+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-13980 | ||||||||||||||||||
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Title | Human mitochondrial ribosome at 2.2 A resolution | ||||||||||||||||||
Map data | Local_masked_refined_composite_map | ||||||||||||||||||
Sample |
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Keywords | ribosome / mitochondrial translation / tRNA / mRNA / 2Fe-2S clusters / polyamines / rRNA modifications / post-translation modifications / cryo EM | ||||||||||||||||||
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 / positive regulation of mitochondrial translation / microprocessor complex / Mitochondrial translation elongation ...mitochondrial ribosome binding / rRNA import into mitochondrion / mitochondrial transcription / mitochondrial translational termination / mitochondrial translational elongation / 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 large ribosomal subunit / negative regulation of mitotic nuclear division / 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 / small ribosomal subunit rRNA binding / cell junction / regulation of translation / ribosomal small subunit assembly / small ribosomal subunit / large ribosomal subunit rRNA binding / 5S rRNA binding / nuclear membrane / endonuclease activity / cell population proliferation / tRNA binding / mitochondrial inner membrane / negative regulation of translation / nuclear body / rRNA binding / ribosome / mitochondrial matrix / structural constituent of ribosome / 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 / 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: 2.21 Å | ||||||||||||||||||
Authors | Singh V / Itoh Y / Andrell J / Aibara S / Amunts A | ||||||||||||||||||
Funding support | Sweden, European Union, 5 items
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Citation | Journal: bioRxiv / Year: 2023 Title: Structure of mitoribosome reveals mechanism of mRNA binding, tRNA interactions with L1 stalk, roles of cofactors and rRNA modifications. Authors: Vivek Singh / Yuzuru Itoh / Samuel Del'Olio / Asem Hassan / Andreas Naschberger / Rasmus Kock Flygaard / Yuko Nobe / Keiichi Izumikawa / Shintaro Aibara / Juni Andréll / Paul C Whitford / ...Authors: Vivek Singh / Yuzuru Itoh / Samuel Del'Olio / Asem Hassan / Andreas Naschberger / Rasmus Kock Flygaard / Yuko Nobe / Keiichi Izumikawa / Shintaro Aibara / Juni Andréll / Paul C Whitford / Antoni Barrientos / Masato Taoka / Alexey Amunts Abstract: The mitoribosome translates mitochondrial mRNAs and regulates energy conversion that is a signature of aerobic life forms. We present a 2.2 Å resolution structure of human mitoribosome together with ...The mitoribosome translates mitochondrial mRNAs and regulates energy conversion that is a signature of aerobic life forms. We present a 2.2 Å resolution structure of human mitoribosome together with validated mitoribosomal RNA (rRNA) modifications, including aminoacylated CP-tRNA . The structure shows how mitoribosomal proteins stabilise binding of mRNA and tRNA helping to align it in the decoding center, whereas the GDP-bound mS29 stabilizes intersubunit communication. Comparison between different states, with respect to tRNA position, allowed to characterize a non-canonical L1 stalk, and molecular dynamics simulations revealed how it facilitates tRNA transition in a way that does not require interactions with rRNA. We also report functionally important polyamines that are depleted when cells are subjected to an antibiotic treatment. The structural, biochemical, and computational data illuminate the principal functional components of the translation mechanism in mitochondria and provide the most complete description so far of the structure and function of the human mitoribosome. | ||||||||||||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_13980.map.gz | 336.9 MB | EMDB map data format | |
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Header (meta data) | emd-13980-v30.xml emd-13980.xml | 124.6 KB 124.6 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_13980_fsc.xml | 19 KB | Display | FSC data file |
Images | emd_13980.png | 152.7 KB | ||
Masks | emd_13980_msk_1.map emd_13980_msk_2.map emd_13980_msk_3.map emd_13980_msk_4.map emd_13980_msk_5.map emd_13980_msk_6.map emd_13980_msk_7.map emd_13980_msk_8.map emd_13980_msk_9.map | 600.7 MB 600.7 MB 600.7 MB 600.7 MB 600.7 MB 600.7 MB 600.7 MB 600.7 MB 600.7 MB | Mask map | |
Filedesc metadata | emd-13980.cif.gz | 24.2 KB | ||
Others | emd_13980_additional_1.map.gz emd_13980_additional_2.map.gz emd_13980_additional_3.map.gz emd_13980_half_map_1.map.gz emd_13980_half_map_2.map.gz | 2.2 GB 336.2 MB 483.2 MB 486 MB 486 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-13980 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-13980 | HTTPS FTP |
-Validation report
Summary document | emd_13980_validation.pdf.gz | 1.1 MB | Display | EMDB validaton report |
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Full document | emd_13980_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | emd_13980_validation.xml.gz | 27.6 KB | Display | |
Data in CIF | emd_13980_validation.cif.gz | 36.4 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-13980 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-13980 | HTTPS FTP |
-Related structure data
Related structure data | 7qi4MC 7qi5C 7qi6C M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_13980.map.gz / Format: CCP4 / Size: 600.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Annotation | Local_masked_refined_composite_map | ||||||||||||||||||||||||||||||||||||
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:
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-Supplemental data
+Mask #1
+Mask #2
+Mask #3
+Mask #4
+Mask #5
+Mask #6
+Mask #7
+Mask #8
+Mask #9
+Additional map: super-sampled local masked refined composite map
+Additional map: local resolution filtered sharpened map
+Additional map: unsharpened map
+Half map: half map 2 unfiltered
+Half map: half map 1 unfiltered
-Sample components
+Entire : Human mitochondrial ribosome
+Supramolecule #1: Human mitochondrial ribosome
+Macromolecule #1: 12S mitochondrial rRNA
+Macromolecule #32: A/A-tRNA
+Macromolecule #33: P/P-tRNA
+Macromolecule #34: mRNA
+Macromolecule #35: 16S mitochondrial rRNA
+Macromolecule #36: mitochondrial tRNAVal
+Macromolecule #89: E/E-tRNA
+Macromolecule #2: 28S ribosomal protein S2, mitochondrial
+Macromolecule #3: 28S ribosomal protein S24, mitochondrial
+Macromolecule #4: 28S ribosomal protein S5, mitochondrial
+Macromolecule #5: 28S ribosomal protein S6, mitochondrial
+Macromolecule #6: 28S ribosomal protein S7, mitochondrial
+Macromolecule #7: 28S ribosomal protein S9, mitochondrial
+Macromolecule #8: 28S ribosomal protein S10, mitochondrial
+Macromolecule #9: 28S ribosomal protein S11, mitochondrial
+Macromolecule #10: 28S ribosomal protein S12, mitochondrial
+Macromolecule #11: 28S ribosomal protein S14, mitochondrial
+Macromolecule #12: 28S ribosomal protein S15, mitochondrial
+Macromolecule #13: 28S ribosomal protein S16, mitochondrial
+Macromolecule #14: 28S ribosomal protein S17, mitochondrial
+Macromolecule #15: 28S ribosomal protein S18b, mitochondrial
+Macromolecule #16: 28S ribosomal protein S18c, mitochondrial
+Macromolecule #17: MRPS21 isoform 1
+Macromolecule #18: 28S ribosomal protein S22, mitochondrial
+Macromolecule #19: 28S ribosomal protein S23, mitochondrial
+Macromolecule #20: 28S ribosomal protein S25, mitochondrial
+Macromolecule #21: 28S ribosomal protein S26, mitochondrial
+Macromolecule #22: 28S ribosomal protein S27, mitochondrial
+Macromolecule #23: 28S ribosomal protein S28, mitochondrial
+Macromolecule #24: 28S ribosomal protein S29, mitochondrial
+Macromolecule #25: 28S ribosomal protein S31, mitochondrial
+Macromolecule #26: 28S ribosomal protein S33, mitochondrial
+Macromolecule #27: 28S ribosomal protein S34, mitochondrial
+Macromolecule #28: 28S ribosomal protein S35, mitochondrial
+Macromolecule #29: Coiled-coil-helix-coiled-coil-helix domain-containing protein 1
+Macromolecule #30: Aurora kinase A-interacting protein
+Macromolecule #31: Pentatricopeptide repeat domain-containing protein 3, mitochondrial
+Macromolecule #37: 39S ribosomal protein L2, mitochondrial
+Macromolecule #38: 39S ribosomal protein L3, mitochondrial
+Macromolecule #39: 39S ribosomal protein L4, mitochondrial
+Macromolecule #40: 39S ribosomal protein L9, mitochondrial
+Macromolecule #41: 39S ribosomal protein L10, mitochondrial
+Macromolecule #42: 39S ribosomal protein L11, mitochondrial
+Macromolecule #43: 39S ribosomal protein L13, mitochondrial
+Macromolecule #44: 39S ribosomal protein L14, mitochondrial
+Macromolecule #45: 39S ribosomal protein L15, mitochondrial
+Macromolecule #46: 39S ribosomal protein L16, mitochondrial
+Macromolecule #47: 39S ribosomal protein L17, mitochondrial
+Macromolecule #48: 39S ribosomal protein L18, mitochondrial
+Macromolecule #49: 39S ribosomal protein L19, mitochondrial
+Macromolecule #50: 39S ribosomal protein L20, mitochondrial
+Macromolecule #51: 39S ribosomal protein L21, mitochondrial
+Macromolecule #52: 39S ribosomal protein L22, mitochondrial
+Macromolecule #53: 39S ribosomal protein L23, mitochondrial
+Macromolecule #54: 39S ribosomal protein L24, mitochondrial
+Macromolecule #55: 39S ribosomal protein L27, mitochondrial
+Macromolecule #56: 39S ribosomal protein L28, mitochondrial
+Macromolecule #57: 39S ribosomal protein L47, mitochondrial
+Macromolecule #58: 39S ribosomal protein L30, mitochondrial
+Macromolecule #59: 39S ribosomal protein L32, mitochondrial
+Macromolecule #60: 39S ribosomal protein L33, mitochondrial
+Macromolecule #61: 39S ribosomal protein L34, mitochondrial
+Macromolecule #62: 39S ribosomal protein L35, mitochondrial
+Macromolecule #63: 39S ribosomal protein L36, mitochondrial
+Macromolecule #64: 39S ribosomal protein L37, mitochondrial
+Macromolecule #65: 39S ribosomal protein L38, mitochondrial
+Macromolecule #66: 39S ribosomal protein L39, mitochondrial
+Macromolecule #67: 39S ribosomal protein L40, mitochondrial
+Macromolecule #68: 39S ribosomal protein L41, mitochondrial
+Macromolecule #69: 39S ribosomal protein L42, mitochondrial
+Macromolecule #70: 39S ribosomal protein L43, mitochondrial
+Macromolecule #71: 39S ribosomal protein L44, mitochondrial
+Macromolecule #72: 39S ribosomal protein L45, mitochondrial
+Macromolecule #73: 39S ribosomal protein L46, mitochondrial
+Macromolecule #74: 39S ribosomal protein L48, mitochondrial
+Macromolecule #75: 39S ribosomal protein L49, mitochondrial
+Macromolecule #76: 39S ribosomal protein L50, mitochondrial
+Macromolecule #77: 39S ribosomal protein L51, mitochondrial
+Macromolecule #78: 39S ribosomal protein L52, mitochondrial
+Macromolecule #79: 39S ribosomal protein L53, mitochondrial
+Macromolecule #80: 39S ribosomal protein L54, mitochondrial
+Macromolecule #81: 39S ribosomal protein L55, mitochondrial
+Macromolecule #82: Ribosomal protein 63, mitochondrial
+Macromolecule #83: Peptidyl-tRNA hydrolase ICT1, mitochondrial
+Macromolecule #84: Growth arrest and DNA damage-inducible proteins-interacting protein 1
+Macromolecule #85: 39S ribosomal protein S18a, mitochondrial
+Macromolecule #86: 39S ribosomal protein S30, mitochondrial
+Macromolecule #87: 39S ribosomal protein L12, mitochondrial
+Macromolecule #88: 39S ribosomal protein L1, mitochondrial
+Macromolecule #90: NICOTINAMIDE-ADENINE-DINUCLEOTIDE
+Macromolecule #91: SPERMINE
+Macromolecule #92: SPERMIDINE
+Macromolecule #93: MAGNESIUM ION
+Macromolecule #94: POTASSIUM ION
+Macromolecule #95: ZINC ION
+Macromolecule #96: FE2/S2 (INORGANIC) CLUSTER
+Macromolecule #97: ADENOSINE-5'-TRIPHOSPHATE
+Macromolecule #98: GUANOSINE-5'-DIPHOSPHATE
+Macromolecule #99: 1,4-DIAMINOBUTANE
+Macromolecule #100: VALINE
+Macromolecule #101: 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 |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Specialist optics | Energy filter - Slit width: 20 eV |
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average electron dose: 30.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.8000000000000003 µm / Nominal defocus min: 0.6 µm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |