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- PDB-6vlz: Structure of the human mitochondrial ribosome-EF-G1 complex (ClassI) -
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Open data
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Basic information
Entry | Database: PDB / ID: 6vlz | ||||||
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Title | Structure of the human mitochondrial ribosome-EF-G1 complex (ClassI) | ||||||
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![]() | RIBOSOME / mitochondrial elongation factor-G1 / 55S ribosome | ||||||
Function / homology | ![]() mitochondrial ribosome binding / mitochondrial transcription / 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 / mitochondrial transcription / 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 / translation elongation factor activity / 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 / GTPase activity / mRNA binding / apoptotic process / synapse / nucleolus / GTP binding / positive regulation of DNA-templated transcription / mitochondrion / RNA binding / nucleoplasm / nucleus / plasma membrane / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.97 Å | ||||||
![]() | Sharma, M.R. / Koripella, R.K. / Agrawal, R.K. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Structures of the human mitochondrial ribosome bound to EF-G1 reveal distinct features of mitochondrial translation elongation. Authors: Ravi Kiran Koripella / Manjuli R Sharma / Kalpana Bhargava / Partha P Datta / Prem S Kaushal / Pooja Keshavan / Linda L Spremulli / Nilesh K Banavali / Rajendra K Agrawal / ![]() ![]() Abstract: The mammalian mitochondrial ribosome (mitoribosome) and its associated translational factors have evolved to accommodate greater participation of proteins in mitochondrial translation. Here we ...The mammalian mitochondrial ribosome (mitoribosome) and its associated translational factors have evolved to accommodate greater participation of proteins in mitochondrial translation. Here we present the 2.68-3.96 Å cryo-EM structures of the human 55S mitoribosome in complex with the human mitochondrial elongation factor G1 (EF-G1) in three distinct conformational states, including an intermediate state and a post-translocational state. These structures reveal the role of several mitochondria-specific (mito-specific) mitoribosomal proteins (MRPs) and a mito-specific segment of EF-G1 in mitochondrial tRNA (tRNA) translocation. In particular, the mito-specific C-terminal extension in EF-G1 is directly involved in translocation of the acceptor arm of the A-site tRNA. In addition to the ratchet-like and independent head-swiveling motions exhibited by the small mitoribosomal subunit, we discover significant conformational changes in MRP mL45 at the nascent polypeptide-exit site within the large mitoribosomal subunit that could be critical for tethering of the elongating mitoribosome onto the inner-mitochondrial membrane. | ||||||
History |
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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 | ![]() | 3.9 MB | Display | ![]() |
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PDB format | ![]() | Display | ![]() | |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.8 MB | Display | ![]() |
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Full document | ![]() | 1.9 MB | Display | |
Data in XML | ![]() | 364.8 KB | Display | |
Data in CIF | ![]() | 606.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 21233MC ![]() 6vmiC M: map data used to model this data C: citing same article ( |
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Similar structure data | |
EM raw data | ![]() Data size: 753.5 Data #1: Aligned single-frame particles of human mitochondrial 55S-EF-Gmt complex [picked particles - single frame - processed]) |
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Links
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Assembly
Deposited unit | ![]()
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Components
-RNA chain , 3 types, 3 molecules AAAB
#1: RNA chain | Mass: 306112.125 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
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#32: RNA chain | Mass: 500019.594 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#33: RNA chain | Mass: 23266.883 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
+28S ribosomal protein ... , 27 types, 27 molecules ABACAEAIAJAKAMANAOAPAQATAWAXAHALARASAUAVAYAZA1A0ADAFAG
-Protein , 10 types, 10 molecules A2A3A4joqPpuv
#16: Protein | Mass: 13498.819 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
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#27: Protein | Mass: 22395.326 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#28: Protein | Mass: 78648.547 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#58: Protein | Mass: 13696.684 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#60: Protein | Mass: 12292.333 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#61: Protein | Mass: 25426.895 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#66: Protein | Mass: 20465.348 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#81: Protein | Mass: 23674.203 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#85: Protein | Mass: 5549.833 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#86: Protein | Mass: 83578.461 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
+39S ribosomal protein ... , 46 types, 48 molecules DFHKLMORSTWXYZ012348begimrJINU...
-DNA chain , 2 types, 2 molecules A5A7
#87: DNA chain | Mass: 3183.098 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
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#88: DNA chain | Mass: 20742.291 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
-Non-polymers , 4 types, 139 molecules ![](data/chem/img/MG.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/GDP.gif)
![](data/chem/img/GCP.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/GDP.gif)
![](data/chem/img/GCP.gif)
#89: Chemical | ChemComp-MG / #90: Chemical | ChemComp-ZN / #91: Chemical | ChemComp-GDP / | #92: Chemical | ChemComp-GCP / | |
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-Details
Has ligand of interest | N |
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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: Human mitochondrial ribosome-EF-G1 complex / Type: COMPLEX / Entity ID: #1-#88 / Source: NATURAL |
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Source (natural) | Organism: ![]() |
Buffer solution | pH: 7.5 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
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: ![]() |
Electron lens | Mode: BRIGHT FIELD |
Image recording | Electron dose: 69.2 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
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Processing
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION |
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3D reconstruction | Resolution: 2.97 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 99804 / Symmetry type: POINT |