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Yorodumi- PDB-6nf8: Structure of human mitochondrial translation initiation factor 3 ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6nf8 | |||||||||
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Title | Structure of human mitochondrial translation initiation factor 3 bound to the small ribosomal subunit -Class I | |||||||||
Components |
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Keywords | RIBOSOMAL PROTEIN / Mitochondrial translation Initiation Factor 3 | |||||||||
Function / homology | Function and homology information Mitochondrial translation elongation / Mitochondrial translation termination / mitochondrial translational initiation / peptide biosynthetic process / mitochondrial ribosome binding / translation factor activity, RNA binding / mitochondrial ribosome assembly / ribosome disassembly / positive regulation of mitochondrial translation / Mitochondrial translation initiation ...Mitochondrial translation elongation / Mitochondrial translation termination / mitochondrial translational initiation / peptide biosynthetic process / mitochondrial ribosome binding / translation factor activity, RNA binding / mitochondrial ribosome assembly / ribosome disassembly / positive regulation of mitochondrial translation / Mitochondrial translation initiation / mitochondrial small ribosomal subunit / mitochondrial ribosome / mitochondrial translation / Mitochondrial protein degradation / ribosomal small subunit binding / translation initiation factor activity / small ribosomal subunit rRNA binding / ribosome binding / kinase activity / regulation of translation / ribosomal small subunit assembly / small ribosomal subunit / cell population proliferation / tRNA binding / mitochondrial inner membrane / rRNA binding / ribosome / structural constituent of ribosome / ribonucleoprotein complex / translation / mRNA binding / apoptotic process / mitochondrion / RNA binding / nucleoplasm Similarity search - Function | |||||||||
Biological species | Bos taurus (cattle) Homo sapiens (human) | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.48 Å | |||||||||
Authors | Sharma, M. / Koripella, R. / Agrawal, R. | |||||||||
Funding support | United States, 2items
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Citation | Journal: iScience / Year: 2019 Title: Structure of Human Mitochondrial Translation Initiation Factor 3 Bound to the Small Ribosomal Subunit. Authors: Ravi K Koripella / Manjuli R Sharma / Md Emdadul Haque / Paul Risteff / Linda L Spremulli / Rajendra K Agrawal / Abstract: The human mitochondrial translational initiation factor 3 (IF3) carries mitochondrial-specific amino acid extensions at both its N and C termini (N- and C-terminal extensions [NTE and CTE, ...The human mitochondrial translational initiation factor 3 (IF3) carries mitochondrial-specific amino acid extensions at both its N and C termini (N- and C-terminal extensions [NTE and CTE, respectively]), when compared with its eubacterial counterpart. Here we present 3.3- to 3.5-Å-resolution cryoelectron microscopic structures of the mammalian 28S mitoribosomal subunit in complex with human IF3. Unique contacts observed between the 28S subunit and N-terminal domain of IF3 explain its unusually high affinity for the 28S subunit, whereas the position of the mito-specific NTE suggests NTE's role in binding of initiator tRNA to the 28S subunit. The location of the C-terminal domain (CTD) clarifies its anti-association activity, whereas the orientation of the mito-specific CTE provides a mechanistic explanation for its role in destabilizing initiator tRNA in the absence of mRNA. Furthermore, our structure hints at a possible role of the CTD in recruiting leaderless mRNAs for translation initiation. Our findings highlight unique features of IF3 in mitochondrial translation initiation. | |||||||||
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 | 6nf8.cif.gz | 1.4 MB | Display | PDBx/mmCIF format |
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PDB format | pdb6nf8.ent.gz | 1.2 MB | Display | PDB format |
PDBx/mmJSON format | 6nf8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6nf8_validation.pdf.gz | 1021.2 KB | Display | wwPDB validaton report |
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Full document | 6nf8_full_validation.pdf.gz | 1 MB | Display | |
Data in XML | 6nf8_validation.xml.gz | 140.3 KB | Display | |
Data in CIF | 6nf8_validation.cif.gz | 233.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nf/6nf8 ftp://data.pdbj.org/pub/pdb/validation_reports/nf/6nf8 | HTTPS FTP |
-Related structure data
Related structure data | 9362MC 9358C 6neqC 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 , 1 types, 1 molecules A
#1: RNA chain | Mass: 306932.719 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) |
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+28S ribosomal protein ... , 26 types, 26 molecules CELPQacdejpGIJNhikBFKORUbf
-Protein , 5 types, 5 molecules gmonz
#17: Protein | Mass: 40505.719 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: A6QQP1 |
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#21: Protein | Mass: 13581.974 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: Q2HJE8 |
#22: Protein | Mass: 60587.832 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: Q2KI62 |
#31: Protein | Mass: 22968.365 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: Q0VCJ1 |
#32: Protein | Mass: 28213.160 Da / Num. of mol.: 1 / Fragment: residues 32-278 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9H2K0 |
-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: all / Source: NATURAL | ||||||||||||
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Source (natural) |
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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 | ||||||||||||
3D reconstruction | Resolution: 3.48 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 99178 / Algorithm: FOURIER SPACE / Symmetry type: POINT | ||||||||||||
Atomic model building | B value: 97 / Protocol: OTHER | ||||||||||||
Atomic model building | PDB-ID: 3JD5 |