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Yorodumi- PDB-6yw5: The structure of the small subunit of the mitoribosome from Neuro... -
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-Basic information
Entry | Database: PDB / ID: 6yw5 | |||||||||||||||
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Title | The structure of the small subunit 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 3-hydroxyisobutyryl-CoA hydrolase activity / valine catabolic process / nuclear pore inner ring / nuclear pore organization / ATPase inhibitor activity / negative regulation of ATP-dependent activity / positive regulation of translational fidelity / mitochondrial large ribosomal subunit / structural constituent of nuclear pore / mitochondrial small ribosomal subunit ...3-hydroxyisobutyryl-CoA hydrolase activity / valine catabolic process / nuclear pore inner ring / nuclear pore organization / ATPase inhibitor activity / negative regulation of ATP-dependent activity / positive regulation of translational fidelity / mitochondrial large ribosomal subunit / structural constituent of nuclear pore / mitochondrial small ribosomal subunit / mitochondrial translation / superoxide dismutase activity / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / mRNA 5'-UTR binding / ribosomal small subunit assembly / small ribosomal subunit / small ribosomal subunit rRNA binding / cytosolic small ribosomal subunit / rRNA binding / ribosome / structural constituent of ribosome / ribonucleoprotein complex / translation / 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: 2.85 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 | 6yw5.cif.gz | 4.1 MB | Display | PDBx/mmCIF format |
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PDB format | pdb6yw5.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 6yw5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6yw5_validation.pdf.gz | 1.5 MB | Display | wwPDB validaton report |
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Full document | 6yw5_full_validation.pdf.gz | 1.6 MB | Display | |
Data in XML | 6yw5_validation.xml.gz | 200.8 KB | Display | |
Data in CIF | 6yw5_validation.cif.gz | 331.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yw/6yw5 ftp://data.pdbj.org/pub/pdb/validation_reports/yw/6yw5 | HTTPS FTP |
-Related structure data
Related structure data | 10958MC 6yweC 6ywsC 6ywvC 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
-Protein , 14 types, 16 molecules AAGGIIVVWWYY223344556677880099V
#1: Protein | Mass: 51596.340 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Neurospora crassa OR74A (fungus) / References: UniProt: A7UWX2 | ||||||||||
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#7: Protein | Mass: 33821.914 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Neurospora crassa OR74A (fungus) / References: UniProt: Q7S6M9 | ||||||||||
#9: Protein | Mass: 35319.570 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Neurospora crassa OR74A (fungus) / References: UniProt: Q7S7R6 | ||||||||||
#22: Protein | Mass: 35312.184 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Neurospora crassa OR74A (fungus) / References: UniProt: Q7SHR9 | ||||||||||
#23: Protein | Mass: 44923.723 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Neurospora crassa OR74A (fungus) / References: UniProt: Q7RYW7 | ||||||||||
#25: Protein | Mass: 12169.154 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Neurospora crassa OR74A (fungus) / References: UniProt: Q1K5R0 | ||||||||||
#28: Protein | Mass: 38126.250 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Neurospora crassa OR74A (fungus) / References: UniProt: Q7SHR6 | ||||||||||
#29: Protein | Mass: 26612.898 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Neurospora crassa OR74A (fungus) / References: UniProt: Q1K6Q3 | ||||||||||
#30: Protein | Mass: 34270.785 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Neurospora crassa OR74A (fungus) / References: UniProt: Q7S2H6 #31: Protein | | Mass: 39274.625 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Neurospora crassa OR74A (fungus) / References: UniProt: Q7SHB2 #32: Protein | | Mass: 43112.672 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Neurospora crassa OR74A (fungus) / References: UniProt: Q7SG49 #33: Protein | | Mass: 56401.191 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Neurospora crassa OR74A (fungus) References: UniProt: Q1K7A4, 3-hydroxyisobutyryl-CoA hydrolase #34: Protein | Mass: 10664.098 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Neurospora crassa OR74A (fungus) / References: UniProt: V5IRA3 #36: 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 |
-Mito ribosomal protein ... , 5 types, 5 molecules BBDDFFRRTT
#2: Protein | Mass: 47197.305 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Neurospora crassa OR74A (fungus) / References: UniProt: V5ILE0 |
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#4: Protein | Mass: 51610.031 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Neurospora crassa OR74A (fungus) / References: UniProt: Q7SA90 |
#6: Protein | Mass: 13304.392 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Neurospora crassa OR74A (fungus) / References: UniProt: Q7SB95 |
#18: Protein | Mass: 28468.594 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Neurospora crassa OR74A (fungus) / References: UniProt: Q1K8E0 |
#20: Protein | Mass: 25679.785 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Neurospora crassa OR74A (fungus) / References: UniProt: Q7SAJ1 |
-Ribosomal protein ... , 3 types, 3 molecules CCOOPP
#3: Protein | Mass: 58907.285 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Neurospora crassa OR74A (fungus) / References: UniProt: P23351 |
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#15: Protein | Mass: 35803.988 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Neurospora crassa OR74A (fungus) / References: UniProt: Q1K5G1 |
#16: Protein | Mass: 12140.166 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Neurospora crassa OR74A (fungus) / References: UniProt: P08580 |
-37S ribosomal protein ... , 5 types, 5 molecules EEJJUUZZ11
#5: Protein | Mass: 53297.543 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Neurospora crassa OR74A (fungus) / References: UniProt: Q1K548 |
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#10: Protein | Mass: 30377.070 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Neurospora crassa OR74A (fungus) / References: UniProt: Q7RYL4 |
#21: Protein | Mass: 29553.588 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Neurospora crassa OR74A (fungus) / References: UniProt: Q873E4 |
#26: Protein | Mass: 44057.090 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Neurospora crassa OR74A (fungus) / References: UniProt: Q1K5Z0 |
#27: Protein | Mass: 9907.534 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Neurospora crassa OR74A (fungus) / References: UniProt: Q7S4Y4 |
-40S ribosomal protein ... , 2 types, 2 molecules HHMM
#8: Protein | Mass: 17743.707 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Neurospora crassa OR74A (fungus) / References: UniProt: Q7SHF3 |
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#13: Protein | Mass: 13503.821 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Neurospora crassa OR74A (fungus) / References: UniProt: Q7S2C2 |
-Mitochondrial ... , 6 types, 6 molecules KKLLNNQQSSXX
#11: Protein | Mass: 42159.832 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Neurospora crassa OR74A (fungus) / References: UniProt: Q7SGU0 |
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#12: Protein | Mass: 18657.877 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Neurospora crassa OR74A (fungus) / References: UniProt: Q7S9I4 |
#14: Protein | Mass: 13210.644 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Neurospora crassa OR74A (fungus) / References: UniProt: Q7SF85 |
#17: Protein | Mass: 18505.701 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Neurospora crassa OR74A (fungus) / References: UniProt: Q7S4E0 |
#19: Protein | Mass: 10408.332 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Neurospora crassa OR74A (fungus) / References: UniProt: Q1K8V2 |
#24: Protein | Mass: 51451.414 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Neurospora crassa OR74A (fungus) / References: UniProt: Q7SD06 |
-RNA chain , 1 types, 1 molecules aa
#35: RNA chain | Mass: 600339.375 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Neurospora crassa OR74A (fungus) |
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-Non-polymers , 3 types, 120 molecules
#37: Chemical | ChemComp-MG / #38: Chemical | ChemComp-ATP / | #39: Chemical | ChemComp-K / |
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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: Mitoribosome of Neurospora crassa / Type: RIBOSOME / Entity ID: #1-#36 / 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 | ||||||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||||||||||||||
3D reconstruction | Resolution: 2.85 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 131806 / Symmetry type: POINT | ||||||||||||||||||||||||
Refinement | Cross valid method: NONE Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2 | ||||||||||||||||||||||||
Displacement parameters | Biso mean: 36.7 Å2 | ||||||||||||||||||||||||
Refine LS restraints |
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