / Rhodanese-like domain / LysM domain / Rhodanese domain profile. / Rhodanese-like domain superfamily / 39S ribosomal protein L43/54S ribosomal protein L51 / Ribosomal protein L47, mitochondrial / MRP-L47 superfamily, mitochondrial / Mitochondrial 39-S ribosomal protein L47 (MRP-L47) / LysM domain / Rhodanese-like domain / Manganese/iron superoxide dismutase, C-terminal / Phosphatidylethanolamine-binding protein, eukaryotic / Manganese/iron superoxide dismutase, C-terminal domain superfamily / Manganese/iron superoxide dismutase, N-terminal domain superfamily / Iron/manganese superoxide dismutases, C-terminal domain / PEBP-like superfamily / DnaJ molecular chaperone homology domain / dnaJ domain profile. / Chaperone J-domain superfamily / DnaJ domain / Cyclophilin-type peptidyl-prolyl cis-trans isomerase / ANL, N-terminal domain / AMP-dependent synthetase/ligase / AMP-binding enzyme / 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 / 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 / NUDIX hydrolase-like domain superfamily / Zinc finger C2H2 superfamily / 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 / 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 / Translation elongation factor EF1B/ribosomal protein S6 / Ribosomal protein L3, bacterial/organelle-type / Ribosomal protein L15, bacterial-type / Ribosomal protein S18 superfamily / 50S ribosomal protein uL4 / : / Ribosomal protein S5, C-terminal / Ribosomal protein S5, C-terminal domain / Ubiquitin family / Ribosomal protein L10e/L16 / Ribosomal protein L10e/L16 superfamily / Ribosomal protein L16p/L10e Similarity search - Domain/homology
GUANOSINE-5'-TRIPHOSPHATE / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / SERINE / SPERMIDINE / SPERMINE / URIDINE 5'-TRIPHOSPHATE / : / RNA / RNA (> 10) / RNA (> 100) ...GUANOSINE-5'-TRIPHOSPHATE / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / SERINE / SPERMIDINE / SPERMINE / URIDINE 5'-TRIPHOSPHATE / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Ribosomal protein S12 / Large ribosomal subunit protein uL4m / Uncharacterized protein / Superoxide dismutase, putative / Uncharacterized protein / Uncharacterized protein / KOW domain-containing protein / Ubiquitin-like domain-containing protein / Uncharacterized protein / T. brucei spp.-specific protein / T. brucei spp.-specific protein / Uncharacterized protein / Chaperone protein DNAj, putative / Tetratricopeptide repeat / Cullin family profile domain-containing protein / Uncharacterized protein / Uncharacterized protein / Large ribosomal subunit protein uL22c / Uncharacterized protein / Large ribosomal subunit protein bL21m / Large ribosomal subunit protein mL46 / T. brucei spp.-specific protein / Uncharacterized protein / Ribosomal protein L30 ferredoxin-like fold domain-containing protein / T. brucei spp.-specific protein / T. brucei spp.-specific protein / T. brucei spp.-specific protein / T. brucei spp.-specific protein / Uncharacterized protein / Uncharacterized protein / Mitochondrial RNA binding protein / T. brucei spp.-specific protein / T. brucei spp.-specific protein / T. brucei spp.-specific protein / T. brucei spp.-specific protein / Maxicircle unassigned reading frame 5 / Uncharacterized protein / Phosphatidylethanolamine-binding protein / Uncharacterized protein / A-kinase anchor protein 7-like phosphoesterase domain-containing protein / Uncharacterized protein / Uncharacterized protein / Uncharacterized protein / Ribosomal protein S24/S35 mitochondrial conserved domain-containing protein / Large ribosomal subunit protein bL20c / 3-hydroxyisobutyryl-CoA hydrolase / Uncharacterized protein / Peptidyl-prolyl cis-trans isomerase / Uncharacterized protein / Uncharacterized protein / Uncharacterized protein / Mitochondrial SSU ribosomal protein / Mitochondrial SSU ribosomal protein / Large ribosomal subunit protein uL23m / Probable Zinc-ribbon domain-containing protein / Uncharacterized protein / Uncharacterized protein / 30S ribosomal protein S8, putative / Uncharacterized protein / Small ribosomal subunit protein mS41 / Uncharacterized protein / Uncharacterized protein / Uncharacterized protein / Mitochondrial ribosomal protein S18 / Small ribosomal subunit protein uS5 C-terminal domain-containing protein / Uncharacterized protein / Uncharacterized protein / Uncharacterized protein / Uncharacterized protein / Uncharacterized protein / Mitochondrial RNA binding complex 1 subunit / Trans-sialidase / Uncharacterized protein / 30S Ribosomal protein S17, putative / Uncharacterized protein / Large ribosomal subunit protein uL29m / Rhodanese domain-containing protein / Uncharacterized protein / Opioid growth factor receptor (OGFr) conserved domain-containing protein / Uncharacterized protein / Uncharacterized protein / Uncharacterized protein / Large ribosomal subunit protein uL15/eL18 domain-containing protein / Ribosomal protein L9 domain-containing protein / Uncharacterized protein / Uncharacterized protein / 50S ribosomal protein L16, putative / Uncharacterized protein / Ribosomal protein S23 mitochondrial conserved domain-containing protein Similarity search - Component
Biological species
Trypanosoma brucei brucei (eukaryote)
Method
ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 7.8 Å
Journal: Science / Year: 2018 Title: Evolutionary shift toward protein-based architecture in trypanosomal mitochondrial ribosomes. Authors: David J F Ramrath / Moritz Niemann / Marc Leibundgut / Philipp Bieri / Céline Prange / Elke K Horn / Alexander Leitner / Daniel Boehringer / André Schneider / Nenad Ban / Abstract: Ribosomal RNA (rRNA) plays key functional and architectural roles in ribosomes. Using electron microscopy, we determined the atomic structure of a highly divergent ribosome found in mitochondria of , ...Ribosomal RNA (rRNA) plays key functional and architectural roles in ribosomes. Using electron microscopy, we determined the atomic structure of a highly divergent ribosome found in mitochondria of , a unicellular parasite that causes sleeping sickness in humans. The trypanosomal mitoribosome features the smallest rRNAs and contains more proteins than all known ribosomes. The structure shows how the proteins have taken over the role of architectural scaffold from the rRNA: They form an autonomous outer shell that surrounds the entire particle and stabilizes and positions the functionally important regions of the rRNA. Our results also reveal the "minimal" set of conserved rRNA and protein components shared by all ribosomes that help us define the most essential functional elements.
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