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Yorodumi- PDB-5oom: Structure of a native assembly intermediate of the human mitochon... -
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-Basic information
Entry | Database: PDB / ID: 5oom | ||||||
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Title | Structure of a native assembly intermediate of the human mitochondrial ribosome with unfolded interfacial rRNA | ||||||
Components |
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Keywords | RIBOSOME / mitochondria / biogenesis / translation / electron cryomicroscopy | ||||||
Function / homology | Function and homology information negative regulation of mitochondrial translation / mitochondrial large ribosomal subunit assembly / negative regulation of ribosome biogenesis / protein lipoylation / Mitochondrial Fatty Acid Beta-Oxidation / Protein lipoylation / rRNA import into mitochondrion / mitochondrial translational elongation / mitochondrial translational termination / iron-sulfur cluster assembly complex ...negative regulation of mitochondrial translation / mitochondrial large ribosomal subunit assembly / negative regulation of ribosome biogenesis / protein lipoylation / Mitochondrial Fatty Acid Beta-Oxidation / Protein lipoylation / rRNA import into mitochondrion / mitochondrial translational elongation / mitochondrial translational termination / iron-sulfur cluster assembly complex / microprocessor complex / translation release factor activity, codon nonspecific / Mitochondrial translation elongation / Mitochondrial translation termination / positive regulation of mitochondrial translation / Mitochondrial translation initiation / mitochondrial large ribosomal subunit binding / mitochondrial fission / mitochondrial large ribosomal subunit / Hydrolases; Acting on ester bonds; Endoribonucleases producing 5'-phosphomonoesters / peptidyl-tRNA hydrolase / [2Fe-2S] cluster assembly / mitochondrial small ribosomal subunit / aminoacyl-tRNA hydrolase activity / iron-sulfur cluster assembly / mitochondrial ribosome / mitochondrial translation / ribosomal large subunit binding / acyl binding / anatomical structure morphogenesis / Complex I biogenesis / acyl carrier activity / Respiratory electron transport / RNA processing / mitochondrial respiratory chain complex I assembly / rescue of stalled ribosome / : / ribosomal large subunit biogenesis / mitochondrial electron transport, NADH to ubiquinone / proton motive force-driven mitochondrial ATP synthesis / cellular response to leukemia inhibitory factor / Mitochondrial protein degradation / fatty acid binding / mitochondrial membrane / aerobic respiration / fibrillar center / fatty acid biosynthetic process / cell junction / double-stranded RNA binding / small ribosomal subunit rRNA binding / 5S rRNA binding / large ribosomal subunit rRNA binding / endonuclease activity / nuclear body / rRNA binding / negative regulation of translation / mitochondrial inner membrane / ribosome / structural constituent of ribosome / mitochondrial matrix / translation / ribonucleoprotein complex / protein domain specific binding / mRNA binding / nucleotide binding / synapse / calcium ion binding / nucleolus / apoptotic process / mitochondrion / RNA binding / extracellular space / nucleoplasm / nucleus / plasma membrane / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.03 Å | ||||||
Authors | Brown, A. / Rathore, S. / Kimanius, D. / Aibara, S. / Bai, X.C. / Rorbach, J. / Amunts, A. / Ramakrishnan, V. | ||||||
Citation | Journal: Nat Struct Mol Biol / Year: 2017 Title: Structures of the human mitochondrial ribosome in native states of assembly. Authors: Alan Brown / Sorbhi Rathore / Dari Kimanius / Shintaro Aibara / Xiao-Chen Bai / Joanna Rorbach / Alexey Amunts / V Ramakrishnan / Abstract: Mammalian mitochondrial ribosomes (mitoribosomes) have less rRNA content and 36 additional proteins compared with the evolutionarily related bacterial ribosome. These differences make the assembly of ...Mammalian mitochondrial ribosomes (mitoribosomes) have less rRNA content and 36 additional proteins compared with the evolutionarily related bacterial ribosome. These differences make the assembly of mitoribosomes more complex than the assembly of bacterial ribosomes, but the molecular details of mitoribosomal biogenesis remain elusive. Here, we report the structures of two late-stage assembly intermediates of the human mitoribosomal large subunit (mt-LSU) isolated from a native pool within a human cell line and solved by cryo-EM to ∼3-Å resolution. Comparison of the structures reveals insights into the timing of rRNA folding and protein incorporation during the final steps of ribosomal maturation and the evolutionary adaptations that are required to preserve biogenesis after the structural diversification of mitoribosomes. Furthermore, the structures redefine the ribosome silencing factor (RsfS) family as multifunctional biogenesis factors and identify two new assembly factors (L0R8F8 and mt-ACP) not previously implicated in mitoribosomal biogenesis. | ||||||
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 | 5oom.cif.gz | 2 MB | Display | PDBx/mmCIF format |
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PDB format | pdb5oom.ent.gz | 1.6 MB | Display | PDB format |
PDBx/mmJSON format | 5oom.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5oom_validation.pdf.gz | 1.5 MB | Display | wwPDB validaton report |
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Full document | 5oom_full_validation.pdf.gz | 1.6 MB | Display | |
Data in XML | 5oom_validation.xml.gz | 222 KB | Display | |
Data in CIF | 5oom_validation.cif.gz | 368.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/oo/5oom ftp://data.pdbj.org/pub/pdb/validation_reports/oo/5oom | HTTPS FTP |
-Related structure data
Related structure data | 3843MC 3842C 5oolC 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 , 2 types, 2 molecules AB
#1: RNA chain | Mass: 500019.594 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: GenBank: 1025814679 |
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#2: RNA chain | Mass: 22022.131 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: GenBank: 1215733170 |
+39S ribosomal protein ... , 46 types, 46 molecules DEFHIJKLMNOPQRSTUVWXYZ01235678...
-Protein , 6 types, 6 molecules opquvw
#47: Protein | Mass: 12292.333 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9BQC6 |
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#48: Protein | Mass: 23674.203 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q14197, peptidyl-tRNA hydrolase |
#49: Protein | Mass: 25426.895 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q8TAE8 |
#53: Protein | Mass: 26203.076 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q96EH3 |
#54: Protein | Mass: 8460.787 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: L0R8F8 |
#55: Protein | Mass: 17434.273 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: O14561 |
-Protein/peptide , 1 types, 1 molecules t
#52: Protein/peptide | Mass: 2400.951 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) |
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-Non-polymers , 3 types, 52 molecules
#56: Chemical | ChemComp-MG / #57: Chemical | #58: Chemical | ChemComp-PNS / | |
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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 |
-Sample preparation
Component | Name: Mitochondrial ribosome large subunit with assembly factor Type: ORGANELLE OR CELLULAR COMPONENT / Entity ID: #1-#55 / Source: NATURAL | |||||||||||||||||||||||||
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Molecular weight | Experimental value: NO | |||||||||||||||||||||||||
Source (natural) | Organism: Homo sapiens (human) | |||||||||||||||||||||||||
Buffer solution | pH: 7.45 Details: 2 mM Synercid (Santa Cruz Biotechnology, Inc) was added to reduce preferential orientation. | |||||||||||||||||||||||||
Buffer component |
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Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES / Details: Sample concentration = 100 nM | |||||||||||||||||||||||||
Specimen support | Grid material: COPPER / Grid mesh size: 400 divisions/in. / Grid type: Quantifoil R2/2 | |||||||||||||||||||||||||
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K / Details: Sample incubated for 30 s prior to freezing. |
-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: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Calibrated magnification: 130841 X / Alignment procedure: COMA FREE |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Average exposure time: 1.5 sec. / Electron dose: 1.56 e/Å2 / Detector mode: INTEGRATING / Film or detector model: FEI FALCON II (4k x 4k) |
Image scans | Movie frames/image: 25 / Used frames/image: 1-25 |
-Processing
Software | Name: PHENIX / Version: 1.11.1-2575_1479: / Classification: refinement | ||||||||||||||||||||||||||||||||||||
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EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 3.03 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 379869 / Symmetry type: POINT | ||||||||||||||||||||||||||||||||||||
Atomic model building | B value: 85 / Protocol: OTHER / Space: REAL / Target criteria: Cross-correlation coefficient | ||||||||||||||||||||||||||||||||||||
Atomic model building | PDB-ID: 3J9M | ||||||||||||||||||||||||||||||||||||
Refine LS restraints |
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