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- EMDB-11643: Structure of the split human mitoribosomal large subunit with res... -
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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-11643 | ||||||||||||
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Title | Structure of the split human mitoribosomal large subunit with rescue factors mtRF-R and MTRES1 | ||||||||||||
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Function / homology | ![]() regulation of mitochondrial transcription / negative regulation of mitochondrial translation / mitochondrial large ribosomal subunit assembly / Complex I biogenesis / negative regulation of ribosome biogenesis / protein lipoylation / translation release factor activity / Mitochondrial Fatty Acid Beta-Oxidation / Protein lipoylation / Respiratory electron transport ...regulation of mitochondrial transcription / negative regulation of mitochondrial translation / mitochondrial large ribosomal subunit assembly / Complex I biogenesis / negative regulation of ribosome biogenesis / protein lipoylation / translation release factor activity / Mitochondrial Fatty Acid Beta-Oxidation / Protein lipoylation / Respiratory electron transport / mitochondrial translational elongation / mitochondrial translational termination / iron-sulfur cluster assembly complex / microprocessor complex / translation release factor activity, codon nonspecific / Mitochondrial translation elongation / Mitochondrial translation termination / positive regulation of mitochondrial translation / Mitochondrial translation initiation / mitochondrial large ribosomal subunit binding / mitochondrial fission / mitochondrial large ribosomal subunit / Hydrolases; Acting on ester bonds; Endoribonucleases producing 5'-phosphomonoesters / peptidyl-tRNA hydrolase / [2Fe-2S] cluster assembly / mitochondrial small ribosomal subunit / aminoacyl-tRNA hydrolase activity / iron-sulfur cluster assembly / mitochondrial ribosome / mitochondrial translation / ribosomal large subunit binding / : / mitochondrial electron transport, NADH to ubiquinone / mitochondrial respiratory chain complex I assembly / proton motive force-driven mitochondrial ATP synthesis / acyl binding / anatomical structure morphogenesis / acyl carrier activity / RNA processing / Mitochondrial protein degradation / aerobic respiration / rescue of stalled ribosome / ribosomal large subunit biogenesis / cellular response to leukemia inhibitory factor / fatty acid binding / mitochondrial membrane / fibrillar center / fatty acid biosynthetic process / large ribosomal subunit / double-stranded RNA binding / cell junction / small ribosomal subunit rRNA binding / 5S rRNA binding / large ribosomal subunit rRNA binding / endonuclease activity / cytosolic large ribosomal subunit / 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 / nucleotide binding / mRNA binding / synapse / calcium ion binding / nucleolus / apoptotic process / mitochondrion / RNA binding / nucleoplasm / nucleus / plasma membrane / cytosol Similarity search - Function | ||||||||||||
Biological species | ![]() ![]() | ||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.3 Å | ||||||||||||
![]() | Desai N / Yang H / Chandrasekaran V / Kazi R / Minczuk M / Ramakrishnan V | ||||||||||||
Funding support | ![]()
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![]() | ![]() 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 |
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 56.8 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 73.7 KB 73.7 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 18.1 KB | Display | ![]() |
Images | ![]() | 174.1 KB | ||
Others | ![]() ![]() ![]() | 412.9 MB 414.8 MB 414.6 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7a5hMC ![]() 7a5fC ![]() 7a5gC ![]() 7a5iC ![]() 7a5jC ![]() 7a5kC M: atomic model generated by this map C: citing same article ( |
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Similar structure data |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
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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
-Additional map: Refined map
File | emd_11643_additional_1.map | ||||||||||||
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Annotation | Refined map | ||||||||||||
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Density Histograms |
-Half map: Half2 map
File | emd_11643_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_11643_half_map_2.map | ||||||||||||
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Annotation | Half1 map | ||||||||||||
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Density Histograms |
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Sample components
+Entire : human mitoribosome
+Supramolecule #1: human mitoribosome
+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 L37, mitochondrial
+Macromolecule #28: 39S ribosomal protein L38, mitochondrial
+Macromolecule #29: 39S ribosomal protein L39, mitochondrial
+Macromolecule #30: 39S ribosomal protein L40, mitochondrial
+Macromolecule #31: 39S ribosomal protein L41, mitochondrial
+Macromolecule #32: 39S ribosomal protein L42, mitochondrial
+Macromolecule #33: 39S ribosomal protein L43, mitochondrial
+Macromolecule #34: 39S ribosomal protein L44, mitochondrial
+Macromolecule #35: 39S ribosomal protein L45, mitochondrial
+Macromolecule #36: 39S ribosomal protein L46, mitochondrial
+Macromolecule #37: 39S ribosomal protein L48, mitochondrial
+Macromolecule #38: 39S ribosomal protein L49, mitochondrial
+Macromolecule #39: 39S ribosomal protein L50, mitochondrial
+Macromolecule #40: 39S ribosomal protein L51, mitochondrial
+Macromolecule #41: cDNA FLJ76418, highly similar to Homo sapiens mitochondrial ribos...
+Macromolecule #42: 39S ribosomal protein L53, mitochondrial
+Macromolecule #43: 39S ribosomal protein L54, mitochondrial
+Macromolecule #44: 39S ribosomal protein L55, mitochondrial
+Macromolecule #45: Ribosomal protein 63, mitochondrial
+Macromolecule #46: Peptidyl-tRNA hydrolase ICT1, mitochondrial
+Macromolecule #47: Growth arrest and DNA damage-inducible proteins-interacting protein 1
+Macromolecule #48: 39S ribosomal protein S18a, mitochondrial
+Macromolecule #49: 39S ribosomal protein S30, mitochondrial
+Macromolecule #50: Unknown protein/protein extension
+Macromolecule #51: Mitochondrial assembly of ribosomal large subunit protein 1
+Macromolecule #52: MIEF1 upstream open reading frame protein
+Macromolecule #53: Acyl carrier protein, mitochondrial
+Macromolecule #57: nascent chain
+Macromolecule #58: Probable peptide chain release factor C12orf65, mitochondrial
+Macromolecule #59: Mitochondrial transcription rescue factor 1
+Macromolecule #54: 16S rRNA
+Macromolecule #55: mt-tRNAVal
+Macromolecule #56: mt-tRNA
+Macromolecule #60: MAGNESIUM ION
+Macromolecule #61: ZINC ION
+Macromolecule #62: 4'-PHOSPHOPANTETHEINE
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Concentration | 0.4 mg/mL |
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Buffer | pH: 7.4 |
Vitrification | Cryogen name: ETHANE |
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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: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |