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Yorodumi- EMDB-11645: Structure of the split human mitoribosomal large subunit with P-a... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-11645 | ||||||||||||
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Title | Structure of the split human mitoribosomal large subunit with P-and E-site mt-tRNAs | ||||||||||||
Map data | postprocessed masked map | ||||||||||||
Sample |
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Function / homology | Function and homology information negative regulation of mitochondrial translation / mitochondrial large ribosomal subunit assembly / Complex I biogenesis / negative regulation of ribosome biogenesis / protein lipoylation / Mitochondrial Fatty Acid Beta-Oxidation / Respiratory electron transport / iron-sulfur cluster assembly complex / mitochondrial translational termination / mitochondrial large ribosomal subunit binding ...negative regulation of mitochondrial translation / mitochondrial large ribosomal subunit assembly / Complex I biogenesis / negative regulation of ribosome biogenesis / protein lipoylation / Mitochondrial Fatty Acid Beta-Oxidation / Respiratory electron transport / iron-sulfur cluster assembly complex / mitochondrial translational termination / mitochondrial large ribosomal subunit binding / 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 / [2Fe-2S] cluster assembly / Glyoxylate metabolism and glycine degradation / mitochondrial fission / mitochondrial large ribosomal subunit / Hydrolases; Acting on ester bonds; Endoribonucleases producing 5'-phosphomonoesters / peptidyl-tRNA hydrolase / mitochondrial small ribosomal subunit / acyl binding / aminoacyl-tRNA hydrolase activity / mitochondrial ribosome / iron-sulfur cluster assembly / acyl carrier activity / mitochondrial translation / proton motive force-driven mitochondrial ATP synthesis / mitochondrial respiratory chain complex I / mitochondrial respiratory chain complex I assembly / mitochondrial electron transport, NADH to ubiquinone / ribosomal large subunit binding / anatomical structure morphogenesis / RNA processing / rescue of stalled ribosome / aerobic respiration / ribosomal large subunit biogenesis / cellular response to leukemia inhibitory factor / fatty acid binding / mitochondrial membrane / small ribosomal subunit rRNA binding / fibrillar center / fatty acid biosynthetic process / large ribosomal subunit rRNA binding / double-stranded RNA binding / large ribosomal subunit / regulation of translation / cell junction / endonuclease activity / mitochondrial inner membrane / tRNA binding / negative regulation of translation / rRNA binding / nuclear body / ribosome / mitochondrial matrix / structural constituent of ribosome / cell cycle / translation / ribonucleoprotein complex / protein domain specific binding / nucleotide binding / mRNA binding / synapse / apoptotic process / calcium ion binding / nucleolus / mitochondrion / RNA binding / nucleoplasm / nucleus / plasma membrane / cytosol / cytoplasm Similarity search - Function | ||||||||||||
Biological species | Homo sapiens (human) / Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039) (bacteria) / human (human) / Thermus thermophilus HB27 (bacteria) | ||||||||||||
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_11645.map.gz | 41.9 MB | EMDB map data format | |
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Header (meta data) | emd-11645-v30.xml emd-11645.xml | 84.5 KB 84.5 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_11645_fsc.xml | 18 KB | Display | FSC data file |
Images | emd_11645.png | 190.5 KB | ||
Masks | emd_11645_msk_1.map | 512 MB | Mask map | |
Others | emd_11645_additional_1.map.gz emd_11645_half_map_1.map.gz emd_11645_half_map_2.map.gz | 412.6 MB 413.9 MB 414 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-11645 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-11645 | HTTPS FTP |
-Related structure data
Related structure data | 7a5jMC 7a5fC 7a5gC 7a5hC 7a5iC 7a5kC M: atomic model generated by this map 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_11645.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_11645_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Additional map: refined map
File | emd_11645_additional_1.map | ||||||||||||
