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Yorodumi- EMDB-11278: Human mitochondrial ribosome in complex with OXA1L, mRNA, A/A tRN... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-11278 | |||||||||
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Title | Human mitochondrial ribosome in complex with OXA1L, mRNA, A/A tRNA, P/P tRNA and nascent polypeptide | |||||||||
Map data | Combined map of five local-masked refined maps with sharpening and local-resolution filtering. | |||||||||
Sample |
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Keywords | mitochondrion / translation / membrane insertion / translocon / peptidyl-tRNA / RIBOSOME | |||||||||
Function / homology | Function and homology information mitochondrial protein quality control / protein insertion into mitochondrial inner membrane from matrix / membrane insertase activity / negative regulation of oxidoreductase activity / Complex I biogenesis / mitochondrial ribosome binding / rRNA import into mitochondrion / mitochondrial transcription / mitochondrial translational termination / mitochondrial translational elongation ...mitochondrial protein quality control / protein insertion into mitochondrial inner membrane from matrix / membrane insertase activity / negative regulation of oxidoreductase activity / Complex I biogenesis / mitochondrial ribosome binding / rRNA import into mitochondrion / mitochondrial transcription / mitochondrial translational termination / mitochondrial translational elongation / negative regulation of ATP-dependent activity / mitochondrial ribosome assembly / translation release factor activity, codon nonspecific / positive regulation of mitochondrial translation / microprocessor complex / Mitochondrial translation elongation / Mitochondrial translation termination / Mitochondrial translation initiation / mitochondrial proton-transporting ATP synthase complex assembly / mitochondrial large ribosomal subunit / negative regulation of mitotic nuclear division / Hydrolases; Acting on ester bonds; Endoribonucleases producing 5'-phosphomonoesters / peptidyl-tRNA hydrolase / mitochondrial ribosome / mitochondrial small ribosomal subunit / mitochondrial translation / aminoacyl-tRNA hydrolase activity / positive regulation of proteolysis / ribosomal small subunit binding / mitochondrial respiratory chain complex I assembly / anatomical structure morphogenesis / RNA processing / Mitochondrial protein degradation / aerobic respiration / rescue of stalled ribosome / apoptotic signaling pathway / cellular response to leukemia inhibitory factor / protein tetramerization / mitochondrial membrane / fibrillar center / double-stranded RNA binding / small ribosomal subunit rRNA binding / cell junction / regulation of translation / ribosomal small subunit assembly / small ribosomal subunit / 5S rRNA binding / large ribosomal subunit 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 / ribonucleoprotein complex / translation / protein domain specific binding / intracellular membrane-bounded organelle / mRNA binding / nucleotide binding / synapse / GTP binding / nucleolus / apoptotic process / positive regulation of DNA-templated transcription / protein homodimerization activity / protein-containing complex / mitochondrion / RNA binding / extracellular space / nucleoplasm / nucleus / plasma membrane / cytosol / cytoplasm Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.89 Å | |||||||||
Authors | Itoh Y / Andrell J | |||||||||
Funding support | Sweden, 1 items
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Citation | Journal: Science / Year: 2021 Title: Mechanism of membrane-tethered mitochondrial protein synthesis. Authors: Yuzuru Itoh / Juni Andréll / Austin Choi / Uwe Richter / Priyanka Maiti / Robert B Best / Antoni Barrientos / Brendan J Battersby / Alexey Amunts / Abstract: Mitochondrial ribosomes (mitoribosomes) are tethered to the mitochondrial inner membrane to facilitate the cotranslational membrane insertion of the synthesized proteins. We report cryo-electron ...Mitochondrial ribosomes (mitoribosomes) are tethered to the mitochondrial inner membrane to facilitate the cotranslational membrane insertion of the synthesized proteins. We report cryo-electron microscopy structures of human mitoribosomes with nascent polypeptide, bound to the insertase oxidase assembly 1-like (OXA1L) through three distinct contact sites. OXA1L binding is correlated with a series of conformational changes in the mitoribosomal large subunit that catalyze the delivery of newly synthesized polypeptides. The mechanism relies on the folding of mL45 inside the exit tunnel, forming two specific constriction sites that would limit helix formation of the nascent chain. A gap is formed between the exit and the membrane, making the newly synthesized proteins accessible. Our data elucidate the basis by which mitoribosomes interact with the OXA1L insertase to couple protein synthesis and membrane delivery. | |||||||||
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_11278.map.gz | 339.3 MB | EMDB map data format | |
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Header (meta data) | emd-11278-v30.xml emd-11278.xml | 133.3 KB 133.3 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_11278_fsc.xml | 19.1 KB | Display | FSC data file |
Images | emd_11278.png | 82.1 KB | ||
Masks | emd_11278_msk_1.map | 600.7 MB | Mask map | |
Filedesc metadata | emd-11278.cif.gz | 23.9 KB | ||
Others | emd_11278_additional_1.map.gz emd_11278_half_map_1.map.gz emd_11278_half_map_2.map.gz | 557.9 MB 486.2 MB 486.2 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-11278 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-11278 | HTTPS FTP |
-Validation report
Summary document | emd_11278_validation.pdf.gz | 462.2 KB | Display | EMDB validaton report |
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Full document | emd_11278_full_validation.pdf.gz | 461.4 KB | Display | |
Data in XML | emd_11278_validation.xml.gz | 25.5 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-11278 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-11278 | HTTPS FTP |
-Related structure data
Related structure data | 6zm5MC 6zm6C 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_11278.map.gz / Format: CCP4 / Size: 600.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Combined map of five local-masked refined maps with sharpening and local-resolution filtering. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.83 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_11278_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Additional map: Combined map of five local-masked refined maps without sharpening.
File | emd_11278_additional_1.map | ||||||||||||
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Annotation | Combined map of five local-masked refined maps without sharpening. | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Local-masked refined map using the mask covering the...
File | emd_11278_half_map_1.map | ||||||||||||
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Annotation | Local-masked refined map using the mask covering the LSU-core and the insertase. | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Local-masked refined map using the mask covering the...
File | emd_11278_half_map_2.map | ||||||||||||
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Annotation | Local-masked refined map using the mask covering the LSU-core and the insertase. | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
+Entire : Translating ribosome with insertase
+Supramolecule #1: Translating ribosome with insertase
+Supramolecule #2: Large subunit of ribosome
+Supramolecule #3: Small subunit of ribosome
+Supramolecule #4: OXA1L insertase
+Macromolecule #1: 16S mitochondrial rRNA
+Macromolecule #2: mitochondrial tRNAVal
+Macromolecule #54: 12S mitochondrial rRNA
+Macromolecule #87: A-site tRNA with aminoacylation
+Macromolecule #88: P-site tRNA
+Macromolecule #89: mRNA
+Macromolecule #3: 39S ribosomal protein L2, mitochondrial
+Macromolecule #4: 39S ribosomal protein L3, mitochondrial
+Macromolecule #5: 39S ribosomal protein L4, mitochondrial
+Macromolecule #6: 39S ribosomal protein L9, mitochondrial
+Macromolecule #7: 39S ribosomal protein L10, mitochondrial
+Macromolecule #8: 39S ribosomal protein L11, mitochondrial
+Macromolecule #9: 39S ribosomal protein L13, mitochondrial
+Macromolecule #10: 39S ribosomal protein L14, mitochondrial
+Macromolecule #11: 39S ribosomal protein L15, mitochondrial
+Macromolecule #12: 39S ribosomal protein L16, mitochondrial
+Macromolecule #13: 39S ribosomal protein L17, mitochondrial
+Macromolecule #14: 39S ribosomal protein L18, mitochondrial
+Macromolecule #15: 39S ribosomal protein L19, mitochondrial
+Macromolecule #16: 39S ribosomal protein L20, mitochondrial
+Macromolecule #17: 39S ribosomal protein L21, mitochondrial
+Macromolecule #18: 39S ribosomal protein L22, mitochondrial
+Macromolecule #19: 39S ribosomal protein L23, mitochondrial
