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Yorodumi- PDB-6ywv: The structure of the Atp25 bound assembly intermediate of the mit... -
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-Basic information
Entry | Database: PDB / ID: 6ywv | |||||||||||||||
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Title | The structure of the Atp25 bound assembly intermediate of the mitoribosome from Neurospora crassa | |||||||||||||||
Components |
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Keywords | TRANSLATION / Neurospora crassa / translating Mitoribosomes / tRNA / mRNA / mL108 | |||||||||||||||
Function / homology | Function and homology information mitochondrial gene expression / mitochondrial genome maintenance / ribonuclease III activity / fungal-type vacuole / mitochondrial proton-transporting ATP synthase complex assembly / DNA strand exchange activity / mitochondrial large ribosomal subunit / mRNA stabilization / mitochondrial translation / RNA processing ...mitochondrial gene expression / mitochondrial genome maintenance / ribonuclease III activity / fungal-type vacuole / mitochondrial proton-transporting ATP synthase complex assembly / DNA strand exchange activity / mitochondrial large ribosomal subunit / mRNA stabilization / mitochondrial translation / RNA processing / large ribosomal subunit / double-stranded RNA binding / single-stranded DNA binding / transferase activity / large ribosomal subunit rRNA binding / cytosolic large ribosomal subunit / rRNA binding / negative regulation of translation / mitochondrial inner membrane / ribosome / structural constituent of ribosome / translation / ribonucleoprotein complex / mRNA binding / mitochondrion / RNA binding / metal ion binding Similarity search - Function | |||||||||||||||
Biological species | Neurospora crassa OR74A (fungus) | |||||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.03 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 | 6ywv.cif.gz | 5.1 MB | Display | PDBx/mmCIF format |
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PDB format | pdb6ywv.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 6ywv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6ywv_validation.pdf.gz | 1.8 MB | Display | wwPDB validaton report |
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Full document | 6ywv_full_validation.pdf.gz | 1.8 MB | Display | |
Data in XML | 6ywv_validation.xml.gz | 214.8 KB | Display | |
Data in CIF | 6ywv_validation.cif.gz | 367.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yw/6ywv ftp://data.pdbj.org/pub/pdb/validation_reports/yw/6ywv | HTTPS FTP |
-Related structure data
Related structure data | 10977MC 6yw5C 6yweC 6ywsC 6ywxC 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 , 1 types, 1 molecules A
#1: RNA chain | Mass: 1114857.375 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Neurospora crassa OR74A (fungus) |
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-60S ribosomal protein ... , 8 types, 8 molecules BCDFgK5a
#2: Protein | Mass: 42260.766 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Neurospora crassa OR74A (fungus) / References: UniProt: Q7SCX7 |
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#3: Protein | Mass: 41262.527 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Neurospora crassa OR74A (fungus) / References: UniProt: Q1K8T6 |
#4: Protein | Mass: 36402.785 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Neurospora crassa OR74A (fungus) / References: UniProt: V5IMN1 |
#6: Protein | Mass: 28629.158 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Neurospora crassa OR74A (fungus) / References: UniProt: Q7RZF0 |
#8: Protein | Mass: 16629.375 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Neurospora crassa OR74A (fungus) / References: UniProt: Q7RX40 |
#12: Protein | Mass: 27443.828 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Neurospora crassa OR74A (fungus) / References: UniProt: F5HIJ5 |
#32: Protein | Mass: 48106.484 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Neurospora crassa OR74A (fungus) / References: UniProt: Q7SA88 |
#39: Protein | Mass: 25439.018 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Neurospora crassa OR74A (fungus) / References: UniProt: Q1K6U7 |
-50S ribosomal protein ... , 5 types, 5 molecules EILSU
#5: Protein | Mass: 39170.875 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Neurospora crassa OR74A (fungus) / References: UniProt: Q1K6P0 |
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#10: Protein | Mass: 14135.630 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Neurospora crassa OR74A (fungus) / References: UniProt: Q7SBJ8 |
#13: Protein | Mass: 22181.545 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Neurospora crassa OR74A (fungus) / References: UniProt: Q1K8C8 |
#20: Protein | Mass: 31501.131 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Neurospora crassa OR74A (fungus) / References: UniProt: Q7SC44 |
#22: Protein | Mass: 18196.393 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Neurospora crassa OR74A (fungus) / References: UniProt: Q1K8Y7 |
-Uncharacterized ... , 11 types, 11 molecules fRVXY2378id
#7: Protein | Mass: 37363.766 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Neurospora crassa OR74A (fungus) / References: UniProt: Q7RZ62 |
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#19: Protein | Mass: 49549.199 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Neurospora crassa OR74A (fungus) / References: UniProt: Q1K730 |
#23: Protein | Mass: 23766.729 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Neurospora crassa OR74A (fungus) / References: UniProt: Q1K7L7 |
#25: Protein | Mass: 7027.574 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Neurospora crassa OR74A (fungus) / References: UniProt: V5IM60 |
#26: Protein | Mass: 14853.288 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Neurospora crassa OR74A (fungus) / References: UniProt: Q1K7P9 |
#29: Protein | Mass: 41496.336 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Neurospora crassa OR74A (fungus) / References: UniProt: A0A0B0DWX0 |
#30: Protein | Mass: 11796.603 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Neurospora crassa OR74A (fungus) / References: UniProt: Q7S5W0 |
#34: Protein | Mass: 18180.738 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Neurospora crassa OR74A (fungus) / References: UniProt: Q7S518 |
#35: Protein | Mass: 49748.516 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Neurospora crassa OR74A (fungus) / References: UniProt: Q7S711 |
#37: Protein | Mass: 23179.602 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Neurospora crassa OR74A (fungus) / References: UniProt: Q7SCZ3 |
#42: Protein | Mass: 32516.111 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Neurospora crassa OR74A (fungus) / References: UniProt: Q7RYM5 |
-Protein , 6 types, 6 molecules HNQ09n
#9: Protein | Mass: 20334.576 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Neurospora crassa OR74A (fungus) / References: UniProt: Q7SBV6 |
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#15: Protein | Mass: 23953.027 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Neurospora crassa OR74A (fungus) / References: UniProt: Q7SGE5 |
#18: Protein | Mass: 45460.117 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Neurospora crassa OR74A (fungus) / References: UniProt: Q7RXU7 |
#27: Protein | Mass: 13960.405 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Neurospora crassa OR74A (fungus) / References: UniProt: Q7S4E7 |
#38: Protein | Mass: 29625.195 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Neurospora crassa OR74A (fungus) / References: UniProt: Q7S1R6 |
#43: Protein | Mass: 77985.422 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Neurospora crassa OR74A (fungus) / References: UniProt: Q7SAC2 |
-50S ribosomal subunit ... , 2 types, 2 molecules J6
#11: Protein | Mass: 33951.125 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Neurospora crassa OR74A (fungus) / References: UniProt: Q7SB98 |
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#33: Protein | Mass: 41322.074 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Neurospora crassa OR74A (fungus) / References: UniProt: Q7S1Z3 |
-Mitochondrial ... , 8 types, 8 molecules MOPW14hb
#14: Protein | Mass: 28235.305 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Neurospora crassa OR74A (fungus) / References: UniProt: Q7RYW8 |
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#16: Protein | Mass: 41565.996 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Neurospora crassa OR74A (fungus) / References: UniProt: Q7S5N0 |
#17: Protein | Mass: 26005.465 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Neurospora crassa OR74A (fungus) / References: UniProt: Q7SA60 |
#24: Protein | Mass: 14114.779 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Neurospora crassa OR74A (fungus) / References: UniProt: Q1K4P1 |
#28: Protein | Mass: 50749.188 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Neurospora crassa OR74A (fungus) / References: UniProt: Q7RXV8 |
#31: Protein | Mass: 15126.693 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Neurospora crassa OR74A (fungus) / References: UniProt: Q7S300 |
#36: Protein | Mass: 11128.777 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Neurospora crassa OR74A (fungus) / References: UniProt: Q7SGH0 |
#40: Protein | Mass: 18745.025 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Neurospora crassa OR74A (fungus) / References: UniProt: Q7SEK9 |
-54S ribosomal protein ... , 2 types, 2 molecules Tc
#21: Protein | Mass: 29645.260 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Neurospora crassa OR74A (fungus) / References: UniProt: Q7S910 |
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#41: Protein | Mass: 13131.485 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Neurospora crassa OR74A (fungus) / References: UniProt: U9W8F2 |
-Non-polymers , 5 types, 171 molecules
#44: Chemical | ChemComp-MG / #45: Chemical | ChemComp-NAD / | #46: Chemical | ChemComp-SPM / | #47: Chemical | ChemComp-K / #48: Chemical | |
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-Details
Has ligand of interest | Y |
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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: Assembly intermediate of the mitoribosome of Neurospora crassa Type: RIBOSOME / Entity ID: #1-#43 / 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: 3.03 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 24142 / Symmetry type: POINT | ||||||||||||||||||||||||
Refinement | Cross valid method: NONE Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2 | ||||||||||||||||||||||||
Displacement parameters | Biso mean: 21.45 Å2 | ||||||||||||||||||||||||
Refine LS restraints |
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