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Yorodumi- PDB-6nu3: Structural insights into unique features of the human mitochondri... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6nu3 | ||||||
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Title | Structural insights into unique features of the human mitochondrial ribosome recycling | ||||||
Components |
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Keywords | RIBOSOME / mitochondrial ribosome recycling Factor / mtRRF / 55S | ||||||
Function / homology | Function and homology information mitochondrial ribosome binding / rRNA import into mitochondrion / mitochondrial translational elongation / mitochondrial translational termination / mitochondrial ribosome assembly / microprocessor complex / translation release factor activity, codon nonspecific / Mitochondrial translation elongation / Mitochondrial translation termination / positive regulation of mitochondrial translation ...mitochondrial ribosome binding / rRNA import into mitochondrion / mitochondrial translational elongation / mitochondrial translational termination / mitochondrial ribosome assembly / microprocessor complex / translation release factor activity, codon nonspecific / Mitochondrial translation elongation / Mitochondrial translation termination / positive regulation of mitochondrial translation / Mitochondrial translation initiation / negative regulation of mitotic nuclear division / mitochondrial large ribosomal subunit / 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 / rescue of stalled ribosome / cellular response to leukemia inhibitory factor / Mitochondrial protein degradation / apoptotic signaling pathway / fibrillar center / cell junction / double-stranded RNA binding / regulation of translation / ribosomal small subunit assembly / small ribosomal subunit / small ribosomal subunit rRNA binding / nuclear membrane / 5S rRNA binding / large ribosomal subunit rRNA binding / endonuclease activity / cell population proliferation / tRNA binding / nuclear body / rRNA binding / negative regulation of translation / mitochondrial inner membrane / ribosome / structural constituent of ribosome / mitochondrial matrix / translation / ribonucleoprotein complex / protein domain specific binding / intracellular membrane-bounded organelle / mRNA binding / nucleotide binding / synapse / nucleolus / GTP binding / apoptotic process / mitochondrion / RNA binding / extracellular space / nucleoplasm / nucleus / plasma membrane / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.4 Å | ||||||
Authors | Sharma, M.R. / Koripella, R.K. / Agrawal, R.K. | ||||||
Funding support | United States, 1items
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Citation | Journal: Proc Natl Acad Sci U S A / Year: 2019 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. | ||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 6nu3.cif.gz | 6.3 MB | Display | PDBx/mmCIF format |
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PDB format | pdb6nu3.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 6nu3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6nu3_validation.pdf.gz | 932.8 KB | Display | wwPDB validaton report |
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Full document | 6nu3_full_validation.pdf.gz | 1014 KB | Display | |
Data in XML | 6nu3_validation.xml.gz | 280.3 KB | Display | |
Data in CIF | 6nu3_validation.cif.gz | 500.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nu/6nu3 ftp://data.pdbj.org/pub/pdb/validation_reports/nu/6nu3 | HTTPS FTP |
-Related structure data
Related structure data | 0515MC 0514C 6nu2C M: map data used to model this data C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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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) Homo sapiens (human) |
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#2: RNA chain | Mass: 17955.715 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) |
#54: RNA chain | Mass: 589.430 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) |
#55: RNA chain | Mass: 296318.281 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) |
+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) Homo sapiens (human) / References: UniProt: B4DEF8, UniProt: Q9BRJ2*PLUS |
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#48: Protein | Mass: 12292.333 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9BQC6 |
#49: Protein | Mass: 23674.203 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q14197, peptidyl-tRNA hydrolase |
#50: Protein | Mass: 25426.895 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q8TAE8 |
#83: Protein | Mass: 13498.819 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q96BP2 |
#84: Protein | Mass: 22395.326 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9NWT8 |
#85: Protein | Mass: 50095.523 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q96EY7 |
-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) Homo sapiens (human) |
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+28S ribosomal protein ... , 27 types, 27 molecules ABACADAEAFAGAHAIAJAKALAMANAOAPAQARASATAUAVAWAXAYAZA0A1
-Non-polymers , 2 types, 134 molecules
#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 |
-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: Homo sapiens (human) |
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 |
-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) |
-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 |