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- EMDB-11641: Structure of the stalled human mitoribosome with P- and E-site mt... -
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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-11641 | ||||||||||||
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Title | Structure of the stalled human mitoribosome with P- and E-site mt-tRNAs | ||||||||||||
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Function / homology | ![]() mitochondrial ribosome binding / rRNA import into mitochondrion / 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 ribosome binding / rRNA import into mitochondrion / 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 / rescue of stalled ribosome / cellular response to leukemia inhibitory factor / Mitochondrial protein degradation / apoptotic signaling pathway / fibrillar center / cell junction / double-stranded RNA binding / regulation of translation / ribosomal small subunit assembly / small ribosomal subunit / small ribosomal subunit rRNA binding / nuclear membrane / 5S rRNA binding / large ribosomal subunit rRNA binding / endonuclease activity / cytosolic large ribosomal subunit / cell population proliferation / tRNA binding / nuclear body / rRNA binding / negative regulation of translation / mitochondrial inner membrane / ribosome / structural constituent of ribosome / mitochondrial matrix / translation / ribonucleoprotein complex / protein domain specific binding / intracellular membrane-bounded organelle / mRNA binding / nucleotide binding / synapse / nucleolus / GTP binding / apoptotic process / mitochondrion / RNA binding / extracellular space / nucleoplasm / nucleus / plasma membrane / cytoplasm / cytosol Similarity search - Function | ||||||||||||
Biological species | ![]() ![]() ![]() ![]() | ||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.4 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 | ![]() | 59.6 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 117.2 KB 117.2 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 18.2 KB | Display | ![]() |
Images | ![]() | 195.6 KB | ||
Masks | ![]() | 512 MB | ![]() | |
Others | ![]() ![]() ![]() | 413.1 MB 411.9 MB 411.9 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7a5fMC ![]() 7a5gC ![]() 7a5hC ![]() 7a5iC ![]() 7a5jC ![]() 7a5kC M: atomic model generated by this map C: citing same article ( |
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Similar structure data | |
EM raw data | ![]() Data size: 45.7 TB Data #1: 7 independent datasets in TIF format from Titan Krios + Falcon III integrating mode [micrographs - multiframe]) |
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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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Annotation | 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
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Density Histograms |
-Additional map: Unprocessed map
File | emd_11641_additional_1.map | ||||||||||||
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Annotation | Unprocessed map | ||||||||||||
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Density Histograms |
-Half map: Half2
File | emd_11641_half_map_1.map | ||||||||||||
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Annotation | Half2 | ||||||||||||
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Density Histograms |
-Half map: Half1 map
File | emd_11641_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
+Supramolecule #2: human mitoribosome
+Supramolecule #3: 50S ribosomal protein L1
+Macromolecule #1: nascent chain
+Macromolecule #4: 39S ribosomal protein L2, mitochondrial
+Macromolecule #5: 39S ribosomal protein L3, mitochondrial
+Macromolecule #6: 39S ribosomal protein L4, mitochondrial
+Macromolecule #7: 39S ribosomal protein L9, mitochondrial
+Macromolecule #8: 39S ribosomal protein L10, mitochondrial
+Macromolecule #9: 39S ribosomal protein L11, mitochondrial
+Macromolecule #10: 39S ribosomal protein L13, mitochondrial
+Macromolecule #11: 39S ribosomal protein L14, mitochondrial
+Macromolecule #12: 39S ribosomal protein L15, mitochondrial
+Macromolecule #13: 39S ribosomal protein L16, mitochondrial
+Macromolecule #14: 39S ribosomal protein L17, mitochondrial
+Macromolecule #15: 39S ribosomal protein L18, mitochondrial
+Macromolecule #16: 39S ribosomal protein L19, mitochondrial
+Macromolecule #17: 39S ribosomal protein L20, mitochondrial
+Macromolecule #18: 39S ribosomal protein L21, mitochondrial
+Macromolecule #19: 39S ribosomal protein L22, mitochondrial
+Macromolecule #20: 39S ribosomal protein L23, mitochondrial
+Macromolecule #21: 39S ribosomal protein L24, mitochondrial
+Macromolecule #22: 39S ribosomal protein L27, mitochondrial
+Macromolecule #23: 39S ribosomal protein L28, mitochondrial
+Macromolecule #24: 39S ribosomal protein L47, mitochondrial
+Macromolecule #25: 39S ribosomal protein L30, mitochondrial
+Macromolecule #26: 39S ribosomal protein L32, mitochondrial
+Macromolecule #27: 39S ribosomal protein L33, mitochondrial
+Macromolecule #28: 39S ribosomal protein L34, mitochondrial
+Macromolecule #29: 39S ribosomal protein L35, mitochondrial
+Macromolecule #30: 39S ribosomal protein L36, mitochondrial
+Macromolecule #31: 39S ribosomal protein L37, mitochondrial
+Macromolecule #32: 39S ribosomal protein L38, mitochondrial
+Macromolecule #33: 39S ribosomal protein L39, mitochondrial
+Macromolecule #34: 39S ribosomal protein L41, mitochondrial
+Macromolecule #35: 39S ribosomal protein L42, mitochondrial
+Macromolecule #36: 39S ribosomal protein L43, mitochondrial
+Macromolecule #37: 39S ribosomal protein L44, mitochondrial
+Macromolecule #38: 39S ribosomal protein L45, mitochondrial
+Macromolecule #39: 39S ribosomal protein L46, mitochondrial
+Macromolecule #40: 39S ribosomal protein L48, mitochondrial
+Macromolecule #41: 39S ribosomal protein L49, mitochondrial
+Macromolecule #42: 39S ribosomal protein L50, mitochondrial
+Macromolecule #43: 39S ribosomal protein L51, mitochondrial
+Macromolecule #44: 39S ribosomal protein L52, mitochondrial
+Macromolecule #45: 39S ribosomal protein L53, mitochondrial
+Macromolecule #46: 39S ribosomal protein L54, mitochondrial
+Macromolecule #47: 39S ribosomal protein L55, mitochondrial
+Macromolecule #48: Ribosomal protein 63, mitochondrial
+Macromolecule #49: Peptidyl-tRNA hydrolase ICT1, mitochondrial
+Macromolecule #50: Growth arrest and DNA damage-inducible proteins-interacting protein 1
+Macromolecule #51: 39S ribosomal protein S18a, mitochondrial
+Macromolecule #52: 39S ribosomal protein S30, mitochondrial,39S ribosomal protein S3...
+Macromolecule #53: Oxa1L
+Macromolecule #54: 28S ribosomal protein S2, mitochondrial
+Macromolecule #55: 28S ribosomal protein S24, mitochondrial
+Macromolecule #56: 28S ribosomal protein S5, mitochondrial
+Macromolecule #57: 28S ribosomal protein S6, mitochondrial
+Macromolecule #58: 28S ribosomal protein S7, mitochondrial
+Macromolecule #59: 28S ribosomal protein S9, mitochondrial
+Macromolecule #60: 28S ribosomal protein S10, mitochondrial
+Macromolecule #61: 28S ribosomal protein S11, mitochondrial
+Macromolecule #62: 28S ribosomal protein S12, mitochondrial
+Macromolecule #63: 28S ribosomal protein S14, mitochondrial
+Macromolecule #64: 28S ribosomal protein S15, mitochondrial
+Macromolecule #65: 28S ribosomal protein S16, mitochondrial
+Macromolecule #66: 28S ribosomal protein S17, mitochondrial
+Macromolecule #67: 28S ribosomal protein S18b, mitochondrial
+Macromolecule #68: 28S ribosomal protein S18c, mitochondrial
+Macromolecule #69: 28S ribosomal protein S21, mitochondrial
+Macromolecule #70: 28S ribosomal protein S22, mitochondrial
+Macromolecule #71: 28S ribosomal protein S23, mitochondrial
+Macromolecule #72: 28S ribosomal protein S25, mitochondrial
+Macromolecule #73: 28S ribosomal protein S26, mitochondrial
+Macromolecule #74: 28S ribosomal protein S27, mitochondrial
+Macromolecule #75: 28S ribosomal protein S28, mitochondrial
+Macromolecule #76: 28S ribosomal protein S29, mitochondrial
+Macromolecule #77: 28S ribosomal protein S31, mitochondrial
+Macromolecule #78: 28S ribosomal protein S33, mitochondrial
+Macromolecule #79: 28S ribosomal protein S34, mitochondrial
+Macromolecule #80: 28S ribosomal protein S35, mitochondrial
+Macromolecule #81: Coiled-coil-helix-coiled-coil-helix domain-containing protein 1
+Macromolecule #82: Aurora kinase A-interacting protein
+Macromolecule #83: Pentatricopeptide repeat domain-containing protein 3, mitochondrial
+Macromolecule #87: 39S ribosomal protein L40, mitochondrial
+Macromolecule #88: 50S ribosomal protein L1
+Macromolecule #2: 16S rRNA
+Macromolecule #3: mt-tRNA Val
+Macromolecule #84: 12S rRNA
+Macromolecule #85: mt-tRNA
+Macromolecule #86: mRNA
+Macromolecule #89: MAGNESIUM ION
+Macromolecule #90: ZINC ION
+Macromolecule #91: GUANOSINE-5'-DIPHOSPHATE
+Macromolecule #92: SULFATE ION
+Macromolecule #93: MALONATE ION
+Macromolecule #94: CHLORIDE ION
+Macromolecule #95: SODIUM ION
+Macromolecule #96: water
-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 |