+Macromolecule #20: 39S ribosomal protein L24, mitochondrial
+Macromolecule #21: 39S ribosomal protein L27, mitochondrial
+Macromolecule #22: 39S ribosomal protein L28, mitochondrial
+Macromolecule #23: 39S ribosomal protein L47, mitochondrial
+Macromolecule #24: 39S ribosomal protein L30, mitochondrial
+Macromolecule #25: 39S ribosomal protein L32, mitochondrial
+Macromolecule #26: 39S ribosomal protein L33, mitochondrial
+Macromolecule #27: 39S ribosomal protein L34, mitochondrial
+Macromolecule #28: 39S ribosomal protein L35, mitochondrial
+Macromolecule #29: 39S ribosomal protein L36, mitochondrial
+Macromolecule #30: 39S ribosomal protein L37, mitochondrial
+Macromolecule #31: 39S ribosomal protein L38, mitochondrial
+Macromolecule #32: 39S ribosomal protein L39, mitochondrial
+Macromolecule #33: 39S ribosomal protein L40, 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
+Macromolecule #53: 39S ribosomal protein L12, mitochondrial
+Macromolecule #55: 28S ribosomal protein S2, mitochondrial
+Macromolecule #56: 28S ribosomal protein S24, mitochondrial
+Macromolecule #57: 28S ribosomal protein S5, mitochondrial
+Macromolecule #58: 28S ribosomal protein S6, mitochondrial
+Macromolecule #59: 28S ribosomal protein S7, mitochondrial
+Macromolecule #60: 28S ribosomal protein S9, mitochondrial
+Macromolecule #61: 28S ribosomal protein S10, mitochondrial
+Macromolecule #62: 28S ribosomal protein S11, mitochondrial
+Macromolecule #63: 28S ribosomal protein S12, mitochondrial
+Macromolecule #64: 28S ribosomal protein S14, mitochondrial
+Macromolecule #65: 28S ribosomal protein S15, mitochondrial
+Macromolecule #66: 28S ribosomal protein S16, mitochondrial
+Macromolecule #67: 28S ribosomal protein S17, mitochondrial
+Macromolecule #68: 28S ribosomal protein S18b, mitochondrial
+Macromolecule #69: 28S ribosomal protein S18c, mitochondrial
+Macromolecule #70: 28S ribosomal protein S21, mitochondrial
+Macromolecule #71: 28S ribosomal protein S22, mitochondrial
+Macromolecule #72: 28S ribosomal protein S23, mitochondrial
+Macromolecule #73: 28S ribosomal protein S25, mitochondrial
+Macromolecule #74: 28S ribosomal protein S26, mitochondrial
+Macromolecule #75: 28S ribosomal protein S27, mitochondrial
+Macromolecule #76: 28S ribosomal protein S28, mitochondrial
+Macromolecule #77: 28S ribosomal protein S29, mitochondrial
+Macromolecule #78: 28S ribosomal protein S31, mitochondrial
+Macromolecule #79: 28S ribosomal protein S33, mitochondrial
+Macromolecule #80: 28S ribosomal protein S34, mitochondrial
+Macromolecule #81: 28S ribosomal protein S35, mitochondrial
+Macromolecule #82: Coiled-coil-helix-coiled-coil-helix domain-containing protein 1
+Macromolecule #83: Aurora kinase A-interacting protein
+Macromolecule #84: Pentatricopeptide repeat domain-containing protein 3, mitochondrial
+Macromolecule #85: Mitochondrial inner membrane protein OXA1L
+Macromolecule #86: Nascent polypeptide
+Macromolecule #90: MAGNESIUM ION
+Macromolecule #91: POTASSIUM ION
+Macromolecule #92: ZINC ION
+Macromolecule #93: FE2/S2 (INORGANIC) CLUSTER
+Macromolecule #94: ADENOSINE-5'-TRIPHOSPHATE
+Macromolecule #95: GUANOSINE-5'-TRIPHOSPHATE
+Macromolecule #96: ALANINE
+Macromolecule #97: water
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.5 Component:
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Grid | Model: Quantifoil R2/2 / Material: COPPER / Support film - Material: CARBON / Support film - topology: HOLEY / Support film - Film thickness: 3 / Pretreatment - Type: GLOW DISCHARGE | ||||||||||||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Specialist optics | Energy filter - Name: GIF Quantum LS / Energy filter - Slit width: 20 eV |
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Digitization - Dimensions - Width: 3838 pixel / Digitization - Dimensions - Height: 3710 pixel / Digitization - Frames/image: 1-20 / Number grids imaged: 2 / Number real images: 19655 / Average exposure time: 4.0 sec. / Average electron dose: 30.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 70.0 µm / Calibrated defocus max: 3.6 µm / Calibrated defocus min: 0.2 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal magnification: 165000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
+Image processing
-Atomic model buiding 1
Initial model |
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Refinement | Space: REAL / Protocol: AB INITIO MODEL / Overall B value: 44 / Target criteria: Correlation coefficient | ||||||||
Output model | PDB-6zm5: |