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- EMDB-4368: Unique features of mammalian mitochondrial translation initiation... -
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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-4368 | ||||||||||||
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Title | Unique features of mammalian mitochondrial translation initiation revealed by cryo-EM. This file contains the complete 55S ribosome. | ||||||||||||
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Function / homology | ![]() Hormone ligand-binding receptors / ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | ||||||||||||
Biological species | ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() | ||||||||||||
Method | ![]() ![]() | ||||||||||||
![]() | Kummer E / Leibundgut M / Boehringer D / Ban N | ||||||||||||
Funding support | ![]()
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![]() | ![]() 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 |
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 28.7 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 109.4 KB 109.4 KB | Display Display | ![]() |
Images | ![]() | 165 KB | ||
Masks | ![]() | 84.6 MB | ![]() | |
Others | ![]() ![]() | 71.7 MB 71.7 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6gawMC ![]() 4369C ![]() 4370C ![]() 6gazC ![]() 6gb2C C: citing same article ( M: atomic model generated by this map |
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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: 1.39 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Mask #1
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Sample components
+Entire : mammalian mitochondrial translation initiation complex
+Supramolecule #1: mammalian mitochondrial translation initiation complex
+Macromolecule #1: Mitochondrial ribosomal protein L12
+Macromolecule #2: Mitochondrial ribosomal protein L27
+Macromolecule #3: Mitochondrial ribosomal protein L28
+Macromolecule #4: Mitochondrial ribosomal protein L47
+Macromolecule #5: uL30m
+Macromolecule #6: 39S ribosomal protein L55, mitochondrial
+Macromolecule #7: bL32m
+Macromolecule #8: bL33m
+Macromolecule #9: Mitochondrial ribosomal protein L34
+Macromolecule #10: Mitochondrial ribosomal protein L35
+Macromolecule #11: Ribosomal protein
+Macromolecule #14: Translation initiation factor IF-2, mitochondrial
+Macromolecule #15: 39S ribosomal protein L2, mitochondrial
+Macromolecule #16: ICT1
+Macromolecule #17: Mitochondrial ribosomal protein L4
+Macromolecule #18: Mitochondrial ribosomal protein L9
+Macromolecule #19: Mitochondrial ribosomal protein L10
+Macromolecule #20: Mitochondrial ribosomal protein L11
+Macromolecule #21: 39S ribosomal protein L13, mitochondrial
+Macromolecule #22: uL14m
+Macromolecule #23: 39S ribosomal protein L15, mitochondrial
+Macromolecule #24: 39S ribosomal protein L16, mitochondrial
+Macromolecule #25: 39S ribosomal protein L17, mitochondrial
+Macromolecule #26: Mitochondrial ribosomal protein L18
+Macromolecule #27: Mitochondrial ribosomal protein L19
+Macromolecule #28: Mitochondrial ribosomal protein L20
+Macromolecule #29: Mitochondrial ribosomal protein L21
+Macromolecule #30: uL22m
+Macromolecule #31: uL23m
+Macromolecule #32: 39S ribosomal protein L24, mitochondrial
+Macromolecule #33: Mitochondrial ribosomal protein L37
+Macromolecule #34: Mitochondrial ribosomal protein L38
+Macromolecule #35: Mitochondrial ribosomal protein L39
+Macromolecule #36: 39S ribosomal protein L40, mitochondrial isoform 1
+Macromolecule #37: Mitochondrial ribosomal protein L41
+Macromolecule #38: mL42
+Macromolecule #39: mL43
+Macromolecule #40: 39S ribosomal protein L44, mitochondrial
+Macromolecule #41: mL45
+Macromolecule #42: Mitochondrial ribosomal protein L46
+Macromolecule #43: Mitochondrial ribosomal protein L48
+Macromolecule #44: 39S ribosomal protein L49, mitochondrial
+Macromolecule #45: mL50
+Macromolecule #46: Mitochondrial ribosomal protein L51
+Macromolecule #47: 39S ribosomal protein L52, mitochondrial
+Macromolecule #48: mL53
+Macromolecule #49: mL54
+Macromolecule #50: Mitochondrial ribosomal protein L57
+Macromolecule #51: Peptidyl-tRNA hydrolase ICT1, mitochondrial
+Macromolecule #52: mL64
+Macromolecule #53: mL65
+Macromolecule #54: Mitochondrial ribosomal protein S18A
+Macromolecule #55: unassigned secondary structure elements
+Macromolecule #57: Mitochondrial ribosomal protein S2
+Macromolecule #58: Mitochondrial ribosomal protein S24
+Macromolecule #59: Mitochondrial ribosomal protein S5
+Macromolecule #60: Mitochondrial ribosomal protein S6
+Macromolecule #61: Mitochondrial ribosomal protein S7
+Macromolecule #62: 28S ribosomal protein S9, mitochondrial
+Macromolecule #63: Mitochondrial ribosomal protein S10
+Macromolecule #64: 28S ribosomal protein S11, mitochondrial
+Macromolecule #65: Mitochondrial ribosomal protein S12
+Macromolecule #66: Mitochondrial ribosomal protein S14
+Macromolecule #67: Uncharacterized protein
+Macromolecule #68: bS16m
+Macromolecule #69: uS17m
+Macromolecule #70: Mitochondrial ribosomal protein S18C
+Macromolecule #71: bS21m
+Macromolecule #74: unassigned secondary structure elements
+Macromolecule #75: Mitochondrial ribosomal protein S22
+Macromolecule #76: 28S ribosomal protein S23, mitochondrial
+Macromolecule #77: Mitochondrial ribosomal protein S25
+Macromolecule #78: Mitochondrial ribosomal protein S26
+Macromolecule #79: mS27
+Macromolecule #80: 28S ribosomal protein S28, mitochondrial
+Macromolecule #81: Death associated protein 3
+Macromolecule #82: mS31
+Macromolecule #83: mS33
+Macromolecule #84: 28S ribosomal protein S34, mitochondrial
+Macromolecule #85: 28S ribosomal protein S35, mitochondrial
+Macromolecule #86: Coiled-coil-helix-coiled-coil-helix domain-containing protein 1
+Macromolecule #87: Aurora kinase A interacting protein 1
+Macromolecule #88: Pentatricopeptide repeat domain-containing protein 3, mitochondrial
+Macromolecule #89: 28S ribosomal protein S18b, mitochondrial
+Macromolecule #12: 16S ribosomal RNA, mitochondrial
+Macromolecule #13: tRNA-Phe, mitochondrial
+Macromolecule #56: 12S ribosomal RNA, mitochondrial
+Macromolecule #72: P-site fMet-tRNAMet, mitochondrial
+Macromolecule #73: MT-CO3 mRNA, mitochondrial
+Macromolecule #90: MAGNESIUM ION
+Macromolecule #91: ZINC ION
+Macromolecule #92: GUANOSINE-5'-MONOPHOSPHATE
+Macromolecule #93: SPERMINE
+Macromolecule #94: 5'-GUANOSINE-DIPHOSPHATE-MONOTHIOPHOSPHATE
+Macromolecule #95: SODIUM ION
+Macromolecule #96: N-FORMYLMETHIONINE
+Macromolecule #97: GUANOSINE-5'-TRIPHOSPHATE
+Macromolecule #98: water
-Experimental details
-Structure determination
Method | ![]() |
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Aggregation state | particle |
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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 |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD![]() |
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 |
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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 / Applied symmetry - Point group: C1 (asymmetric) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 3.2 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: 66.8 |
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Output model | ![]() PDB-6gaw: |