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Yorodumi- EMDB-11397: Human mitochondrial ribosome in complex with mRNA, A-site tRNA, P... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-11397 | |||||||||||||||
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Title | Human mitochondrial ribosome in complex with mRNA, A-site tRNA, P-site tRNA and E-site tRNA | |||||||||||||||
Map data | ||||||||||||||||
Sample |
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Keywords | Mitochondria / Ribosome / mRNA / tRNA / Translation | |||||||||||||||
Function / homology | Function and homology information mitochondrial ribosome binding / rRNA import into mitochondrion / mitochondrial transcription / mitochondrial translational termination / mitochondrial translational elongation / mitochondrial ribosome assembly / translation release factor activity, codon nonspecific / microprocessor complex / Mitochondrial translation elongation / Mitochondrial translation termination ...mitochondrial ribosome binding / rRNA import into mitochondrion / mitochondrial transcription / mitochondrial translational termination / mitochondrial translational elongation / mitochondrial ribosome assembly / translation release factor activity, codon nonspecific / microprocessor complex / Mitochondrial translation elongation / Mitochondrial translation termination / positive regulation of mitochondrial translation / Mitochondrial translation initiation / mitochondrial large ribosomal subunit / negative regulation of mitotic nuclear division / peptidyl-tRNA hydrolase / mitochondrial ribosome / Hydrolases; Acting on ester bonds; Endoribonucleases producing 5'-phosphomonoesters / mitochondrial small ribosomal subunit / mitochondrial translation / aminoacyl-tRNA hydrolase activity / 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 / small ribosomal subunit rRNA binding / cell junction / regulation of translation / ribosomal small subunit assembly / large ribosomal subunit rRNA binding / small ribosomal subunit / 5S rRNA binding / nuclear membrane / endonuclease activity / cell population proliferation / tRNA binding / mitochondrial inner membrane / negative regulation of translation / nuclear body / rRNA binding / 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 / positive regulation of DNA-templated transcription / mitochondrion / RNA binding / extracellular space / nucleoplasm / nucleus / plasma membrane / cytosol / cytoplasm Similarity search - Function | |||||||||||||||
Biological species | Homo sapiens (human) / synthetic construct (others) | |||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.0 Å | |||||||||||||||
Authors | Aibara S / Singh V | |||||||||||||||
Funding support | Sweden, European Union, 4 items
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Citation | Journal: Elife / Year: 2020 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 |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_11397.map.gz | 301.2 MB | EMDB map data format | |
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Header (meta data) | emd-11397-v30.xml emd-11397.xml | 105.2 KB 105.2 KB | Display Display | EMDB header |
Images | emd_11397.png | 68.3 KB | ||
Filedesc metadata | emd-11397.cif.gz | 21.9 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-11397 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-11397 | HTTPS FTP |
-Validation report
Summary document | emd_11397_validation.pdf.gz | 438.1 KB | Display | EMDB validaton report |
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Full document | emd_11397_full_validation.pdf.gz | 437.7 KB | Display | |
Data in XML | emd_11397_validation.xml.gz | 7.7 KB | Display | |
Data in CIF | emd_11397_validation.cif.gz | 8.8 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-11397 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-11397 | HTTPS FTP |
-Related structure data
Related structure data | 6zsgMC 6zs9C 6zsaC 6zsbC 6zscC 6zsdC 6zseC 7og4C 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_11397.map.gz / Format: CCP4 / Size: 536.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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
-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 #87: 39S ribosomal protein S30, mitochondrial
+Macromolecule #88: 39S ribosomal protein L12, mitochondrial
+Macromolecule #89: Quinupristin
+Macromolecule #11: 16S mitochondrial rRNA
+Macromolecule #17: 12S mitochondrial rRNA
+Macromolecule #43: mitochondrial tRNAVal
+Macromolecule #83: mRNA
+Macromolecule #84: A-site tRNA
+Macromolecule #85: P-site tRNA
+Macromolecule #86: E-site tRNA
+Macromolecule #90: ZINC ION
+Macromolecule #91: MAGNESIUM ION
+Macromolecule #92: 5-(2-DIETHYLAMINO-ETHANESULFONYL)-21-HYDROXY-10-ISOPROPYL-11,19-D...
+Macromolecule #93: GUANOSINE-5'-TRIPHOSPHATE
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.5 |
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Vitrification | Cryogen name: ETHANE |
-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: FIELD EMISSION GUN |
Electron optics | Illumination mode: OTHER / Imaging mode: BRIGHT FIELD |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Startup model | Type of model: PDB ENTRY |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 4.0 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 13350 |
Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |