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- PDB-6hiy: Cryo-EM structure of the Trypanosoma brucei mitochondrial ribosom... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6hiy | ||||||
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Title | Cryo-EM structure of the Trypanosoma brucei mitochondrial ribosome - This entry contains the body of the small mitoribosomal subunit in complex with mt-IF-3 | ||||||
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Function / homology | ![]() modulation of formation of structure involved in a symbiotic process / organellar small ribosomal subunit / ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Ramrath, D.J.F. / Niemann, M. / Leibundgut, M. / Bieri, P. / Prange, C. / Horn, E.K. / Leitner, A. / Boehringer, D. / Schneider, A. / Ban, N. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Evolutionary shift toward protein-based architecture in trypanosomal mitochondrial ribosomes. Authors: David J F Ramrath / Moritz Niemann / Marc Leibundgut / Philipp Bieri / Céline Prange / Elke K Horn / Alexander Leitner / Daniel Boehringer / André Schneider / Nenad Ban / ![]() Abstract: Ribosomal RNA (rRNA) plays key functional and architectural roles in ribosomes. Using electron microscopy, we determined the atomic structure of a highly divergent ribosome found in mitochondria of , ...Ribosomal RNA (rRNA) plays key functional and architectural roles in ribosomes. Using electron microscopy, we determined the atomic structure of a highly divergent ribosome found in mitochondria of , a unicellular parasite that causes sleeping sickness in humans. The trypanosomal mitoribosome features the smallest rRNAs and contains more proteins than all known ribosomes. The structure shows how the proteins have taken over the role of architectural scaffold from the rRNA: They form an autonomous outer shell that surrounds the entire particle and stabilizes and positions the functionally important regions of the rRNA. Our results also reveal the "minimal" set of conserved rRNA and protein components shared by all ribosomes that help us define the most essential functional elements. | ||||||
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 | ![]() | 2.4 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 | ![]() 0232MC ![]() 0229C ![]() 0230C ![]() 0231C ![]() 0233C ![]() 6hivC ![]() 6hiwC ![]() 6hixC ![]() 6hizC 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
+Protein , 37 types, 37 molecules DADDDIDLDMDNDODPDQDRDSDUDZDaCECFCHCICKCLCOCPCQCRCUCZCaCbCdCj...
-RNA chain , 1 types, 1 molecules CA
#37: RNA chain | Mass: 198481.422 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() ![]() |
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-Protein/peptide , 3 types, 3 molecules UQURUT
#38: Protein/peptide | Mass: 2741.370 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: unassigned UNK residues / Source: (natural) ![]() ![]() ![]() |
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#39: Protein/peptide | Mass: 698.854 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: unassigned UNK residues / Source: (natural) ![]() ![]() ![]() |
#41: Protein/peptide | Mass: 3762.629 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: unassigned UNK residues / Source: (natural) ![]() ![]() ![]() |
-Non-polymers , 4 types, 43 molecules ![](data/chem/img/ZN.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/SPD.gif)
![](data/chem/img/SPM.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/SPD.gif)
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#42: Chemical | ChemComp-ZN / #43: Chemical | ChemComp-MG / #44: Chemical | ![]() #45: Chemical | ChemComp-SPM / | ![]() |
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-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: body of the T. brucei mitoribosome small subunit in complex with mt-IF-3 Type: RIBOSOME / Entity ID: #1-#41 / Source: NATURAL |
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Molecular weight | Value: 1.35 MDa / Experimental value: YES |
Source (natural) | Organism: ![]() ![]() ![]() |
Buffer solution | pH: 7.4 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied![]() ![]() |
Vitrification![]() | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE-PROPANE / Humidity: 98 % / Chamber temperature: 278 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![]() |
Image recording | Electron dose: 40 e/Å2 / Film or detector model: FEI FALCON III (4k x 4k) |
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Processing
EM software |
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CTF correction![]() | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | |||||||||||||||||||||
3D reconstruction![]() | Resolution: 3.27 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 31911 / Algorithm: FOURIER SPACE / Symmetry type: POINT | |||||||||||||||||||||
Atomic model building | B value: 41.4 / Protocol: AB INITIO MODEL Details: We used Coot and O for initial model building and refined the structure using Phenix |