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Yorodumi- EMDB-11636: Cryo-EM structure of the human mitoribosome in the rotated-1 stat... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-11636 | ||||||||||||
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Title | Cryo-EM structure of the human mitoribosome in the rotated-1 state with A/A and P/E mt-tRNAs | ||||||||||||
Map data | postprocessed masked map | ||||||||||||
Sample |
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Function / homology | Function and homology information mitochondrial ribosome binding / rRNA import into mitochondrion / mitochondrial translational termination / mitochondrial ribosome assembly / mitochondrial translational elongation / translation release factor activity, codon nonspecific / microprocessor complex / Mitochondrial translation elongation / positive regulation of mitochondrial translation / Mitochondrial translation termination ...mitochondrial ribosome binding / rRNA import into mitochondrion / mitochondrial translational termination / mitochondrial ribosome assembly / mitochondrial translational elongation / translation release factor activity, codon nonspecific / microprocessor complex / Mitochondrial translation elongation / positive regulation of mitochondrial translation / Mitochondrial translation termination / 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 / rescue of stalled ribosome / cellular response to leukemia inhibitory factor / apoptotic signaling pathway / small ribosomal subunit rRNA binding / fibrillar center / ribosomal small subunit assembly / large ribosomal subunit rRNA binding / double-stranded RNA binding / large ribosomal subunit / regulation of translation / cell junction / small ribosomal subunit / 5S rRNA binding / endonuclease activity / nuclear membrane / mitochondrial inner membrane / cell population proliferation / tRNA binding / negative regulation of translation / rRNA binding / nuclear body / ribosome / mitochondrial matrix / structural constituent of ribosome / cell cycle / ribonucleoprotein complex / translation / protein domain specific binding / nucleotide binding / mRNA binding / intracellular membrane-bounded organelle / synapse / apoptotic process / GTP binding / nucleolus / mitochondrion / extracellular space / RNA binding / nucleoplasm / nucleus / plasma membrane / cytosol / cytoplasm Similarity search - Function | ||||||||||||
Biological species | Homo sapiens (human) | ||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.9 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_11636.map.gz | 57.9 MB | EMDB map data format | |
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Header (meta data) | emd-11636-v30.xml emd-11636.xml | 26.3 KB 26.3 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_11636_fsc.xml | 18.2 KB | Display | FSC data file |
Images | emd_11636.png | 175.2 KB | ||
Masks | emd_11636_msk_1.map | 512 MB | Mask map | |
Others | emd_11636_additional_1.map.gz emd_11636_half_map_1.map.gz emd_11636_half_map_2.map.gz | 409.5 MB 410.7 MB 411 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-11636 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-11636 | 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_11636.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: 1.04 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_11636_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Additional map: refined map
File | emd_11636_additional_1.map | ||||||||||||
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Annotation | refined map | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Half2 map
File | emd_11636_half_map_1.map | ||||||||||||
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Annotation | Half2 map | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Half1 map
File | emd_11636_half_map_2.map | ||||||||||||
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Annotation | Half1 map | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : human mitoribosome
Entire | Name: human mitoribosomeMitochondrial ribosome |
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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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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy |
Image recording | Film or detector model: FEI FALCON III (4k x 4k) / Detector mode: INTEGRATING / Average electron dose: 60.0 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |