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Yorodumi- EMDB-11637: Cryo-EM structure of Oxa1L-bound human mitoribosomal large subunit -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-11637 | ||||||||||||
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Title | Cryo-EM structure of Oxa1L-bound human mitoribosomal large subunit | ||||||||||||
Map data | postprocessed masked map | ||||||||||||
Sample |
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Function / homology | Function and homology information mitochondrial ribosome binding / mitochondrial translational elongation / mitochondrial translational termination / mitochondrial ribosome assembly / microprocessor complex / translation release factor activity, codon nonspecific / Mitochondrial translation elongation / Mitochondrial translation termination / positive regulation of mitochondrial translation / Mitochondrial translation initiation ...mitochondrial ribosome binding / mitochondrial translational elongation / mitochondrial translational termination / mitochondrial ribosome assembly / microprocessor complex / translation release factor activity, codon nonspecific / Mitochondrial translation elongation / Mitochondrial translation termination / positive regulation of mitochondrial translation / Mitochondrial translation initiation / negative regulation of mitotic nuclear division / mitochondrial large ribosomal subunit / Hydrolases; Acting on ester bonds; Endoribonucleases producing 5'-phosphomonoesters / peptidyl-tRNA hydrolase / mitochondrial small ribosomal subunit / aminoacyl-tRNA hydrolase activity / mitochondrial ribosome / mitochondrial translation / positive regulation of proteolysis / ribosomal small subunit binding / anatomical structure morphogenesis / RNA processing / Mitochondrial protein degradation / rescue of stalled ribosome / cellular response to leukemia inhibitory factor / apoptotic signaling pathway / fibrillar center / large ribosomal subunit / double-stranded RNA binding / cell junction / regulation of translation / ribosomal small subunit assembly / small ribosomal subunit / small ribosomal subunit rRNA binding / 5S rRNA binding / large ribosomal subunit rRNA binding / nuclear membrane / endonuclease activity / cytosolic large ribosomal subunit / cell population proliferation / mitochondrial inner membrane / tRNA binding / nuclear body / rRNA binding / negative regulation of translation / ribosome / structural constituent of ribosome / mitochondrial matrix / ribonucleoprotein complex / translation / protein domain specific binding / intracellular membrane-bounded organelle / nucleotide binding / mRNA binding / synapse / nucleolus / GTP binding / apoptotic process / mitochondrion / RNA binding / nucleoplasm / nucleus / plasma membrane / cytosol / cytoplasm Similarity search - Function | ||||||||||||
Biological species | Homo sapiens (human) | ||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.1 Å | ||||||||||||
Authors | Desai N / Yang H / Chandrasekaran V / Kazi R / Minczuk M / Ramakrishnan V | ||||||||||||
Funding support | United Kingdom, 3 items
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Citation | Journal: Science / Year: 2020 Title: Elongational stalling activates mitoribosome-associated quality control. Authors: Nirupa Desai / Hanting Yang / Viswanathan Chandrasekaran / Razina Kazi / Michal Minczuk / V Ramakrishnan / Abstract: The human mitochondrial ribosome (mitoribosome) and associated proteins regulate the synthesis of 13 essential subunits of the oxidative phosphorylation complexes. We report the discovery of a ...The human mitochondrial ribosome (mitoribosome) and associated proteins regulate the synthesis of 13 essential subunits of the oxidative phosphorylation complexes. We report the discovery of a mitoribosome-associated quality control pathway that responds to interruptions during elongation, and we present structures at 3.1- to 3.3-angstrom resolution of mitoribosomal large subunits trapped during ribosome rescue. Release factor homolog C12orf65 (mtRF-R) and RNA binding protein C6orf203 (MTRES1) eject the nascent chain and peptidyl transfer RNA (tRNA), respectively, from stalled ribosomes. Recruitment of mitoribosome biogenesis factors to these quality control intermediates suggests additional roles for these factors during mitoribosome rescue. We also report related cryo-electron microscopy structures (3.7 to 4.4 angstrom resolution) of elongating mitoribosomes bound to tRNAs, nascent polypeptides, the guanosine triphosphatase elongation factors mtEF-Tu and mtEF-G1, and the Oxa1L translocase. | ||||||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_11637.map.gz | 41.9 MB | EMDB map data format | |
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Header (meta data) | emd-11637-v30.xml emd-11637.xml | 26.3 KB 26.3 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_11637_fsc.xml | 18 KB | Display | FSC data file |
Images | emd_11637.png | 197.2 KB | ||
Masks | emd_11637_msk_1.map | 512 MB | Mask map | |
Others | emd_11637_additional_1.map.gz emd_11637_half_map_1.map.gz emd_11637_half_map_2.map.gz | 412.1 MB 413.6 MB 413.7 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-11637 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-11637 | HTTPS FTP |
-Related structure data
Related structure data | 7a5fC 7a5gC 7a5hC 7a5iC 7a5jC 7a5kC C: citing same article (ref.) |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_11637.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | postprocessed masked map | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.25938 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Mask #1
File | emd_11637_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Additional map: refined map
File | emd_11637_additional_1.map | ||||||||||||
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Annotation | refined map | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Half1 map
File | emd_11637_half_map_1.map | ||||||||||||
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Annotation | Half1 map | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Half2 map
File | emd_11637_half_map_2.map | ||||||||||||
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Annotation | Half2 map | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : human mitoribosome
Entire | Name: human mitoribosome |
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Components |
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-Supramolecule #1: human mitoribosome
Supramolecule | Name: human mitoribosome / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#88 |
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Source (natural) | Organism: Homo sapiens (human) |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.4 mg/mL |
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Buffer | pH: 7.4 |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: FEI FALCON III (4k x 4k) / Detector mode: INTEGRATING / Average electron dose: 60.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |