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Yorodumi- EMDB-4369: Unique features of mammalian mitochondrial translation initiation... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-4369 | ||||||||||||
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Title | Unique features of mammalian mitochondrial translation initiation revealed by cryo-EM. This file contains the 28S ribosomal subunit. | ||||||||||||
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Sample |
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Function / homology | Function and homology information Hormone ligand-binding receptors / gonadotropin-releasing hormone receptor binding / gonadotropin hormone-releasing hormone activity / G alpha (q) signalling events / Mitochondrial translation elongation / Mitochondrial translation termination / mitochondrial translational initiation / : / translation factor activity, RNA binding / ribosome disassembly ...Hormone ligand-binding receptors / gonadotropin-releasing hormone receptor binding / gonadotropin hormone-releasing hormone activity / G alpha (q) signalling events / Mitochondrial translation elongation / Mitochondrial translation termination / mitochondrial translational initiation / : / translation factor activity, RNA binding / ribosome disassembly / mitochondrial ribosome assembly / Mitochondrial translation initiation / mitochondrial small ribosomal subunit / regulation of translational initiation / mitochondrial ribosome / mitochondrial translation / positive regulation of proteolysis / ribosomal small subunit binding / organelle membrane / translation initiation factor activity / small ribosomal subunit rRNA binding / ribosomal small subunit assembly / regulation of translation / cell junction / small ribosomal subunit / nuclear membrane / rRNA binding / ribosome / mitochondrial matrix / structural constituent of ribosome / ribonucleoprotein complex / translation / mRNA binding / intracellular membrane-bounded organelle / GTPase activity / apoptotic process / GTP binding / nucleolus / mitochondrion / extracellular space / RNA binding / nucleoplasm / cytoplasm Similarity search - Function | ||||||||||||
Biological species | Sus scrofa (pig) / Homo sapiens (human) / Pig (pig) | ||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.1 Å | ||||||||||||
Authors | Kummer E / Leibundgut M / Boehringer D / Ban N | ||||||||||||
Funding support | Switzerland, 3 items
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Citation | Journal: Nature / Year: 2018 Title: Unique features of mammalian mitochondrial translation initiation revealed by cryo-EM. Authors: Eva Kummer / Marc Leibundgut / Oliver Rackham / Richard G Lee / Daniel Boehringer / Aleksandra Filipovska / Nenad Ban / Abstract: Mitochondria maintain their own specialized protein synthesis machinery, which in mammals is used exclusively for the synthesis of the membrane proteins responsible for oxidative phosphorylation. The ...Mitochondria maintain their own specialized protein synthesis machinery, which in mammals is used exclusively for the synthesis of the membrane proteins responsible for oxidative phosphorylation. The initiation of protein synthesis in mitochondria differs substantially from bacterial or cytosolic translation systems. Mitochondrial translation initiation lacks initiation factor 1, which is essential in all other translation systems from bacteria to mammals. Furthermore, only one type of methionyl transfer RNA (tRNA) is used for both initiation and elongation, necessitating that the initiation factor specifically recognizes the formylated version of tRNA (fMet-tRNA). Lastly, most mitochondrial mRNAs do not possess 5' leader sequences to promote mRNA binding to the ribosome. There is currently little mechanistic insight into mammalian mitochondrial translation initiation, and it is not clear how mRNA engagement, initiator-tRNA recruitment and start-codon selection occur. Here we determine the cryo-EM structure of the complete translation initiation complex from mammalian mitochondria at 3.2 Å. We describe the function of an additional domain insertion that is present in the mammalian mitochondrial initiation factor 2 (mtIF2). By closing the decoding centre, this insertion stabilizes the binding of leaderless mRNAs and induces conformational changes in the rRNA nucleotides involved in decoding. We identify unique features of mtIF2 that are required for specific recognition of fMet-tRNA and regulation of its GTPase activity. Finally, we observe that the ribosomal tunnel in the initiating ribosome is blocked by insertion of the N-terminal portion of mitochondrial protein mL45, which becomes exposed as the ribosome switches to elongation mode and may have an additional role in targeting of mitochondrial ribosomes to the protein-conducting pore in the inner mitochondrial membrane. | ||||||||||||
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_4369.map.gz | 12.7 MB | EMDB map data format | |
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Header (meta data) | emd-4369-v30.xml emd-4369.xml | 63.9 KB 63.9 KB | Display Display | EMDB header |
Images | emd_4369.png | 122.8 KB | ||
Masks | emd_4369_msk_1.map | 84.6 MB | Mask map | |
Others | emd_4369_half_map_1.map.gz emd_4369_half_map_2.map.gz | 71.5 MB 71.5 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-4369 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-4369 | HTTPS FTP |
-Related structure data
Related structure data | 6gazMC 4368C 4370C 6gawC 6gb2C C: citing same article (ref.) M: atomic model generated by this map |
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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_4369.map.gz / Format: CCP4 / Size: 84.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Voxel size | X=Y=Z: 1.39 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_4369_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_4369_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_4369_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
+Entire : mammalian mitochondrial translation initiation complex
+Supramolecule #1: mammalian mitochondrial translation initiation complex
+Supramolecule #2: Porcine Ribosome
+Supramolecule #3: Translation initiation factor IF-2, mitochondrial
+Supramolecule #4: Nucleic acids
+Macromolecule #1: Translation initiation factor IF-2, mitochondrial
+Macromolecule #2: Mitochondrial ribosomal protein L19
+Macromolecule #4: Mitochondrial ribosomal protein S2
+Macromolecule #5: Mitochondrial ribosomal protein S24
+Macromolecule #6: Mitochondrial ribosomal protein S5
+Macromolecule #7: Mitochondrial ribosomal protein S6
+Macromolecule #8: Mitochondrial ribosomal protein S7
+Macromolecule #9: Mitochondrial ribosomal protein S9
+Macromolecule #10: Mitochondrial ribosomal protein S10
+Macromolecule #11: Mitochondrial ribosomal protein S11
+Macromolecule #12: Mitochondrial ribosomal protein S12
+Macromolecule #13: Mitochondrial ribosomal protein S14
+Macromolecule #14: Mitochondrial ribosomal protein S15
+Macromolecule #15: bS16m, MRPS16
+Macromolecule #16: Mitochondrial ribosomal protein S17
+Macromolecule #17: Mitochondrial ribosomal protein S18C
+Macromolecule #18: Mitochondrial ribosomal protein S21
+Macromolecule #21: unassigned secondary structure elements
+Macromolecule #22: Mitochondrial ribosomal protein S22
+Macromolecule #23: Mitochondrial ribosomal protein S23
+Macromolecule #24: Mitochondrial ribosomal protein S25
+Macromolecule #25: Mitochondrial ribosomal protein S26
+Macromolecule #26: Mitochondrial ribosomal protein S27
+Macromolecule #27: Mitoribosomal protein ms28, mrps28
+Macromolecule #28: Death associated protein 3
+Macromolecule #29: mS31, MRPS31
+Macromolecule #30: Mitochondrial ribosomal protein S33
+Macromolecule #31: Mitochondrial ribosomal protein S34
+Macromolecule #32: Mitochondrial ribosomal protein S35
+Macromolecule #33: Mitochondrial ribosomal protein S37
+Macromolecule #34: Aurora kinase A interacting protein 1
+Macromolecule #35: Mitochondrial ribosomal protein S39
+Macromolecule #36: 28S ribosomal protein S18b, mitochondrial
+Macromolecule #3: 12S ribosomal RNA, mitochondrial
+Macromolecule #19: P-site fMet-tRNAMet, mitochondrial
+Macromolecule #20: MT-CO3 mRNA, mitochondrial
+Macromolecule #37: 5'-GUANOSINE-DIPHOSPHATE-MONOTHIOPHOSPHATE
+Macromolecule #38: MAGNESIUM ION
+Macromolecule #39: SODIUM ION
+Macromolecule #40: SPERMINE
+Macromolecule #41: ZINC ION
+Macromolecule #42: N-FORMYLMETHIONINE
+Macromolecule #43: GUANOSINE-5'-TRIPHOSPHATE
+Macromolecule #44: water
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.171 mg/mL |
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Buffer | pH: 7.6 |
Grid | Model: Quantifoil R2/2 / Material: COPPER / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Pretreatment - Type: GLOW DISCHARGE |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV |
Details | contains 55S mitochondrial ribosome, mitochondrial initiation factor 2, mitochondrial formyl-Met-tRNAMet and MT-CO3 mRNA |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy |
Image recording | Film or detector model: FEI FALCON III (4k x 4k) / Detector mode: INTEGRATING / Digitization - Dimensions - Width: 4096 pixel / Digitization - Dimensions - Height: 4096 pixel / Number real images: 13936 / Average exposure time: 1.4 sec. / Average electron dose: 40.0 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Particle selection | Number selected: 1366787 |
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CTF correction | Software - Name: RELION (ver. 2.1) |
Startup model | Type of model: PDB ENTRY PDB model - PDB ID: |
Initial angle assignment | Type: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 2.1) |
Final angle assignment | Type: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 2.1) |
Final reconstruction | Number classes used: 1 / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 2.1) / Number images used: 139206 |
-Atomic model buiding 1
Refinement | Space: RECIPROCAL / Protocol: OTHER / Overall B value: 73.8 |
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Output model | PDB-6gaz: |