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- PDB-3jd5: Cryo-EM structure of the small subunit of the mammalian mitochond... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3jd5 | |||||||||
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Title | Cryo-EM structure of the small subunit of the mammalian mitochondrial ribosome | |||||||||
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![]() | RIBOSOME / mitoribosome / mammalian 55S mitoribosome / protein synthesis / RNA-protein complex | |||||||||
Function / homology | ![]() Mitochondrial translation elongation / Mitochondrial translation termination / peptide biosynthetic process / mitochondrial ribosome binding / mitochondrial ribosome assembly / positive regulation of mitochondrial translation / mitochondrial small ribosomal subunit / mitochondrial ribosome / mitochondrial translation / Mitochondrial protein degradation ...Mitochondrial translation elongation / Mitochondrial translation termination / peptide biosynthetic process / mitochondrial ribosome binding / mitochondrial ribosome assembly / positive regulation of mitochondrial translation / mitochondrial small ribosomal subunit / mitochondrial ribosome / mitochondrial translation / Mitochondrial protein degradation / ribosomal small subunit binding / kinase activity / regulation of translation / ribosomal small subunit assembly / small ribosomal subunit rRNA binding / cytosolic small ribosomal subunit / cell population proliferation / mitochondrial inner membrane / tRNA binding / rRNA binding / ribosome / structural constituent of ribosome / ribonucleoprotein complex / translation / phosphorylation / mRNA binding / apoptotic process / mitochondrion / RNA binding / nucleoplasm Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 7 Å | |||||||||
![]() | Kaushal, P.S. / Sharma, M.R. / Booth, T.M. / Haque, E.M. / Tung, C.S. / Sanbonmatsu, K.Y. / Spremulli, L.L. / Agrawal, R.K. | |||||||||
![]() | ![]() Title: Cryo-EM structure of the small subunit of the mammalian mitochondrial ribosome. Authors: Prem S Kaushal / Manjuli R Sharma / Timothy M Booth / Emdadul M Haque / Chang-Shung Tung / Karissa Y Sanbonmatsu / Linda L Spremulli / Rajendra K Agrawal / ![]() Abstract: The mammalian mitochondrial ribosomes (mitoribosomes) are responsible for synthesizing 13 membrane proteins that form essential components of the complexes involved in oxidative phosphorylation or ...The mammalian mitochondrial ribosomes (mitoribosomes) are responsible for synthesizing 13 membrane proteins that form essential components of the complexes involved in oxidative phosphorylation or ATP generation for the eukaryotic cell. The mammalian 55S mitoribosome contains significantly smaller rRNAs and a large mass of mitochondrial ribosomal proteins (MRPs), including large mito-specific amino acid extensions and insertions in MRPs that are homologous to bacterial ribosomal proteins and an additional 35 mito-specific MRPs. Here we present the cryo-EM structure analysis of the small (28S) subunit (SSU) of the 55S mitoribosome. We find that the mito-specific extensions in homologous MRPs generally are involved in inter-MRP contacts and in contacts with mito-specific MRPs, suggesting a stepwise evolution of the current architecture of the mitoribosome. Although most of the mito-specific MRPs and extensions of homologous MRPs are situated on the peripheral regions, they also contribute significantly to the formation of linings of the mRNA and tRNA paths, suggesting a tailor-made structural organization of the mito-SSU for the recruitment of mito-specific mRNAs, most of which do not possess a 5' leader sequence. In addition, docking of previously published coordinates of the large (39S) subunit (LSU) into the cryo-EM map of the 55S mitoribosome reveals that mito-specific MRPs of both the SSU and LSU are involved directly in the formation of six of the 15 intersubunit bridges. | |||||||||
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 | ![]() | 1.4 MB | Display | ![]() |
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PDB format | ![]() | 1.1 MB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
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-Validation report
Summary document | ![]() | 975.1 KB | Display | ![]() |
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Full document | ![]() | 994.3 KB | Display | |
Data in XML | ![]() | 133.9 KB | Display | |
Data in CIF | ![]() | 220.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5941MC M: map data used to model this data C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Components
+28S ribosomal protein ... , 27 types, 27 molecules BCEFGIJKLNOPQRUabcdefghijkp
-Protein , 3 types, 3 molecules mno
#28: Protein | Mass: 13581.974 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
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#29: Protein | Mass: 22968.365 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#30: Protein | Mass: 60587.832 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
-RNA chain / Protein/peptide , 2 types, 3 molecules Asz
#1: RNA chain | Mass: 306932.719 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
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#32: Protein/peptide | Mass: 1464.797 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
-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: small subunit of mitochondrial ribosome / Type: RIBOSOME |
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Buffer solution | Name: 20 mM HEPES-KOH, pH 7.6, 20 mM MgCl2, 40 mM KCl, 20 mM DTT pH: 7.6 Details: 20 mM HEPES-KOH, pH 7.6, 20 mM MgCl2, 40 mM KCl, 20 mM DTT |
Specimen | Conc.: 0.86 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Details: 300 mesh Quantifoil holey carbon copper grid, carbon support, glow-discharged in a plasma cleaner |
Vitrification | Instrument: FEI VITROBOT MARK I / Cryogen name: ETHANE / Humidity: 100 % / Details: Plunged into liquid ethane (FEI VITROBOT MARK I). / Method: flash freezing |
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Electron microscopy imaging
Microscopy | Model: JEOL 3200FS / Date: Oct 10, 2009 |
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Electron gun | Electron source: ![]() |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 60000 X / Calibrated magnification: 59717 X / Nominal defocus max: 4500 nm / Nominal defocus min: 1000 nm / Camera length: 800 mm |
Specimen holder | Specimen holder model: GATAN LIQUID NITROGEN / Temperature: 100 K / Temperature (max): 105 K / Temperature (min): 80 K |
Image recording | Electron dose: 9 e/Å2 / Film or detector model: GATAN ULTRASCAN 1000 (2k x 2k) |
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Processing
EM software |
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CTF correction | Details: CTFFIND3 | ||||||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||||||||||||||
3D reconstruction | Method: single particle reconstruction / Resolution: 7 Å / Num. of particles: 307556 / Nominal pixel size: 1.17 Å / Actual pixel size: 1.17 Å Details: A total of 866553 particle images were picked and subjected to supervised classification. Based on statistical information derived from Relion classification, ~28% of the particles - those ...Details: A total of 866553 particle images were picked and subjected to supervised classification. Based on statistical information derived from Relion classification, ~28% of the particles - those with low cross-correlation coefficient values with the 55S reference projections - were removed. Symmetry type: POINT | ||||||||||||||||||||||||
Atomic model building | Protocol: FLEXIBLE FIT / Space: REAL / Target criteria: Cross-correlation coefficient Details: METHOD--Flexible fitting REFINEMENT PROTOCOL--rigid body | ||||||||||||||||||||||||
Atomic model building |
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Refinement step | Cycle: LAST
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Refine LS restraints |
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