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- PDB-6ywy: The structure of the mitoribosome from Neurospora crassa with bou... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6ywy | |||||||||||||||
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Title | The structure of the mitoribosome from Neurospora crassa with bound tRNA at the P-site | |||||||||||||||
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Function / homology | ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | |||||||||||||||
Biological species | ![]() ![]() | |||||||||||||||
Method | ![]() ![]() ![]() | |||||||||||||||
![]() | Amunts, A. / Itoh, Y. / Naschberger, A. | |||||||||||||||
Funding support | ![]()
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![]() | ![]() 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 |
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Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 9.6 MB | Display | ![]() |
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PDB format | ![]() | Display | ![]() | |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 10985MC ![]() 6yw5C ![]() 6yweC ![]() 6ywsC ![]() 6ywvC ![]() 6ywxC M: map data used to model this data C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Components
+RNA chain , 4 types, 4 molecules Aaabbee
+60S ribosomal protein ... , 3 types, 3 molecules BDe
+Related to ribosomal protein ... , 12 types, 12 molecules CEfKNUVWYaEEOO
+Protein , 44 types, 46 molecules FGgHLMPQRSX01235678i9bdAABBDDGGHHIIJJ...
+Ribosomal protein ... , 7 types, 7 molecules IJCCFFLLRRSS
+Mitochondrial ... , 3 types, 3 molecules ONNXX
+54S ribosomal protein ... , 2 types, 2 molecules Tc
+L51 S25 CI-B8 domain-containing ... , 2 types, 2 molecules 4j
+Probable ribosomal protein ... , 2 types, 2 molecules hMM
+37S ribosomal protein ... , 3 types, 3 molecules UUZZ11
+Protein/peptide , 1 types, 1 molecules cc
+Non-polymers , 6 types, 304 molecules ![](data/chem/img/MG.gif)
![](data/chem/img/SPM.gif)
![](data/chem/img/K.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/NAD.gif)
![](data/chem/img/ATP.gif)
![](data/chem/img/SPM.gif)
![](data/chem/img/K.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/NAD.gif)
![](data/chem/img/ATP.gif)
+Details
-Experimental details
-Experiment
Experiment | Method: ![]() |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: ![]() |
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Sample preparation
Component | Name: Mitoribosome of Neurospora crassa in the tRNA bound state (P-site). Type: RIBOSOME / Entity ID: #1-#83 / Source: NATURAL | |||||||||||||||||||||||||||||||||||
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Molecular weight | Experimental value: NO | |||||||||||||||||||||||||||||||||||
Source (natural) | Organism: ![]() ![]() | |||||||||||||||||||||||||||||||||||
Buffer solution | pH: 7.5 | |||||||||||||||||||||||||||||||||||
Buffer component |
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Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied![]() ![]() | |||||||||||||||||||||||||||||||||||
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 |
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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![]() ![]() |
Electron lens | Mode: BRIGHT FIELD![]() |
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![]() |
Image scans | Movie frames/image: 20 / Used frames/image: 1-20 |
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Processing
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EM software |
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CTF correction![]() | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
3D reconstruction![]() | Resolution: 3.05 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 24601 / Symmetry type: POINT | ||||||||||||||||||||||||
Refinement | Cross valid method: NONE Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2 | ||||||||||||||||||||||||
Displacement parameters | Biso mean: 21.41 Å2 | ||||||||||||||||||||||||
Refine LS restraints |
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