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Yorodumi- PDB-7of4: Structure of mature human mitochondrial ribosome large subunit in... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7of4 | ||||||||||||||||||
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Title | Structure of mature human mitochondrial ribosome large subunit in complex with GTPBP6 (PTC conformation 1). | ||||||||||||||||||
Components |
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Keywords | RIBOSOME / Mitochondria / Biogenesis / GTPase / NSUN4 / MTERF4 | ||||||||||||||||||
Function / homology | Function and homology information rRNA import into mitochondrion / mitochondrial translational elongation / mitochondrial translational termination / microprocessor complex / translation release factor activity, codon nonspecific / Mitochondrial translation elongation / Mitochondrial translation termination / Mitochondrial translation initiation / mitochondrial large ribosomal subunit / Hydrolases; Acting on ester bonds; Endoribonucleases producing 5'-phosphomonoesters ...rRNA import into mitochondrion / mitochondrial translational elongation / mitochondrial translational termination / microprocessor complex / translation release factor activity, codon nonspecific / Mitochondrial translation elongation / Mitochondrial translation termination / Mitochondrial translation initiation / mitochondrial large ribosomal subunit / Hydrolases; Acting on ester bonds; Endoribonucleases producing 5'-phosphomonoesters / peptidyl-tRNA hydrolase / mitochondrial small ribosomal subunit / aminoacyl-tRNA hydrolase activity / mitochondrial ribosome / mitochondrial translation / anatomical structure morphogenesis / RNA processing / Mitochondrial protein degradation / rescue of stalled ribosome / cellular response to leukemia inhibitory factor / fibrillar center / double-stranded RNA binding / cell junction / ribosome binding / small ribosomal subunit rRNA binding / 5S rRNA binding / large ribosomal subunit rRNA binding / endonuclease activity / cytosolic large ribosomal subunit / mitochondrial inner membrane / cytoplasmic translation / nuclear body / rRNA binding / negative regulation of translation / ribosome / mitochondrial matrix / structural constituent of ribosome / ribonucleoprotein complex / cell cycle / translation / protein domain specific binding / nucleotide binding / mRNA binding / apoptotic process / synapse / nucleolus / GTP binding / mitochondrion / RNA binding / extracellular space / nucleoplasm / nucleus / metal ion binding / plasma membrane / cytoplasm / cytosol Similarity search - Function | ||||||||||||||||||
Biological species | Homo sapiens (human) | ||||||||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.7 Å | ||||||||||||||||||
Authors | Hillen, H.S. / Lavdovskaia, E. / Nadler, F. / Hanitsch, E. / Linden, A. / Bohnsack, K.E. / Urlaub, H. / Richter-Dennerlein, R. | ||||||||||||||||||
Funding support | Germany, 5items
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Citation | Journal: Nat Commun / Year: 2021 Title: Structural basis of GTPase-mediated mitochondrial ribosome biogenesis and recycling. Authors: Hauke S Hillen / Elena Lavdovskaia / Franziska Nadler / Elisa Hanitsch / Andreas Linden / Katherine E Bohnsack / Henning Urlaub / Ricarda Richter-Dennerlein / Abstract: Ribosome biogenesis requires auxiliary factors to promote folding and assembly of ribosomal proteins and RNA. Particularly, maturation of the peptidyl transferase center (PTC) is mediated by ...Ribosome biogenesis requires auxiliary factors to promote folding and assembly of ribosomal proteins and RNA. Particularly, maturation of the peptidyl transferase center (PTC) is mediated by conserved GTPases, but the molecular basis is poorly understood. Here, we define the mechanism of GTPase-driven maturation of the human mitochondrial large ribosomal subunit (mtLSU) using endogenous complex purification, in vitro reconstitution and cryo-EM. Structures of transient native mtLSU assembly intermediates that accumulate in GTPBP6-deficient cells reveal how the biogenesis factors GTPBP5, MTERF4 and NSUN4 facilitate PTC folding. Addition of recombinant GTPBP6 reconstitutes late mtLSU biogenesis in vitro and shows that GTPBP6 triggers a molecular switch and progression to a near-mature PTC state. Additionally, cryo-EM analysis of GTPBP6-treated mature mitochondrial ribosomes reveals the structural basis for the dual-role of GTPBP6 in ribosome biogenesis and recycling. Together, these results provide a framework for understanding step-wise PTC folding as a critical conserved quality control checkpoint. #1: Journal: Biorxiv / Year: 2021 Title: Structural basis of GTPase-mediated mitochondrial ribosome biogenesis and recycling Authors: Hillen, H.S. / Lavdovskaia, E. / Nadler, F. / Hanitsch, E. / Linden, A. / Bohnsack, K.E. / Urlaub, H. / Richter-Dennerlein, R. | ||||||||||||||||||
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 | 7of4.cif.gz | 2.2 MB | Display | PDBx/mmCIF format |
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PDB format | pdb7of4.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 7of4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7of4_validation.pdf.gz | 1.9 MB | Display | wwPDB validaton report |
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Full document | 7of4_full_validation.pdf.gz | 1.9 MB | Display | |
Data in XML | 7of4_validation.xml.gz | 205 KB | Display | |
Data in CIF | 7of4_validation.cif.gz | 356.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/of/7of4 ftp://data.pdbj.org/pub/pdb/validation_reports/of/7of4 | HTTPS FTP |
-Related structure data
Related structure data | 12869MC 7of0C 7of2C 7of3C 7of5C 7of6C 7of7C 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
+39S ribosomal protein ... , 47 types, 47 molecules 0123456789DEFHIJKLMNOPQRSTUVWX...
-RNA chain , 2 types, 2 molecules AB
#11: RNA chain | Mass: 500061.656 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Strain: HEK293 Flp-In T-Rex |
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#12: RNA chain | Mass: 22022.131 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: GenBank: 1485738021 |
-Protein , 4 types, 4 molecules Copq
#13: Protein | Mass: 56984.414 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: GTPBP6, PGPL / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): RIL / References: UniProt: O43824 |
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#49: Protein | Mass: 12292.333 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9BQC6 |
#50: 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 |
#51: Protein | Mass: 25426.895 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q8TAE8 |
-Non-polymers , 3 types, 95 molecules
#54: Chemical | #55: Chemical | ChemComp-MG / #56: Chemical | |
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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 |
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Molecular weight | Experimental value: NO | ||||||||||||||||||||||||
Source (natural) |
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Source (recombinant) | Organism: Escherichia coli BL21(DE3) (bacteria) | ||||||||||||||||||||||||
Buffer solution | pH: 7.4 | ||||||||||||||||||||||||
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | ||||||||||||||||||||||||
Specimen support | Grid type: Quantifoil R3.5/1 | ||||||||||||||||||||||||
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277.15 K |
-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: SPOT SCAN |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 81000 X / Calibrated defocus min: 300 nm / Calibrated defocus max: 2800 nm / Alignment procedure: COMA FREE |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Electron dose: 36 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) |
EM imaging optics | Energyfilter name: GIF Bioquantum / Energyfilter slit width: 20 eV |
-Processing
EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | |||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 2540514 | |||||||||||||||||||||||||||
3D reconstruction | Resolution: 2.7 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 137890 / Num. of class averages: 1 / Symmetry type: POINT | |||||||||||||||||||||||||||
Atomic model building | Protocol: FLEXIBLE FIT / Space: REAL | |||||||||||||||||||||||||||
Atomic model building | PDB-ID: 5OOL Accession code: 5OOL / Source name: PDB / Type: experimental model |