- EMDB-51104: LSU structure derived from the LSU sample of the mitoribosome fro... -
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Basic information
Entry
Database: EMDB / ID: EMD-51104
Title
LSU structure derived from the LSU sample of the mitoribosome from T. gondii.
Map data
DeepEMhanced map of the LSU structure derived from the LSU sample of the mitoribosome from T. gondii.
Sample
Complex: LSU structure derived from the LSU sample of the mitoribosome from T. gondii.
Protein or peptide: x 71 types
RNA: x 33 types
Keywords
Complex / translation / rRNA / RIBOSOME
Function / homology
Function and homology information
regulation of mitochondrial mRNA stability / ribonucleoprotein granule / mitochondrial RNA processing / mitochondrial large ribosomal subunit / mitochondrial translation / cyclosporin A binding / peptidylprolyl isomerase / peptidyl-prolyl cis-trans isomerase activity / ubiquitin-protein transferase activity / protein folding ...regulation of mitochondrial mRNA stability / ribonucleoprotein granule / mitochondrial RNA processing / mitochondrial large ribosomal subunit / mitochondrial translation / cyclosporin A binding / peptidylprolyl isomerase / peptidyl-prolyl cis-trans isomerase activity / ubiquitin-protein transferase activity / protein folding / large ribosomal subunit / transferase activity / 5S rRNA binding / large ribosomal subunit rRNA binding / cytosolic large ribosomal subunit / negative regulation of translation / rRNA binding / structural constituent of ribosome / ribosome / mitochondrial matrix / translation / DNA-binding transcription factor activity / ribonucleoprotein complex / mRNA binding / DNA binding / RNA binding / nucleus / membrane / cytoplasm Similarity search - Function
HECTD4 / : / : / : / Domain of unknown function (DUF6831) / Domain of unknown function (DUF6832) / Apicomplexa microprotein / Apicomplexa microprotein / RAP domain / RAP domain ...HECTD4 / : / : / : / Domain of unknown function (DUF6831) / Domain of unknown function (DUF6832) / Apicomplexa microprotein / Apicomplexa microprotein / RAP domain / RAP domain / RAP domain profile. / RAP / AP2 domain / AP2/ERF domain / : / FAS1 domain / FAS1 domain superfamily / FAS1/BIgH3 domain profile. / Ribosomal protein L37, mitochondrial / Mitochondrial ribosomal protein L37 / Ribosomal protein L49/IMG2 / Mitochondrial large subunit ribosomal protein (Img2) / Ribosomal protein L27/L41, mitochondrial / Mitochondrial ribosomal protein L27 / 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) / HECT domain / HECT, E3 ligase catalytic domain / HECT-domain (ubiquitin-transferase) / HECT domain profile. / Domain Homologous to E6-AP Carboxyl Terminus with / ANL, N-terminal domain / 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 / Cyclophilin-like domain superfamily / Ribosomal protein/NADH dehydrogenase domain / Mitochondrial ribosomal protein L51 / S25 / CI-B8 domain / 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/L12 / Ribosomal protein L11, RNA binding domain / Ribosomal protein L28/L24 superfamily / Ribosomal protein L25/Gln-tRNA synthetase, anti-codon-binding domain superfamily / Eukaryotic RNA Recognition Motif (RRM) profile. / RNA recognition motif domain / Ribosomal protein L9, N-terminal domain superfamily / Ribosomal protein L9 / Ribosomal protein L9, N-terminal / Ribosomal protein L9, N-terminal domain / Ribosomal protein L9/RNase H1, N-terminal / Ribosomal protein L5, bacterial-type / RNA-binding domain superfamily / Ribosomal protein L2, bacterial/organellar-type / Ribosomal protein L33 / Ribosomal protein L33 / Ribosomal protein L33 superfamily / Ribosomal protein L16 / Ribosomal protein L28/L24 / L28p-like / Ribosomal protein L27 / Ribosomal L27 protein / Ribosomal protein L20 / Ribosomal protein L20 / Ribosomal protein L20, C-terminal / Ribosomal protein L17 / Ribosomal protein L17 superfamily / Ribosomal protein L17 / Ribosomal proteins 50S L24/mitochondrial 39S L24 / 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 L13, bacterial-type / : / Ribosomal protein L10e/L16 / Ribosomal protein L10e/L16 superfamily / Ribosomal protein L16p/L10e / Prokaryotic membrane lipoprotein lipid attachment site profile. / Ribosomal protein L2, domain 3 / Ribosomal Proteins L2, C-terminal domain / Ribosomal protein L2, C-terminal / Ribosomal Proteins L2, C-terminal domain / Ribosomal Proteins L2, RNA binding domain / Ribosomal Proteins L2, RNA binding N-terminal domain / Ribosomal Proteins L2, RNA binding domain / Ribosomal protein L2 / KOW (Kyprides, Ouzounis, Woese) motif. Similarity search - Domain/homology
Uncharacterized protein / Uncharacterized protein / Large ribosomal subunit protein uL24c / Ribosomal protein L11, putative / Uncharacterized protein / Ribosomal protein RPL22 / Large ribosomal subunit protein mL49 / Uncharacterized protein / Putative 50S ribosomal protein L33 / Uncharacterized protein ...Uncharacterized protein / Uncharacterized protein / Large ribosomal subunit protein uL24c / Ribosomal protein L11, putative / Uncharacterized protein / Ribosomal protein RPL22 / Large ribosomal subunit protein mL49 / Uncharacterized protein / Putative 50S ribosomal protein L33 / Uncharacterized protein / Large ribosomal subunit protein uL24c / Putative 60S ribosomal protein L27 / Uncharacterized protein / Large ribosomal subunit protein uL4m / BIR protein / Putative 50S ribosomal protein L13 / Putative ribosomal protein L28 / Large ribosomal subunit protein uL29m / Uncharacterized protein / AP2 domain transcription factor AP2VIIb-2 / Large ribosomal subunit protein uL23m / Large ribosomal subunit protein uL3m / RAP domain-containing protein / Ribosomal L22p/L17e protein / Transmembrane protein / Large ribosomal subunit protein bL21m / Putative 50S ribosomal protein L16 / Uncharacterized protein / Uncharacterized protein / Uncharacterized protein / Uncharacterized protein / Transmembrane protein / DUF6832 domain-containing protein / Large ribosomal subunit protein mL43 / Uncharacterized protein / Uncharacterized protein / AP2 domain transcription factor AP2IV-1 / Uncharacterized protein / Putative 50S ribosomal protein L17 / Uncharacterized protein / Putative ribosomal protein L20 / Uncharacterized protein / RAP domain-containing protein / Ribosomal l25 family protein / Uncharacterized protein / RAP domain-containing protein / Ribosomal protein L46 / Large ribosomal subunit protein mL54 / RAP domain-containing protein / Large ribosomal subunit protein uL2m / RRM domain-containing protein / FAS1 domain-containing protein / AMP-dependent synthetase/ligase domain-containing protein / Peptidyl-prolyl cis-trans isomerase / RAP domain-containing protein / Uncharacterized protein / Ribosomal protein L9, N-terminal domain-containing protein / RAP domain-containing protein / Macro domain-containing protein / RAP domain-containing protein / Ribosomal protein L15, putative / HECT-domain (Ubiquitin-transferase) domain-containing protein Similarity search - Component
Biological species
Toxoplasma gondii (eukaryote)
Method
single particle reconstruction / cryo EM / Resolution: 2.89 Å
Journal: Acta Crystallogr D Struct Biol / Year: 2018 Title: ISOLDE: a physically realistic environment for model building into low-resolution electron-density maps. Authors: Tristan Ian Croll / Abstract: This paper introduces ISOLDE, a new software package designed to provide an intuitive environment for high-fidelity interactive remodelling/refinement of macromolecular models into electron-density ...This paper introduces ISOLDE, a new software package designed to provide an intuitive environment for high-fidelity interactive remodelling/refinement of macromolecular models into electron-density maps. ISOLDE combines interactive molecular-dynamics flexible fitting with modern molecular-graphics visualization and established structural biology libraries to provide an immersive interface wherein the model constantly acts to maintain physically realistic conformations as the user interacts with it by directly tugging atoms with a mouse or haptic interface or applying/removing restraints. In addition, common validation tasks are accelerated and visualized in real time. Using the recently described 3.8 Å resolution cryo-EM structure of the eukaryotic minichromosome maintenance (MCM) helicase complex as a case study, it is demonstrated how ISOLDE can be used alongside other modern refinement tools to avoid common pitfalls of low-resolution modelling and improve the quality of the final model. A detailed analysis of changes between the initial and final model provides a somewhat sobering insight into the dangers of relying on a small number of validation metrics to judge the quality of a low-resolution model.
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