Pseudouridine synthase, TruD / GTPase Der, C-terminal KH-domain-like / KH-domain-like of EngA bacterial GTPase enzymes, C-terminal / Pseudouridine synthase, RsuA/RluA-like / RNA pseudouridylate synthase / tRNA/rRNA methyltransferase, SpoU type / SpoU rRNA Methylase family / Fungal lipase-like domain / Lipase (class 3) / Pseudouridine synthase, catalytic domain superfamily ...Pseudouridine synthase, TruD / GTPase Der, C-terminal KH-domain-like / KH-domain-like of EngA bacterial GTPase enzymes, C-terminal / Pseudouridine synthase, RsuA/RluA-like / RNA pseudouridylate synthase / tRNA/rRNA methyltransferase, SpoU type / SpoU rRNA Methylase family / Fungal lipase-like domain / Lipase (class 3) / Pseudouridine synthase, catalytic domain superfamily / Protein Iojap/ribosomal silencing factor RsfS / Pentatricopeptide (PPR) repeat profile. / GTP-binding protein, orthogonal bundle domain superfamily / LIM domain / Zinc-binding domain present in Lin-11, Isl-1, Mec-3. / Zinc finger, LIM-type / Pentatricopeptide repeat / LIM domain profile. / DnaJ domain / 39S ribosomal protein L43/54S ribosomal protein L51 / Ribosomal protein L47, mitochondrial / MRP-L47 superfamily, mitochondrial / Mitochondrial 39-S ribosomal protein L47 (MRP-L47) / Rhodanese-like domain superfamily / DnaJ molecular chaperone homology domain / dnaJ domain profile. / Chaperone J-domain superfamily / DnaJ domain / tRNA (guanine-N1-)-methyltransferase, N-terminal / Cyclophilin-type peptidyl-prolyl cis-trans isomerase / Alpha/beta knot methyltransferases / 50S ribosome-binding GTPase / RNA helicase, DEAD-box type, Q motif / DEAD-box RNA helicase Q motif profile. / GTP binding 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 / Complex 1 LYR protein domain / Cyclophilin-like domain superfamily / Complex 1 protein (LYR family) / Ribosomal protein/NADH dehydrogenase domain / Mitochondrial ribosomal protein L51 / S25 / CI-B8 domain / Mitochondrial ribosomal protein L51 / S25 / CI-B8 domain / Acyl carrier protein (ACP) / Phosphopantetheine attachment site / DEAD/DEAH box helicase / DEAD/DEAH box helicase domain / Phosphopantetheine attachment site. / Nucleotidyltransferase superfamily / Phosphopantetheine attachment site / 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 / ACP-like superfamily / Ribosomal protein L28/L24 superfamily / Carrier protein (CP) domain profile. / Phosphopantetheine binding ACP domain / Ribosomal protein L9 / Ribosomal protein L9, N-terminal / Ribosomal protein L9, N-terminal domain / 50S ribosomal protein L30e-like / Helicase conserved C-terminal domain / Ribosomal protein L22, bacterial/chloroplast-type / Ribosomal protein L28/L24 / 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 / K homology domain-like, alpha/beta / Tetratricopeptide-like helical domain superfamily / Small GTP-binding protein domain / helicase superfamily c-terminal domain / Ribosomal protein L13 / Ribosomal protein L13 / Ribosomal protein L13 superfamily / 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 Similarity search - Domain/homology
Uncharacterized protein / Uncharacterized protein / Peptidyl-prolyl cis-trans isomerase / Uncharacterized protein / Uncharacterized protein / Ribosomal protein L4/L1 family / Uncharacterized protein / Ribosomal protein L23 / Uncharacterized protein / Uncharacterized protein ...Uncharacterized protein / Uncharacterized protein / Peptidyl-prolyl cis-trans isomerase / Uncharacterized protein / Uncharacterized protein / Ribosomal protein L4/L1 family / Uncharacterized protein / Ribosomal protein L23 / Uncharacterized protein / Uncharacterized protein / Uncharacterized protein / Uncharacterized protein / Uncharacterized protein / Uncharacterized protein / Mitochondrial RNA binding complex 1 subunit / Uncharacterized protein / GTP-binding protein / Uncharacterized protein / Lipase (Class 3) / SpoU rRNA Methylase family / Uncharacterized protein / Replication