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Yorodumi- PDB-6ywx: The structure of the mitoribosome from Neurospora crassa with tRN... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6ywx | |||||||||||||||
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Title | The structure of the mitoribosome from Neurospora crassa with tRNA bound to the E-site | |||||||||||||||
Components |
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Keywords | TRANSLATION / Neurospora crassa / translating Mitoribosomes / tRNA / mRNA / mL108 | |||||||||||||||
Function / homology | Function and homology information 3-hydroxyisobutyryl-CoA hydrolase activity / valine catabolic process / nuclear pore inner ring / nuclear pore organization / mitochondrial genome maintenance / ribonuclease III activity / ATPase inhibitor activity / negative regulation of ATP-dependent activity / fungal-type vacuole / DNA strand exchange activity ...3-hydroxyisobutyryl-CoA hydrolase activity / valine catabolic process / nuclear pore inner ring / nuclear pore organization / mitochondrial genome maintenance / ribonuclease III activity / ATPase inhibitor activity / negative regulation of ATP-dependent activity / fungal-type vacuole / DNA strand exchange activity / positive regulation of translational fidelity / mitochondrial large ribosomal subunit / structural constituent of nuclear pore / mitochondrial small ribosomal subunit / mitochondrial translation / superoxide dismutase activity / RNA processing / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / mRNA 5'-UTR binding / large ribosomal subunit / double-stranded RNA binding / single-stranded DNA binding / ribosomal small subunit assembly / small ribosomal subunit / small ribosomal subunit rRNA binding / transferase activity / large ribosomal subunit rRNA binding / cytosolic large ribosomal subunit / rRNA binding / negative regulation of translation / ribosome / structural constituent of ribosome / translation / ribonucleoprotein complex / mRNA binding / mitochondrion / RNA binding / metal ion binding / cytoplasm Similarity search - Function | |||||||||||||||
Biological species | Neurospora crassa OR74A (fungus) | |||||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.1 Å | |||||||||||||||
Authors | Amunts, A. / Itoh, Y. / Naschberger, A. | |||||||||||||||
Funding support | Sweden, European Union, 4items
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Citation | Journal: Nat Commun / Year: 2020 Title: Analysis of translating mitoribosome reveals functional characteristics of translation in mitochondria of fungi. Authors: Yuzuru Itoh / Andreas Naschberger / Narges Mortezaei / Johannes M Herrmann / Alexey Amunts / Abstract: Mitoribosomes are specialized protein synthesis machineries in mitochondria. However, how mRNA binds to its dedicated channel, and tRNA moves as the mitoribosomal subunit rotate with respect to each ...Mitoribosomes are specialized protein synthesis machineries in mitochondria. However, how mRNA binds to its dedicated channel, and tRNA moves as the mitoribosomal subunit rotate with respect to each other is not understood. We report models of the translating fungal mitoribosome with mRNA, tRNA and nascent polypeptide, as well as an assembly intermediate. Nicotinamide adenine dinucleotide (NAD) is found in the central protuberance of the large subunit, and the ATPase inhibitory factor 1 (IF) in the small subunit. The models of the active mitoribosome explain how mRNA binds through a dedicated protein platform on the small subunit, tRNA is translocated with the help of the protein mL108, bridging it with L1 stalk on the large subunit, and nascent polypeptide paths through a newly shaped exit tunnel involving a series of structural rearrangements. An assembly intermediate is modeled with the maturation factor Atp25, providing insight into the biogenesis of the mitoribosomal large subunit and translation regulation. | |||||||||||||||
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 | 6ywx.cif.gz | 9.5 MB | Display | PDBx/mmCIF format |
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PDB format | pdb6ywx.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 6ywx.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6ywx_validation.pdf.gz | 1.9 MB | Display | wwPDB validaton report |
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Full document | 6ywx_full_validation.pdf.gz | 1.9 MB | Display | |
Data in XML | 6ywx_validation.xml.gz | 325.5 KB | Display | |
Data in CIF | 6ywx_validation.cif.gz | 632.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yw/6ywx ftp://data.pdbj.org/pub/pdb/validation_reports/yw/6ywx | HTTPS FTP |
-Related structure data
Related structure data | 10978MC 6yw5C 6yweC 6ywsC 6ywvC 6ywyC 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 , 3 types, 3 molecules Aaabb
+60S ribosomal protein ... , 9 types, 9 molecules BCDFgK5ae
+50S ribosomal protein ... , 5 types, 5 molecules EILSU
+Protein , 29 types, 31 molecules GfNQRVXY02378i9dAAGGVVWWYY223344556677880099j
+Ribosomal protein ... , 4 types, 4 molecules HCCOOPP
+50S ribosomal subunit ... , 2 types, 2 molecules J6
+Mitochondrial ... , 14 types, 14 molecules MOPW14hbKKLLNNQQSSXX
+54S ribosomal protein ... , 2 types, 2 molecules Tc
+Mito ribosomal protein ... , 5 types, 5 molecules BBDDFFRRTT
+37S ribosomal protein ... , 6 types, 6 molecules EEIIJJUUZZ11
+40S ribosomal protein ... , 2 types, 2 molecules HHMM
+Non-polymers , 6 types, 304 molecules
+Details
-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: Mitoribosome of Neurospora crassa with tRNA in the E-site Type: RIBOSOME / Entity ID: #1-#81 / Source: NATURAL | |||||||||||||||||||||||||||||||||||
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Molecular weight | Experimental value: NO | |||||||||||||||||||||||||||||||||||
Source (natural) | Organism: Neurospora crassa OR74A (fungus) | |||||||||||||||||||||||||||||||||||
Buffer solution | pH: 7.5 | |||||||||||||||||||||||||||||||||||
Buffer component |
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Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | |||||||||||||||||||||||||||||||||||
Specimen support | Grid material: COPPER / Grid type: Quantifoil R2/2 | |||||||||||||||||||||||||||||||||||
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 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: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Calibrated magnification: 130000 X / C2 aperture diameter: 70 µm / Alignment procedure: COMA FREE |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Electron dose: 35 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Num. of real images: 3172 |
EM imaging optics | Energyfilter name: GIF Quantum LS / Energyfilter slit width: 20 eV |
Image scans | Movie frames/image: 20 / Used frames/image: 1-20 |
-Processing
Software |
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EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
3D reconstruction | Resolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 23802 / Symmetry type: POINT | ||||||||||||||||||||||||
Refinement | Cross valid method: NONE Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2 | ||||||||||||||||||||||||
Displacement parameters | Biso mean: 47.48 Å2 | ||||||||||||||||||||||||
Refine LS restraints |
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