Pseudouridine synthase, TruD, catalytic domain / EngB-type guanine nucleotide-binding (G) domain profile. / Pseudouridine synthase, TruD / EngB-type guanine nucleotide-binding (G) domain / 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 ...Pseudouridine synthase, TruD, catalytic domain / EngB-type guanine nucleotide-binding (G) domain profile. / Pseudouridine synthase, TruD / EngB-type guanine nucleotide-binding (G) domain / 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) / Ribosomal silencing factor during starvation / Protein Iojap/ribosomal silencing factor RsfS / Pseudouridine synthase, catalytic domain superfamily / GTP-binding protein, orthogonal bundle domain superfamily / 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 / 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) / 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) / Acyl carrier protein (ACP) / Ribosomal protein/NADH dehydrogenase domain / Mitochondrial ribosomal protein L51 / S25 / CI-B8 domain / Mitochondrial ribosomal protein L51 / S25 / CI-B8 domain / Phosphopantetheine attachment site / DEAD/DEAH box helicase / DEAD/DEAH box helicase domain / Phosphopantetheine attachment site. / Nucleotidyltransferase superfamily / Phosphopantetheine attachment site / ACP-like 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 / 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 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 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 Similarity search - Domain/homology
ADENOSINE-5'-TRIPHOSPHATE / GUANOSINE-5'-TRIPHOSPHATE / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Chem-PM8 / SPERMIDINE / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) ...ADENOSINE-5'-TRIPHOSPHATE / GUANOSINE-5'-TRIPHOSPHATE / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Chem-PM8 / SPERMIDINE / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Lipase (Class 3) / Replication restart DNA helicase PriA / Uncharacterized protein / Uncharacterized protein / Tetratricopeptide repeat / KOW domain-containing protein / Uncharacterized protein / Importin-beta N-terminal domain-containing protein / Uncharacterized protein / Chaperone protein DNAj, putative / Large ribosomal subunit protein uL22c / Large ribosomal subunit protein bL21m / T. brucei spp.-specific protein / Uncharacterized protein / Uncharacterized protein / SpoU_methylase domain-containing protein / Mitochondrial RNA binding complex 1 subunit / Uncharacterized protein / T. brucei spp.-specific protein / Uncharacterized protein / Uncharacterized protein / T. brucei spp.-specific protein / Uncharacterized protein / DEAD-box helicase, putative / EngB-type G domain-containing protein / Ribosomal protein S24/S35 mitochondrial conserved domain-containing protein / Large ribosomal subunit protein bL20c / Uncharacterized protein / Mitochondrial ribosomal protein L23 / Uncharacterized protein / Peptidyl-prolyl cis-trans isomerase / TRUD domain-containing protein / Uncharacterized protein / Uncharacterized protein / Uncharacterized protein / Large ribosomal subunit protein uL23m / Uncharacterized protein / Uncharacterized protein / Uncharacterized protein / Uncharacterized protein / Uncharacterized protein / SpoU_methylase domain-containing protein / GTP-binding protein, putative / Uncharacterized protein / Large ribosomal subunit protein uL29m / Rhodanese domain-containing protein / Uncharacterized protein / Pseudouridylate synthase, putative / WHIM1 domain-containing protein / Uncharacterized protein / GTP-binding protein, putative / Large ribosomal subunit protein uL15/eL18 domain-containing protein / Ribosomal protein L9 domain-containing protein / Uncharacterized protein / Peptidyl-prolyl cis-trans isomerase / Uncharacterized protein / Uncharacterized protein / Acyl carrier protein / 50S ribosomal protein L17, putative / Uncharacterized protein / Uncharacterized protein / 50S ribosomal protein L13, putative / Ribosomal protein L3 mitochondrial, putative / Large ribosomal subunit protein mL43 / Uncharacterized 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: 3.1 Å
Journal: Mol Cell / Year: 2020 Title: Structural Insights into the Mechanism of Mitoribosomal Large Subunit Biogenesis. Authors: Mateusz Jaskolowski / David J F Ramrath / Philipp Bieri / Moritz Niemann / Simone Mattei / Salvatore Calderaro / Marc Leibundgut / Elke K Horn / Daniel Boehringer / André Schneider / Nenad Ban / Abstract: In contrast to the bacterial translation machinery, mitoribosomes and mitochondrial translation factors are highly divergent in terms of composition and architecture. There is increasing evidence ...In contrast to the bacterial translation machinery, mitoribosomes and mitochondrial translation factors are highly divergent in terms of composition and architecture. There is increasing evidence that the biogenesis of mitoribosomes is an intricate pathway, involving many assembly factors. To better understand this process, we investigated native assembly intermediates of the mitoribosomal large subunit from the human parasite Trypanosoma brucei using cryo-electron microscopy. We identify 28 assembly factors, 6 of which are homologous to bacterial and eukaryotic ribosome assembly factors. They interact with the partially folded rRNA by specifically recognizing functionally important regions such as the peptidyltransferase center. The architectural and compositional comparison of the assembly intermediates indicates a stepwise modular assembly process, during which the rRNA folds toward its mature state. During the process, several conserved GTPases and a helicase form highly intertwined interaction networks that stabilize distinct assembly intermediates. The presented structures provide general insights into mitoribosomal maturation.
Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen support
Grid type: Quantifoil R2/2
Vitrification
Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE-PROPANE / Humidity: 100 % / Chamber temperature: 277 K Details: 3.5 uL of the sample was blotted for 7-9 sec before plunging
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Electron microscopy imaging
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
Microscopy
Model: FEI TITAN KRIOS
Electron gun
Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lens
Mode: BRIGHT FIELD / Cs: 2.7 mm / C2 aperture diameter: 100 µm / Alignment procedure: COMA FREE
Electron dose: 75 e/Å2 / Detector mode: INTEGRATING / Film or detector model: FEI FALCON III (4k x 4k)
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Processing
EM software
Name: RELION / Version: 3 / Category: 3D reconstruction
CTF correction
Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Symmetry
Point symmetry: C1 (asymmetric)
3D reconstruction
Resolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 98508 / Symmetry type: POINT
Atomic model building
Details: Initial models of ribosomal proteins of the T. brucei mitochondrial ribosomal large subunit were taken from PDB 6HIX. Assembly factors of the mitoribosomal large subunit were built de novo.
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