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Annotation | refined map | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Half2 map
File | emd_11645_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_11645_half_map_2.map | ||||||||||||
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Annotation | Half1 map | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
+Entire : human mitoribosome
+Supramolecule #1: human mitoribosome
+Supramolecule #2: ribosome
+Supramolecule #3: 50S ribosomal protein L1
+Macromolecule #1: 39S ribosomal protein L2, mitochondrial
+Macromolecule #2: 39S ribosomal protein L3, mitochondrial
+Macromolecule #3: 39S ribosomal protein L4, mitochondrial
+Macromolecule #4: 39S ribosomal protein L9, mitochondrial
+Macromolecule #5: 39S ribosomal protein L10, mitochondrial
+Macromolecule #6: 39S ribosomal protein L11, mitochondrial
+Macromolecule #7: 39S ribosomal protein L13, mitochondrial
+Macromolecule #8: 39S ribosomal protein L14, mitochondrial
+Macromolecule #9: 39S ribosomal protein L15, mitochondrial
+Macromolecule #10: 39S ribosomal protein L16, mitochondrial
+Macromolecule #11: 39S ribosomal protein L17, mitochondrial
+Macromolecule #12: Mitochondrial ribosomal protein L18, isoform CRA_b
+Macromolecule #13: 39S ribosomal protein L19, mitochondrial
+Macromolecule #14: 39S ribosomal protein L20, mitochondrial
+Macromolecule #15: 39S ribosomal protein L21, mitochondrial
+Macromolecule #16: 39S ribosomal protein L22, mitochondrial
+Macromolecule #17: 39S ribosomal protein L23, mitochondrial
+Macromolecule #18: 39S ribosomal protein L24, mitochondrial
+Macromolecule #19: 39S ribosomal protein L27, mitochondrial
+Macromolecule #20: 39S ribosomal protein L28, mitochondrial
+Macromolecule #21: 39S ribosomal protein L47, mitochondrial
+Macromolecule #22: 39S ribosomal protein L30, mitochondrial
+Macromolecule #23: 39S ribosomal protein L32, mitochondrial
+Macromolecule #24: 39S ribosomal protein L33, mitochondrial
+Macromolecule #25: 39S ribosomal protein L34, mitochondrial
+Macromolecule #26: 39S ribosomal protein L35, mitochondrial
+Macromolecule #27: 39S ribosomal protein L36, mitochondrial
+Macromolecule #28: 39S ribosomal protein L37, mitochondrial
+Macromolecule #29: 39S ribosomal protein L38, mitochondrial
+Macromolecule #30: 39S ribosomal protein L39, mitochondrial
+Macromolecule #31: 39S ribosomal protein L40, mitochondrial
+Macromolecule #32: 39S ribosomal protein L41, mitochondrial
+Macromolecule #33: 39S ribosomal protein L42, mitochondrial
+Macromolecule #34: 39S ribosomal protein L43, mitochondrial
+Macromolecule #35: 39S ribosomal protein L44, mitochondrial
+Macromolecule #36: 39S ribosomal protein L45, mitochondrial
+Macromolecule #37: 39S ribosomal protein L46, mitochondrial
+Macromolecule #38: 39S ribosomal protein L48, mitochondrial
+Macromolecule #39: 39S ribosomal protein L49, mitochondrial
+Macromolecule #40: 39S ribosomal protein L50, mitochondrial
+Macromolecule #41: 39S ribosomal protein L51, mitochondrial
+Macromolecule #42: cDNA FLJ76418, highly similar to Homo sapiens mitochondrial ribos...
+Macromolecule #43: 39S ribosomal protein L53, mitochondrial
+Macromolecule #44: 39S ribosomal protein L54, mitochondrial
+Macromolecule #45: 39S ribosomal protein L55, mitochondrial
+Macromolecule #46: Ribosomal protein 63, mitochondrial
+Macromolecule #47: Peptidyl-tRNA hydrolase ICT1, mitochondrial
+Macromolecule #48: Growth arrest and DNA damage-inducible proteins-interacting protein 1
+Macromolecule #49: 39S ribosomal protein S18a, mitochondrial
+Macromolecule #50: 39S ribosomal protein S30, mitochondrial
+Macromolecule #51: Unknown protein/protein extension
+Macromolecule #52: Mitochondrial assembly of ribosomal large subunit protein 1
+Macromolecule #53: MIEF1 upstream open reading frame protein
+Macromolecule #54: Acyl carrier protein, mitochondrial
+Macromolecule #55: 50S ribosomal protein L1
+Macromolecule #58: nascent chain
+Macromolecule #60: Unknown protein/protein extension
+Macromolecule #61: unknown protein/protein extension
+Macromolecule #56: 16S rRNA
+Macromolecule #57: mt-tRNAVal
+Macromolecule #59: mt-tRNA
+Macromolecule #62: MAGNESIUM ION
+Macromolecule #63: ZINC ION
+Macromolecule #64: CHLORIDE ION
+Macromolecule #65: SODIUM ION
-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 |