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Yorodumi- PDB-3jd5: Cryo-EM structure of the small subunit of the mammalian mitochond... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3jd5 | |||||||||
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Title | Cryo-EM structure of the small subunit of the mammalian mitochondrial ribosome | |||||||||
Components |
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Keywords | RIBOSOME / mitoribosome / mammalian 55S mitoribosome / protein synthesis / RNA-protein complex | |||||||||
Function / homology | Function and homology information 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 / ribosomal small subunit binding ...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 / ribosomal small subunit binding / small ribosomal subunit rRNA binding / ribosomal small subunit assembly / regulation of translation / kinase activity / mitochondrial inner membrane / cell population proliferation / tRNA binding / rRNA binding / ribosome / structural constituent of ribosome / translation / ribonucleoprotein complex / protein domain specific binding / phosphorylation / mRNA binding / apoptotic process / nucleolus / mitochondrion / RNA binding / nucleoplasm Similarity search - Function | |||||||||
Biological species | Bos taurus (cattle) | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 7 Å | |||||||||
Authors | Kaushal, P.S. / Sharma, M.R. / Booth, T.M. / Haque, E.M. / Tung, C.S. / Sanbonmatsu, K.Y. / Spremulli, L.L. / Agrawal, R.K. | |||||||||
Citation | Journal: Proc Natl Acad Sci U S A / Year: 2014 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
Movie |
Movie viewer |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 3jd5.cif.gz | 1.4 MB | Display | PDBx/mmCIF format |
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PDB format | pdb3jd5.ent.gz | 1.1 MB | Display | PDB format |
PDBx/mmJSON format | 3jd5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jd/3jd5 ftp://data.pdbj.org/pub/pdb/validation_reports/jd/3jd5 | HTTPS FTP |
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-Related structure data
Related structure data | 5941MC 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
+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) Bos taurus (cattle) / Organ: liver / Organelle: mitochondrion / References: UniProt: Q2HJE8 |
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#29: Protein | Mass: 22968.365 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / Organ: liver / Organelle: mitochondrion / References: UniProt: Q0VCJ1 |
#30: Protein | Mass: 60587.832 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / Organ: liver / Organelle: mitochondrion / References: UniProt: Q2KI62 |
-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) Bos taurus (cattle) / Organ: liver / Organelle: mitochondrion |
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#32: Protein/peptide | Mass: 1464.797 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / Organ: liver / Organelle: mitochondrion |
-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: 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 |
-Electron microscopy imaging
Microscopy | Model: JEOL 3200FS / Date: Oct 10, 2009 |
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Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: SPOT SCAN |
Electron lens | Mode: BRIGHT FIELDBright-field microscopy / 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) |
-Processing
EM software |
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CTF correction | Details: CTFFIND3 | ||||||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||||||||||||||
3D reconstruction | Method: single particle reconstructionSingle particle analysis 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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