restart DNA helicase PriA / Uncharacterized protein / Uncharacterized protein / Uncharacterized protein / Uncharacterized protein / Ribosomal protein L22p/L17e / Uncharacterized protein / LIM domain containing protein / Uncharacterized protein / Uncharacterized protein / Ribosomal_L18e/L15P domain-containing protein / Oligomerization domain containing protein / Uncharacterized protein / Complex1-LYR-like / Uncharacterized protein / RIBOSOMAL_L9 domain-containing protein / Ribosomal protein L21 / Tetratricopeptide repeat / 50S ribosomal protein L13 / 50S ribosomal protein L17 / Uncharacterized protein / Mitochondrial ribosomal protein L51 / S25 / CI-B8 domain containing protein / Uncharacterized protein / Uncharacterized protein / Uncharacterized protein / 50S ribosomal protein L14 / Ribosomal protein L11 / KOW domain-containing protein / Uncharacterized protein / Chaperone protein DNAj, putative / GTP-binding protein, putative / Uncharacterized protein / T. brucei spp.-specific protein / Uncharacterized protein / Mitochondrial RNA binding protein / Uncharacterized protein / DEAD-box helicase, putative / Uncharacterized protein / Large ribosomal subunit protein uL29m / Uncharacterized protein / Pseudouridylate synthase, putative / WHIM1 domain-containing protein / Uncharacterized protein / Peptidyl-prolyl cis-trans isomerase / Uncharacterized protein / Acyl carrier protein / Uncharacterized protein / Ribosomal protein L3 mitochondrial, putative Similarity search - Component
Biological species
Trypanosoma brucei (eukaryote)
Method
single particle reconstruction / cryo EM / Resolution: 3.5 Å
Journal: EMBO J / Year: 2021 Title: Interconnected assembly factors regulate the biogenesis of mitoribosomal large subunit. Authors: Victor Tobiasson / Ondřej Gahura / Shintaro Aibara / Rozbeh Baradaran / Alena Zíková / Alexey Amunts / Abstract: Mitoribosomes consist of ribosomal RNA and protein components, coordinated assembly of which is critical for function. We used mitoribosomes from Trypanosoma brucei with reduced RNA and increased ...Mitoribosomes consist of ribosomal RNA and protein components, coordinated assembly of which is critical for function. We used mitoribosomes from Trypanosoma brucei with reduced RNA and increased protein mass to provide insights into the biogenesis of the mitoribosomal large subunit. Structural characterization of a stable assembly intermediate revealed 22 assembly factors, some of which have orthologues/counterparts/homologues in mammalian genomes. These assembly factors form a protein network that spans a distance of 180 Å, shielding the ribosomal RNA surface. The central protuberance and L7/L12 stalk are not assembled entirely and require removal of assembly factors and remodeling of the mitoribosomal proteins to become functional. The conserved proteins GTPBP7 and mt-EngA are bound together at the subunit interface in proximity to the peptidyl transferase center. A mitochondrial acyl-carrier protein plays a role in docking the L1 stalk, which needs to be repositioned during maturation. Additional enzymatically deactivated factors scaffold the assembly while the exit tunnel is blocked. Together, this extensive network of accessory factors stabilizes the immature sites and connects the functionally important regions of the mitoribosomal large subunit.
History
Deposition
Oct 14, 2020
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Header (metadata) release
Dec 2, 2020
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Map release
Dec 2, 2020
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Update
Mar 24, 2021
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Current status
Mar 24, 2021
Processing site: PDBe / Status: Released
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Structure visualization
Movie
Surface view with section colored by density value
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