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Yorodumi- PDB-2ftc: Structural Model for the Large Subunit of the Mammalian Mitochond... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2ftc | ||||||
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Title | Structural Model for the Large Subunit of the Mammalian Mitochondrial Ribosome | ||||||
Components |
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Keywords | RIBOSOME / MITOCHONDRIAL RIBOSOME / LARGE RIBOSOMAL SUBUNIT / RIBOSOMAL RNA | ||||||
Function / homology | Function and homology information Mitochondrial translation elongation / Mitochondrial translation termination / mitochondrial transcription / mitochondrial large ribosomal subunit / mitochondrial ribosome / mitochondrial translation / maturation of LSU-rRNA / ribosomal large subunit assembly / large ribosomal subunit rRNA binding / cytosolic large ribosomal subunit ...Mitochondrial translation elongation / Mitochondrial translation termination / mitochondrial transcription / mitochondrial large ribosomal subunit / mitochondrial ribosome / mitochondrial translation / maturation of LSU-rRNA / ribosomal large subunit assembly / large ribosomal subunit rRNA binding / cytosolic large ribosomal subunit / rRNA binding / negative regulation of translation / mitochondrial inner membrane / ribosome / structural constituent of ribosome / translation / mRNA binding / positive regulation of DNA-templated transcription / mitochondrion / RNA binding / nucleoplasm Similarity search - Function | ||||||
Biological species | Bos taurus (cattle) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 12.1 Å | ||||||
Authors | Mears, J.A. / Sharma, M.R. / Gutell, R.R. / Richardson, P.E. / Agrawal, R.K. / Harvey, S.C. | ||||||
Citation | Journal: J Mol Biol / Year: 2006 Title: A structural model for the large subunit of the mammalian mitochondrial ribosome. Authors: Jason A Mears / Manjuli R Sharma / Robin R Gutell / Amanda S McCook / Paul E Richardson / Thomas R Caulfield / Rajendra K Agrawal / Stephen C Harvey / Abstract: Protein translation is essential for all forms of life and is conducted by a macromolecular complex, the ribosome. Evolutionary changes in protein and RNA sequences can affect the 3D organization of ...Protein translation is essential for all forms of life and is conducted by a macromolecular complex, the ribosome. Evolutionary changes in protein and RNA sequences can affect the 3D organization of structural features in ribosomes in different species. The most dramatic changes occur in animal mitochondria, whose genomes have been reduced and altered significantly. The RNA component of the mitochondrial ribosome (mitoribosome) is reduced in size, with a compensatory increase in protein content. Until recently, it was unclear how these changes affect the 3D structure of the mitoribosome. Here, we present a structural model of the large subunit of the mammalian mitoribosome developed by combining molecular modeling techniques with cryo-electron microscopic data at 12.1A resolution. The model contains 93% of the mitochondrial rRNA sequence and 16 mitochondrial ribosomal proteins in the large subunit of the mitoribosome. Despite the smaller mitochondrial rRNA, the spatial positions of RNA domains known to be involved directly in protein synthesis are essentially the same as in bacterial and archaeal ribosomes. However, the dramatic reduction in rRNA content necessitates evolution of unique structural features to maintain connectivity between RNA domains. The smaller rRNA sequence also limits the likelihood of tRNA binding at the E-site of the mitoribosome, and correlates with the reduced size of D-loops and T-loops in some animal mitochondrial tRNAs, suggesting co-evolution of mitochondrial rRNA and tRNA structures. | ||||||
History |
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Remark 999 | SEQUENCE SINCE THE SEQUENCE OF THE HUMAN AND BOVINE MITOCHONDRIAL PROTEINS ARE ESSENTIALLY ...SEQUENCE SINCE THE SEQUENCE OF THE HUMAN AND BOVINE MITOCHONDRIAL PROTEINS ARE ESSENTIALLY IDENTICAL, THE SEQUENCE DATABASE REFERENCE FOR THE PROTEINS USED IN MODELLING FOR THIS DEPOSITION WAS FROM A HUNAN SOURCE (AND NOT BOVINE).THUS THE REFERENCE USED FOR THE PROTEIN CHAINS ARE LISTED BELOW CHAIN ID DATABASE REFERENCE A GB AAH14356 B GB NP_057034 C SWS RM03_HUMAN D GB NP_666499 E GB NP_963900 F GB NP_963900 G SWS RM11_HUMAN H SWS RM13_HUMAN I GB AAH01040 J GB AAH12306 K SWS RM19_HUMAN L GB AAH59945 M GB NP_054899 N GB CAI16343 O SWS RM27_HUMAN P GB NP_004882 Q SWS RM34_HUMAN |
-Structure visualization
Movie |
Movie viewer |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 2ftc.cif.gz | 133.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2ftc.ent.gz | 71.5 KB | Display | PDB format |
PDBx/mmJSON format | 2ftc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2ftc_validation.pdf.gz | 351 KB | Display | wwPDB validaton report |
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Full document | 2ftc_full_validation.pdf.gz | 351.9 KB | Display | |
Data in XML | 2ftc_validation.xml.gz | 1.7 KB | Display | |
Data in CIF | 2ftc_validation.cif.gz | 32.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ft/2ftc ftp://data.pdbj.org/pub/pdb/validation_reports/ft/2ftc | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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-Components
-Mitochondrial ribosomal protein ... , 8 types, 8 molecules ABDIJMNP
#2: Protein | Mass: 21224.551 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: A6QPQ5*PLUS |
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#3: Protein | Mass: 14442.636 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: Q2TA12*PLUS |
#5: Protein | Mass: 19707.887 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: Q32PI6*PLUS |
#9: Protein | Mass: 13107.179 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: Q3T0J3*PLUS |
#10: Protein | Mass: 13682.971 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: Q3T0L3*PLUS |
#13: Protein | Mass: 12914.133 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: Q3SZX5*PLUS |
#14: Protein | Mass: 11010.680 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: Q3SYS0*PLUS |
#16: Protein | Mass: 6092.276 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: Q3SZ47*PLUS |
-Mitochondrial 39S ribosomal protein ... , 2 types, 2 molecules CO
#4: Protein | Mass: 23396.496 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: Q3ZBX6*PLUS |
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#15: Protein | Mass: 7520.631 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: Q32PC3*PLUS |
-39S ribosomal protein ... , 5 types, 6 molecules EFGHKQ
#6: Protein | Mass: 14831.392 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: Q7YR75 #7: Protein | | Mass: 15606.364 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: Q2YDI0*PLUS #8: Protein | | Mass: 16958.729 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: Q3SYS1*PLUS #11: Protein | | Mass: 11098.766 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: Q2HJI0*PLUS #17: Protein/peptide | | Mass: 4485.404 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: A8NN94*PLUS |
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-RNA chain / Protein , 2 types, 2 molecules RL
#12: Protein | Mass: 14125.866 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: Q2TBR2*PLUS |
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#1: RNA chain | Mass: 504151.281 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: GenBank: 56411146 |
-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: Mammalian Mitochondrial Ribosome Large Subunit / Type: RIBOSOME |
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Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
-Electron microscopy imaging
Experimental equipment | Model: Tecnai F20 / Image courtesy: FEI Company |
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Microscopy | Model: FEI TECNAI F20 |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 4600 nm / Nominal defocus min: 1200 nm |
Image scans | Num. digital images: 194 / Scanner model: ZEISS SCAI |
-Processing
Software | Name: YAMMP / Classification: refinement | |||||||||||||||||||||||||||||||||||
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Symmetry | Point symmetry: C1 (asymmetric) | |||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 12.1 Å / Symmetry type: POINT | |||||||||||||||||||||||||||||||||||
Atomic model building | Protocol: RIGID BODY FIT / Space: REAL / Details: REFINEMENT PROTOCOL--rigid body | |||||||||||||||||||||||||||||||||||
Atomic model building |
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Refinement step | Cycle: LAST
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