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Yorodumi- PDB-6hiw: Cryo-EM structure of the Trypanosoma brucei mitochondrial ribosom... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6hiw | ||||||
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Title | Cryo-EM structure of the Trypanosoma brucei mitochondrial ribosome - This entry contains the complete small mitoribosomal subunit in complex with mt-IF-3 | ||||||
Components |
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Keywords | RIBOSOME / mitoribosome / translation / Trypanosoma / small ribosomal subunit / 9S rRNA / ribosomal protein / mitochondrial initiation factor IF-3 | ||||||
Function / homology | Function and homology information modulation of formation of structure involved in a symbiotic process / organellar small ribosomal subunit / 3-hydroxyisobutyryl-CoA hydrolase / 3-hydroxyisobutyryl-CoA hydrolase activity / mitochondrial mRNA editing complex / mitochondrial RNA processing / kinetoplast / thiosulfate sulfurtransferase activity / quorum sensing / nuclear lumen ...modulation of formation of structure involved in a symbiotic process / organellar small ribosomal subunit / 3-hydroxyisobutyryl-CoA hydrolase / 3-hydroxyisobutyryl-CoA hydrolase activity / mitochondrial mRNA editing complex / mitochondrial RNA processing / kinetoplast / thiosulfate sulfurtransferase activity / quorum sensing / nuclear lumen / enoyl-CoA hydratase activity / regulation of protein kinase A signaling / ciliary plasm / mRNA stabilization / mitochondrial small ribosomal subunit / superoxide dismutase / fatty acid beta-oxidation / protein kinase A regulatory subunit binding / superoxide dismutase activity / RNA processing / mitochondrion organization / ribosome / structural constituent of ribosome / hydrolase activity / translation / mRNA binding / mitochondrion / RNA binding / nucleoplasm / nucleus / metal ion binding / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Trypanosoma brucei brucei (eukaryote) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.37 Å | ||||||
Authors | Ramrath, D. / Niemann, M. / Leibundgut, M. / Bieri, P. / Prange, C. / Horn, E.K. / Leitner, A. / Boehringer, D. / 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 | 6hiw.cif.gz | 4.3 MB | Display | PDBx/mmCIF format |
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PDB format | pdb6hiw.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 6hiw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6hiw_validation.pdf.gz | 1.6 MB | Display | wwPDB validaton report |
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Full document | 6hiw_full_validation.pdf.gz | 1.7 MB | Display | |
Data in XML | 6hiw_validation.xml.gz | 413.5 KB | Display | |
Data in CIF | 6hiw_validation.cif.gz | 733.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hi/6hiw ftp://data.pdbj.org/pub/pdb/validation_reports/hi/6hiw | HTTPS FTP |
-Related structure data
Related structure data | 0230MC 0229C 0231C 0232C 0233C 6hivC 6hixC 6hiyC 6hizC 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 , 57 types, 57 molecules DADDDIDLDMDNDODPDQDRDSDUDZDaDBDCDEDFDGDHDJDKDTDVDWDXDYCCCECF...
-RNA chain , 1 types, 1 molecules CA
#57: RNA chain | Mass: 198442.391 Da / Num. of mol.: 1 / Source method: isolated from a natural source Details: post-transcriptional addition of 7 U residues at the 3' end Source: (natural) Trypanosoma brucei brucei (eukaryote) / Variant: Lister 427 / References: GenBank: 343546 |
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-Protein/peptide , 5 types, 5 molecules UOUPUQURUT
#58: Protein/peptide | Mass: 443.539 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: residues built as UNK / Source: (natural) Trypanosoma brucei brucei (eukaryote) / Variant: Lister 427 |
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#59: Protein/peptide | Mass: 613.749 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: residues built as UNK / Source: (natural) Trypanosoma brucei brucei (eukaryote) / Variant: Lister 427 |
#60: Protein/peptide | Mass: 2741.370 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: residues built as UNK / Source: (natural) Trypanosoma brucei brucei (eukaryote) / Variant: Lister 427 |
#61: Protein/peptide | Mass: 698.854 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: residues built as UNK / Source: (natural) Trypanosoma brucei brucei (eukaryote) / Variant: Lister 427 |
#63: Protein/peptide | Mass: 3762.629 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / Variant: Lister 427 |
-Non-polymers , 7 types, 53 molecules
#64: Chemical | ChemComp-ZN / #65: Chemical | ChemComp-UTP / | #66: Chemical | ChemComp-MG / #67: Chemical | ChemComp-GTP / | #68: Chemical | ChemComp-SPD / #69: Chemical | ChemComp-SPM / | #70: 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: small subunit of the T. brucei mitoribosome in complex with mt-IF-3 Type: RIBOSOME / Entity ID: #1-#63 / Source: NATURAL |
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Molecular weight | Value: 2.4 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: 3.37 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 31911 / Algorithm: FOURIER SPACE / Num. of class averages: 1 / Symmetry type: POINT | ||||||||||||||||||||||||||||
Atomic model building | B value: 46.4 / Protocol: AB INITIO MODEL Details: We used Coot and O for initial model building and refined the structure using PHENIX |