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- EMDB-11392: Human mitochondrial ribosome in complex with mRNA and P-site tRNA -
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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-11392 | |||||||||||||||
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Title | Human mitochondrial ribosome in complex with mRNA and P-site tRNA | |||||||||||||||
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![]() | Mitochondria / Ribosome / mRNA / tRNA / Translation | |||||||||||||||
Function / homology | ![]() mitochondrial ribosome binding / rRNA import into mitochondrion / mitochondrial transcription / mitochondrial translational elongation / mitochondrial translational termination / mitochondrial ribosome assembly / microprocessor complex / translation release factor activity, codon nonspecific / Mitochondrial translation elongation / Mitochondrial translation termination ...mitochondrial ribosome binding / rRNA import into mitochondrion / mitochondrial transcription / 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 / 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 / cytosolic small ribosomal subunit / endonuclease activity / cell population proliferation / 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 / intracellular membrane-bounded organelle / nucleotide binding / mRNA binding / synapse / apoptotic process / nucleolus / GTP binding / positive regulation of DNA-templated transcription / mitochondrion / RNA binding / extracellular space / nucleoplasm / nucleus / plasma membrane / cytosol / cytoplasm Similarity search - Function | |||||||||||||||
Biological species | ![]() | |||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.5 Å | |||||||||||||||
![]() | Aibara S / Singh V | |||||||||||||||
Funding support | ![]()
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![]() | ![]() Title: Structural basis of mitochondrial translation. Authors: Shintaro Aibara / Vivek Singh / Angelika Modelska / Alexey Amunts / ![]() ![]() Abstract: Translation of mitochondrial messenger RNA (mt-mRNA) is performed by distinct mitoribosomes comprising at least 36 mitochondria-specific proteins. How these mitoribosomal proteins assist in the ...Translation of mitochondrial messenger RNA (mt-mRNA) is performed by distinct mitoribosomes comprising at least 36 mitochondria-specific proteins. How these mitoribosomal proteins assist in the binding of mt-mRNA and to what extent they are involved in the translocation of transfer RNA (mt-tRNA) is unclear. To visualize the process of translation in human mitochondria, we report ~3.0 Å resolution structure of the human mitoribosome, including the L7/L12 stalk, and eight structures of its functional complexes with mt-mRNA, mt-tRNAs, recycling factor and additional trans factors. The study reveals a transacting protein module LRPPRC-SLIRP that delivers mt-mRNA to the mitoribosomal small subunit through a dedicated platform formed by the mitochondria-specific protein mS39. Mitoribosomal proteins of the large subunit mL40, mL48, and mL64 coordinate translocation of mt-tRNA. The comparison between those structures shows dynamic interactions between the mitoribosome and its ligands, suggesting a sequential mechanism of conformational changes. | |||||||||||||||
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 | ![]() | 300.2 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 103 KB 103 KB | Display Display | ![]() |
Images | ![]() | 85.6 KB | ||
Filedesc metadata | ![]() | 21.8 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6zsbMC ![]() 6zs9C ![]() 6zsaC ![]() 6zscC ![]() 6zsdC ![]() 6zseC ![]() 6zsgC ![]() 7og4C 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: 1.05 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
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Sample components
+Entire : human mitochondrial ribosome
+Supramolecule #1: human mitochondrial ribosome
+Macromolecule #1: 39S ribosomal protein L32, mitochondrial
+Macromolecule #2: 39S ribosomal protein L33, mitochondrial
+Macromolecule #3: 39S ribosomal protein L34, mitochondrial
+Macromolecule #4: 39S ribosomal protein L35, mitochondrial
+Macromolecule #5: 39S ribosomal protein L36, mitochondrial
+Macromolecule #6: 39S ribosomal protein L37, mitochondrial
+Macromolecule #7: 39S ribosomal protein L38, mitochondrial
+Macromolecule #8: 39S ribosomal protein L39, mitochondrial
+Macromolecule #9: 39S ribosomal protein L40, mitochondrial
+Macromolecule #10: 39S ribosomal protein L41, mitochondrial
+Macromolecule #12: 28S ribosomal protein S34, mitochondrial
+Macromolecule #13: 28S ribosomal protein S35, mitochondrial
+Macromolecule #14: Coiled-coil-helix-coiled-coil-helix domain-containing protein 1
+Macromolecule #15: Aurora kinase A-interacting protein
+Macromolecule #16: Pentatricopeptide repeat domain-containing protein 3, mitochondrial
+Macromolecule #18: 28S ribosomal protein S2, mitochondrial
