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Yorodumi- PDB-6hiz: Cryo-EM structure of the Trypanosoma brucei mitochondrial ribosom... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6hiz | ||||||
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Title | Cryo-EM structure of the Trypanosoma brucei mitochondrial ribosome - This entry contains the head of the small mitoribosomal subunit | ||||||
Components |
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Keywords | RIBOSOME / mitoribosome / translation / Trypanosoma / small ribosomal subunit / 9S rRNA / ribosomal protein | ||||||
Function / homology | Function and homology information mitochondrial mRNA editing complex / mitochondrial RNA processing / kinetoplast / thiosulfate sulfurtransferase activity / nuclear lumen / ciliary plasm / mRNA stabilization / mitochondrial small ribosomal subunit / RNA processing / mitochondrion organization ...mitochondrial mRNA editing complex / mitochondrial RNA processing / kinetoplast / thiosulfate sulfurtransferase activity / nuclear lumen / ciliary plasm / mRNA stabilization / mitochondrial small ribosomal subunit / RNA processing / mitochondrion organization / structural constituent of ribosome / translation / mRNA binding / mitochondrion / RNA binding / nucleoplasm / nucleus / cytoplasm Similarity search - Function | ||||||
Biological species | Trypanosoma brucei brucei (eukaryote) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.08 Å | ||||||
Authors | Ramrath, D.J.F. / Niemann, M. / Leibundgut, M. / Bieri, P. / Prange, C. / Horn, E.K. / Leitner, A. / Boehringer, A. / Schneider, A. / Ban, N. | ||||||
Funding support | Switzerland, 1items
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Citation | Journal: Science / Year: 2018 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 |
Movie viewer |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 6hiz.cif.gz | 1.9 MB | Display | PDBx/mmCIF format |
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PDB format | pdb6hiz.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 6hiz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6hiz_validation.pdf.gz | 1.3 MB | Display | wwPDB validaton report |
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Full document | 6hiz_full_validation.pdf.gz | 1.4 MB | Display | |
Data in XML | 6hiz_validation.xml.gz | 195.2 KB | Display | |
Data in CIF | 6hiz_validation.cif.gz | 338.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hi/6hiz ftp://data.pdbj.org/pub/pdb/validation_reports/hi/6hiz | HTTPS FTP |
-Related structure data
Related structure data | 0233MC 0229C 0230C 0231C 0232C 6hivC 6hiwC 6hixC 6hiyC 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 , 25 types, 25 molecules DADLDBDCDEDFDGDHDJDKDTDVDWDXDYCCCICJCKCNCRCSCgCiCk
-RNA chain , 1 types, 1 molecules CA
#26: RNA chain | Mass: 195379.688 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / Variant: Lister 427 / References: GenBank: 343546 |
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-Protein/peptide , 2 types, 2 molecules UOUP
#27: Protein/peptide | Mass: 443.539 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / Variant: Lister 427 |
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#28: Protein/peptide | Mass: 613.749 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / Variant: Lister 427 |
-Non-polymers , 5 types, 10 molecules
#29: Chemical | #30: Chemical | ChemComp-UTP / | #31: Chemical | ChemComp-GTP / | #32: Chemical | #33: Water | ChemComp-HOH / | |
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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: head of the T. brucei mitoribosome small subunit / Type: RIBOSOME / Entity ID: #1-#28 / Source: NATURAL |
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Molecular weight | Value: 1.25 MDa / Experimental value: YES |
Source (natural) | Organism: Trypanosoma brucei brucei (eukaryote) / Strain: Lister 427 |
Buffer solution | pH: 7.4 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE-PROPANE / Humidity: 98 % / Chamber temperature: 278 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 |
Image recording | Electron dose: 40 e/Å2 / Detector mode: INTEGRATING / Film or detector model: FEI FALCON III (4k x 4k) |
-Processing
EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||
3D reconstruction | Resolution: 3.08 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 101308 / Algorithm: FOURIER SPACE / Symmetry type: POINT | ||||||||||||||||||
Atomic model building | B value: 45 / Protocol: AB INITIO MODEL Details: We used Coot and O for initial model building and refined the structure using Phenix |