- PDB-6hix: Cryo-EM structure of the Trypanosoma brucei mitochondrial ribosom... -
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Basic information
Entry
Database: PDB / ID: 6hix
Title
Cryo-EM structure of the Trypanosoma brucei mitochondrial ribosome - This entry contains the large mitoribosomal subunit
Components
(50S ribosomal protein ...) x 3
(Peptidyl-prolyl cis-trans ...) x 2
(Ribosomal protein ...) x 3
(UNK) x 13
(bL12m) x 3
12S rRNA
Chaperone protein DNAj, putative
bl19m
bl20m
bl21m
bl27m
bl28m
bl31m
bl32m
bl33m
bl35m
bl36m
bl9m
mL70
ml100
ml38
ml40
ml41
ml42
ml43
ml46
ml49
ml52
ml53
ml63
ml64
ml67
ml68
ml69
ml71
ml72
ml73
ml74
ml75
ml76
ml78
ml79
ml80
ml81
ml82
ml84
ml85
ml86
ml87
ml88
ml89
ml90
ml91
ml93
ml94
ml95
ml96
ml97
ml98
ml99
ul10m
ul15m
ul22m
ul23m
ul24m
ul29m
ul30m
Keywords
RIBOSOME / mitoribosome / translation / Trypanosoma / large ribosomal subunit / 12S rRNA / ribosomal protein
Function / homology
Function and homology information
: / organellar large ribosomal subunit / mitochondrial mRNA editing complex / mitochondrial RNA processing / kinetoplast / nuclear lumen / mitochondrial large ribosomal subunit / ciliary plasm / mitochondrial ribosome / post-transcriptional regulation of gene expression ...: / organellar large ribosomal subunit / mitochondrial mRNA editing complex / mitochondrial RNA processing / kinetoplast / nuclear lumen / mitochondrial large ribosomal subunit / ciliary plasm / mitochondrial ribosome / post-transcriptional regulation of gene expression / cyclosporin A binding / mitochondrial translation / ciliary basal body / peptidylprolyl isomerase / peptidyl-prolyl cis-trans isomerase activity / large ribosomal subunit / protein folding / large ribosomal subunit rRNA binding / cytosolic large ribosomal subunit / rRNA binding / negative regulation of translation / ribosome / structural constituent of ribosome / translation / ribonucleoprotein complex / mRNA binding / mitochondrion / RNA binding / nucleus / metal ion binding / cytoplasm / cytosol Similarity search - Function
: / 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 ...: / 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 / DnaJ domain / 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) / Phosphatidylethanolamine-binding protein, eukaryotic / 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 / 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 / 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 / Ribosomal protein L3, bacterial/organelle-type / Ribosomal protein L15, bacterial-type / 50S ribosomal protein uL4 / Prokaryotic membrane lipoprotein lipid attachment site profile. / Ribosomal protein L10e/L16 / Ribosomal protein L10e/L16 superfamily / Ribosomal protein L16p/L10e / Tetratricopeptide-like helical domain superfamily / 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 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) / Large ribosomal subunit protein uL4m / Replication restart DNA helicase PriA / 39S ribosomal protein L55, mitochondrial / KOW domain-containing protein ...NICOTINAMIDE-ADENINE-DINUCLEOTIDE / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Large ribosomal subunit protein uL4m / Replication restart DNA helicase PriA / 39S ribosomal protein L55, mitochondrial / KOW domain-containing protein / 39S ribosomal protein L32, mitochondrial / LETM1 domain-containing protein / Uncharacterized protein / Chaperone protein DNAj, putative / TPR_REGION domain-containing protein / Large ribosomal subunit protein uL22c / Large ribosomal subunit protein bL21m / MRP-L46 domain-containing protein / T. brucei spp.-specific protein / Uncharacterized protein / Ribosomal protein L30 ferredoxin-like fold domain-containing protein / Uncharacterized protein / Uncharacterized 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 / Uncharacterized protein / Uncharacterized protein / Uncharacterized protein / Uncharacterized protein / Uncharacterized protein / Ribosomal protein S24/S35 mitochondrial conserved domain-containing protein / Large ribosomal subunit protein bL20c / Uncharacterized protein / Peptidyl-prolyl cis-trans isomerase / Uncharacterized protein / Large ribosomal subunit protein uL23m / Zn_Tnp_IS91 domain-containing protein / Uncharacterized protein / Uncharacterized protein / Uncharacterized protein / Uncharacterized protein / Mitochondrial RNA binding complex 1 subunit / Large ribosomal subunit protein uL29m / Rhodanese domain-containing protein / Uncharacterized protein / Uncharacterized protein / Large ribosomal subunit protein uL15/eL18 domain-containing protein / Ribosomal protein L9 domain-containing protein / 50S ribosomal protein L16, putative / Peptidyl-prolyl cis-trans isomerase / Uncharacterized protein / Uncharacterized protein / AB hydrolase-1 domain-containing protein / Uncharacterized protein / 50S ribosomal protein L17, putative / Uncharacterized protein / 50S ribosomal protein L13, putative / Ribosomal protein L3 mitochondrial, putative / C2H2-type domain-containing protein / Uncharacterized protein / Large ribosomal subunit protein mL43 / Uncharacterized protein / AMP-binding domain-containing protein / Uncharacterized protein / LIM zinc-binding domain-containing protein / 39S ribosomal protein L28, mitochondrial / Uncharacterized protein / Large ribosomal subunit protein uL11m / Uncharacterized protein Similarity search - Component
Biological species
Trypanosoma brucei brucei (eukaryote)
Method
ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.39 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.
History
Deposition
Aug 31, 2018
Deposition site: PDBE / Processing site: PDBE
Revision 1.0
Sep 26, 2018
Provider: repository / Type: Initial release
Revision 1.1
Nov 7, 2018
Group: Data collection / Database references / Source and taxonomy Category: citation / entity_src_gen Item: _citation.journal_volume / _entity_src_gen.gene_src_strain / _entity_src_gen.pdbx_gene_src_scientific_name
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