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- PDB-6nu3: Structural insights into unique features of the human mitochondri... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6nu3 | ||||||
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Title | Structural insights into unique features of the human mitochondrial ribosome recycling | ||||||
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![]() | RIBOSOME / mitochondrial ribosome recycling Factor / mtRRF / 55S | ||||||
Function / homology | ![]() mitochondrial ribosome binding / rRNA import into mitochondrion / mitochondrial translational elongation / mitochondrial translational termination / mitochondrial ribosome assembly / translation release factor activity, codon nonspecific / microprocessor complex / Mitochondrial translation elongation / Mitochondrial translation termination / Mitochondrial translation initiation ...mitochondrial ribosome binding / rRNA import into mitochondrion / mitochondrial translational elongation / mitochondrial translational termination / mitochondrial ribosome assembly / translation release factor activity, codon nonspecific / microprocessor complex / Mitochondrial translation elongation / Mitochondrial translation termination / Mitochondrial translation initiation / positive regulation of mitochondrial translation / negative regulation of mitotic nuclear division / Hydrolases; Acting on ester bonds; Endoribonucleases producing 5'-phosphomonoesters / mitochondrial large ribosomal subunit / 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 / cell junction / regulation of translation / ribosomal small subunit assembly / small ribosomal subunit / small ribosomal subunit rRNA binding / 5S rRNA binding / large ribosomal subunit rRNA binding / endonuclease activity / nuclear membrane / cytosolic small ribosomal subunit / cell population proliferation / cytosolic large ribosomal subunit / mitochondrial inner membrane / tRNA binding / cytoplasmic translation / nuclear body / rRNA binding / negative regulation of translation / ribosome / structural constituent of ribosome / mitochondrial matrix / ribonucleoprotein complex / translation / cell cycle / protein domain specific binding / intracellular membrane-bounded organelle / nucleotide binding / mRNA binding / apoptotic process / synapse / nucleolus / GTP binding / mitochondrion / RNA binding / extracellular space / nucleoplasm / nucleus / plasma membrane / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.4 Å | ||||||
![]() | Sharma, M.R. / Koripella, R.K. / Agrawal, R.K. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Structural insights into unique features of the human mitochondrial ribosome recycling. Authors: Ravi K Koripella / Manjuli R Sharma / Paul Risteff / Pooja Keshavan / Rajendra K Agrawal / ![]() Abstract: Mammalian mitochondrial ribosomes (mitoribosomes) are responsible for synthesizing proteins that are essential for oxidative phosphorylation (ATP generation). Despite their common ancestry with ...Mammalian mitochondrial ribosomes (mitoribosomes) are responsible for synthesizing proteins that are essential for oxidative phosphorylation (ATP generation). Despite their common ancestry with bacteria, the composition and structure of the human mitoribosome and its translational factors are significantly different from those of their bacterial counterparts. The mammalian mitoribosome recycling factor (RRF) carries a mito-specific N terminus extension (NTE), which is necessary for the function of RRF Here we present a 3.9-Å resolution cryo-electron microscopic (cryo-EM) structure of the human 55S mitoribosome-RRF complex, which reveals α-helix and loop structures for the NTE that makes multiple mito-specific interactions with functionally critical regions of the mitoribosome. These include ribosomal RNA segments that constitute the peptidyl transferase center (PTC) and those that connect PTC with the GTPase-associated center and with mitoribosomal proteins L16 and L27. Our structure reveals the presence of a tRNA in the pe/E position and a rotation of the small mitoribosomal subunit on RRF binding. In addition, we observe an interaction between the pe/E tRNA and a mito-specific protein, mL64. These findings help understand the unique features of mitoribosome recycling. | ||||||
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Structure visualization
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Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 6.3 MB | Display | ![]() |
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PDB format | ![]() | Display | ![]() | |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 932.8 KB | Display | ![]() |
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Full document | ![]() | 1014 KB | Display | |
Data in XML | ![]() | 280.3 KB | Display | |
Data in CIF | ![]() | 500.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 0515MC ![]() 0514C ![]() 6nu2C M: map data used to model this data C: citing same article ( |
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Similar structure data |
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Assembly
Deposited unit | ![]()
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Components
-RNA chain , 4 types, 4 molecules ABuAA
#1: RNA chain | Mass: 472442.969 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
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#2: RNA chain | Mass: 17955.715 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#54: RNA chain | Mass: 589.430 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#55: RNA chain | Mass: 296318.281 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
+39S ribosomal protein ... , 46 types, 46 molecules DEFHIJKLMNOPQRSTUVWXYZ01234567...
-Protein , 7 types, 7 molecules dopqA2A3A4
#38: Protein | Mass: 35342.820 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
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#48: Protein | Mass: 12292.333 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#49: Protein | Mass: 23674.203 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#50: Protein | Mass: 25426.895 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#83: Protein | Mass: 13498.819 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#84: Protein | Mass: 22395.326 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#85: Protein | Mass: 50095.523 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
-Protein/peptide , 1 types, 1 molecules t
#53: Protein/peptide | Mass: 2400.951 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
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+28S ribosomal protein ... , 27 types, 27 molecules ABACADAEAFAGAHAIAJAKALAMANAOAPAQARASATAUAVAWAXAYAZA0A1
-Non-polymers , 2 types, 134 molecules ![](data/chem/img/MG.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/ZN.gif)
#86: Chemical | ChemComp-MG / #87: Chemical | ChemComp-ZN / |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
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Sample preparation
Component | Name: Structure of human mitochondrial translation initiation factor 3 bound to the small ribosomal subunit Type: RIBOSOME Details: Structure of human mitochondrial translation initiation factor 3 bound to the small ribosomal subunit Entity ID: #1-#85 / Source: NATURAL |
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Source (natural) | Organism: ![]() |
Buffer solution | pH: 7.6 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Details: unspecified |
Vitrification | Cryogen name: ETHANE |
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Electron microscopy imaging
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: OTHER / Accelerating voltage: 300 kV / Illumination mode: OTHER |
Electron lens | Mode: OTHER |
Image recording | Electron dose: 70 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
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Processing
EM software |
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CTF correction | Type: NONE | ||||||||||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 144057 | ||||||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 4.4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 26195 / Symmetry type: POINT | ||||||||||||||||||||||||||||||||||||
Atomic model building | B value: 88.8 / Protocol: OTHER | ||||||||||||||||||||||||||||||||||||
Atomic model building | PDB-ID: 3J9M |