+Macromolecule #19: 28S ribosomal protein S24, mitochondrial
+Macromolecule #20: 28S ribosomal protein S5, mitochondrial
+Macromolecule #21: 28S ribosomal protein S6, mitochondrial
+Macromolecule #22: 28S ribosomal protein S7, mitochondrial
+Macromolecule #23: 28S ribosomal protein S9, mitochondrial
+Macromolecule #24: 28S ribosomal protein S10, mitochondrial
+Macromolecule #25: 28S ribosomal protein S11, mitochondrial
+Macromolecule #26: 28S ribosomal protein S12, mitochondrial
+Macromolecule #27: 28S ribosomal protein S14, mitochondrial
+Macromolecule #28: 28S ribosomal protein S15, mitochondrial
+Macromolecule #29: 28S ribosomal protein S16, mitochondrial
+Macromolecule #30: 28S ribosomal protein S17, mitochondrial
+Macromolecule #31: 28S ribosomal protein S18b, mitochondrial
+Macromolecule #32: 28S ribosomal protein S18c, mitochondrial
+Macromolecule #33: 28S ribosomal protein S21, mitochondrial
+Macromolecule #34: 28S ribosomal protein S22, mitochondrial
+Macromolecule #35: 28S ribosomal protein S23, mitochondrial
+Macromolecule #36: 28S ribosomal protein S25, mitochondrial
+Macromolecule #37: 28S ribosomal protein S26, mitochondrial
+Macromolecule #38: 28S ribosomal protein S27, mitochondrial
+Macromolecule #39: 28S ribosomal protein S28, mitochondrial
+Macromolecule #40: 28S ribosomal protein S29, mitochondrial
+Macromolecule #41: 28S ribosomal protein S31, mitochondrial
+Macromolecule #42: 28S ribosomal protein S33, mitochondrial
+Macromolecule #44: 39S ribosomal protein L2, mitochondrial
+Macromolecule #45: 39S ribosomal protein L3, mitochondrial
+Macromolecule #46: 39S ribosomal protein L4, mitochondrial
+Macromolecule #47: 39S ribosomal protein L9, mitochondrial
+Macromolecule #48: 39S ribosomal protein L10, mitochondrial
+Macromolecule #49: 39S ribosomal protein L11, mitochondrial
+Macromolecule #50: 39S ribosomal protein L13, mitochondrial
+Macromolecule #51: 39S ribosomal protein L14, mitochondrial
+Macromolecule #52: 39S ribosomal protein L15, mitochondrial
+Macromolecule #53: 39S ribosomal protein L16, mitochondrial
+Macromolecule #54: 39S ribosomal protein L17, mitochondrial
+Macromolecule #55: 39S ribosomal protein L18, mitochondrial
+Macromolecule #56: 39S ribosomal protein L19, mitochondrial
+Macromolecule #57: 39S ribosomal protein L20, mitochondrial
+Macromolecule #58: 39S ribosomal protein L21, mitochondrial
+Macromolecule #59: 39S ribosomal protein L22, mitochondrial
+Macromolecule #60: 39S ribosomal protein L23, mitochondrial
+Macromolecule #61: 39S ribosomal protein L24, mitochondrial
+Macromolecule #62: 39S ribosomal protein L27, mitochondrial
+Macromolecule #63: 39S ribosomal protein L28, mitochondrial
+Macromolecule #64: 39S ribosomal protein L47, mitochondrial
+Macromolecule #65: 39S ribosomal protein L30, mitochondrial
+Macromolecule #66: 39S ribosomal protein L42, mitochondrial
+Macromolecule #67: 39S ribosomal protein L43, mitochondrial
+Macromolecule #68: 39S ribosomal protein L44, mitochondrial
+Macromolecule #69: 39S ribosomal protein L45, mitochondrial
+Macromolecule #70: 39S ribosomal protein L46, mitochondrial
+Macromolecule #71: 39S ribosomal protein L48, mitochondrial
+Macromolecule #72: 39S ribosomal protein L49, mitochondrial
+Macromolecule #73: 39S ribosomal protein L50, mitochondrial
+Macromolecule #74: 39S ribosomal protein L51, mitochondrial
+Macromolecule #75: 39S ribosomal protein L52, mitochondrial
+Macromolecule #76: 39S ribosomal protein L53, mitochondrial
+Macromolecule #77: 39S ribosomal protein L54, mitochondrial
+Macromolecule #78: 39S ribosomal protein L55, mitochondrial
+Macromolecule #79: Ribosomal protein 63, mitochondrial
+Macromolecule #80: Peptidyl-tRNA hydrolase ICT1, mitochondrial
+Macromolecule #81: Growth arrest and DNA damage-inducible proteins-interacting protein 1
+Macromolecule #82: 39S ribosomal protein S18a, mitochondrial
+Macromolecule #85: 39S ribosomal protein S30, mitochondrial
+Macromolecule #86: 39S ribosomal protein L12, mitochondrial
+Macromolecule #87: Quinupristin
+Macromolecule #11: 16S mitochondrial rRNA
+Macromolecule #17: 12S mitochondrial rRNA
+Macromolecule #43: mitochondrial tRNAVal
+Macromolecule #83: mRNA
+Macromolecule #84: P-site tRNA
+Macromolecule #88: ZINC ION
+Macromolecule #89: MAGNESIUM ION
+Macromolecule #90: 5-(2-DIETHYLAMINO-ETHANESULFONYL)-21-HYDROXY-10-ISOPROPYL-11,19-D...
+Macromolecule #91: GUANOSINE-5'-TRIPHOSPHATE
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Buffer | pH: 7.5 |
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Vitrification | Cryogen name: ETHANE |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 30.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: OTHER / Imaging mode: BRIGHT FIELD |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Image processing
Startup model | Type of model: PDB ENTRY |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 4.5 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 6692 |
Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |