+Open data
-Basic information
Entry | Database: PDB / ID: 6sgb | ||||||
---|---|---|---|---|---|---|---|
Title | mt-SSU assemblosome of Trypanosoma brucei | ||||||
Components |
| ||||||
Keywords | RIBOSOME / mitochondrial ribosome / assembly intermediate / translation | ||||||
Function / homology | Function and homology information modulation of formation of structure involved in a symbiotic process / rRNA (cytosine-N4-)-methyltransferase activity / mitochondrial mRNA editing complex / mitochondrial RNA processing / ATP-activated inward rectifier potassium channel activity / kinetoplast / thiosulfate sulfurtransferase activity / quorum sensing / nuclear lumen / rRNA base methylation ...modulation of formation of structure involved in a symbiotic process / rRNA (cytosine-N4-)-methyltransferase activity / mitochondrial mRNA editing complex / mitochondrial RNA processing / ATP-activated inward rectifier potassium channel activity / kinetoplast / thiosulfate sulfurtransferase activity / quorum sensing / nuclear lumen / rRNA base methylation / response to arsenic-containing substance / ciliary plasm / mRNA stabilization / mitochondrial small ribosomal subunit / : / voltage-gated potassium channel activity / acyl binding / acyl carrier activity / voltage-gated potassium channel complex / Transferases; Transferring one-carbon groups; Methyltransferases / methyltransferase activity / protein homooligomerization / potassium ion transport / fatty acid biosynthetic process / mitochondrial matrix / structural constituent of ribosome / translation / mRNA binding / mitochondrion / RNA binding / membrane / metal ion binding / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Trypanosoma brucei brucei (eukaryote) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.3 Å | ||||||
Authors | Saurer, M. / Ramrath, D.J.F. / Niemann, M. / Calderaro, S. / Prange, C. / Mattei, S. / Scaiola, A. / Leitner, A. / Bieri, P. / Horn, E.K. ...Saurer, M. / Ramrath, D.J.F. / Niemann, M. / Calderaro, S. / Prange, C. / Mattei, S. / Scaiola, A. / Leitner, A. / Bieri, P. / Horn, E.K. / Leibundgut, M. / Boehringer, D. / Schneider, A. / Ban, N. | ||||||
Funding support | Switzerland, 1items
| ||||||
Citation | Journal: Science / Year: 2019 Title: Mitoribosomal small subunit biogenesis in trypanosomes involves an extensive assembly machinery. Authors: Martin Saurer / David J F Ramrath / Moritz Niemann / Salvatore Calderaro / Céline Prange / Simone Mattei / Alain Scaiola / Alexander Leitner / Philipp Bieri / Elke K Horn / Marc Leibundgut ...Authors: Martin Saurer / David J F Ramrath / Moritz Niemann / Salvatore Calderaro / Céline Prange / Simone Mattei / Alain Scaiola / Alexander Leitner / Philipp Bieri / Elke K Horn / Marc Leibundgut / Daniel Boehringer / André Schneider / Nenad Ban / Abstract: Mitochondrial ribosomes (mitoribosomes) are large ribonucleoprotein complexes that synthesize proteins encoded by the mitochondrial genome. An extensive cellular machinery responsible for ribosome ...Mitochondrial ribosomes (mitoribosomes) are large ribonucleoprotein complexes that synthesize proteins encoded by the mitochondrial genome. An extensive cellular machinery responsible for ribosome assembly has been described only for eukaryotic cytosolic ribosomes. Here we report that the assembly of the small mitoribosomal subunit in involves a large number of factors and proceeds through the formation of assembly intermediates, which we analyzed by using cryo-electron microscopy. One of them is a 4-megadalton complex, referred to as the small subunit assemblosome, in which we identified 34 factors that interact with immature ribosomal RNA (rRNA) and recognize its functionally important regions. The assembly proceeds through large-scale conformational changes in rRNA coupled with successive incorporation of mitoribosomal proteins, providing an example for the complexity of the ribosomal assembly process in mitochondria. | ||||||
History |
|
-Structure visualization
Movie |
Movie viewer |
---|---|
Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 6sgb.cif.gz | 5.3 MB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb6sgb.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 6sgb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6sgb_validation.pdf.gz | 2.1 MB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 6sgb_full_validation.pdf.gz | 2.2 MB | Display | |
Data in XML | 6sgb_validation.xml.gz | 599.9 KB | Display | |
Data in CIF | 6sgb_validation.cif.gz | 1000.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/sg/6sgb ftp://data.pdbj.org/pub/pdb/validation_reports/sg/6sgb | HTTPS FTP |
-Related structure data
Related structure data | 10180MC 6sg9C 6sgaC M: map data used to model this data C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
|
---|---|
1 |
|
-Components
+Protein , 82 types, 88 molecules CECFCHCKCOCPCQCRCaCbCdCjCnCpDDDIDLDODPDRDUDZF2F3F5F6F7F8F9FA...
-Protein/peptide , 20 types, 27 molecules UAUBUkUCUDUMUQUfUEUPUFUmUGUHUIUNUJUKULUOUaUbUcUeUiUjUl
#46: Protein/peptide | Mass: 1805.216 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / Strain: Lister strain 427 | ||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
#47: Protein/peptide | Mass: 2315.846 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / Strain: Lister strain 427 #48: Protein/peptide | | Mass: 869.063 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / Strain: Lister strain 427 #49: Protein/peptide | Mass: 783.958 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / Strain: Lister strain 427 #50: Protein/peptide | Mass: 3847.734 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / Strain: Lister strain 427 #51: Protein/peptide | Mass: 954.168 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / Strain: Lister strain 427 #52: Protein/peptide | | Mass: 1464.797 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / Strain: Lister strain 427 #53: Protein/peptide | | Mass: 443.539 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / Strain: Lister strain 427 #54: Protein/peptide | Mass: 698.854 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / Strain: Lister strain 427 #55: Protein/peptide | | Mass: 1379.692 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / Strain: Lister strain 427 #56: Protein/peptide | | Mass: 2060.531 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / Strain: Lister strain 427 #57: Protein/peptide | | Mass: 1890.321 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / Strain: Lister strain 427 #58: Protein/peptide | | Mass: 2571.161 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / Strain: Lister strain 427 #93: Protein/peptide | | Mass: 4017.944 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / Strain: Lister strain 427 #94: Protein/peptide | | Mass: 3592.419 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / Strain: Lister strain 427 #95: Protein/peptide | | Mass: 1039.273 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / Strain: Lister strain 427 #97: Protein/peptide | | Mass: 2486.056 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / Strain: Lister strain 427 #100: Protein/peptide | | Mass: 2741.370 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / Strain: Lister strain 427 #101: Protein/peptide | | Mass: 1635.006 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / Strain: Lister strain 427 #102: Protein/peptide | | Mass: 1209.482 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / Strain: Lister strain 427 |
-RNA chain , 1 types, 1 molecules CA
#60: RNA chain | Mass: 198215.203 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / Strain: Lister strain 427 |
---|
-Non-polymers , 7 types, 19 molecules
#104: Chemical | ChemComp-MG / #105: Chemical | ChemComp-PO4 / | #106: Chemical | ChemComp-PM8 / | #107: Chemical | ChemComp-ZN / #108: Chemical | ChemComp-GTP / | #109: Chemical | #110: Water | ChemComp-HOH / | |
---|
-Details
Has ligand of interest | N |
---|
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
---|---|
EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: mt-SSU assemblosome / Type: RIBOSOME / Entity ID: #1-#103 / Source: NATURAL |
---|---|
Source (natural) | Organism: Trypanosoma brucei brucei (eukaryote) / Strain: Lister strain 427 |
Buffer solution | pH: 7.4 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES Details: Mitochondrial ribosomal small subunit assemblosome of Trypanosoma brucei brucei Lister strain 427 |
Specimen support | Grid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R2/2 |
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE-PROPANE / Humidity: 90 % / Chamber temperature: 278 K |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
---|---|
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 / Nominal magnification: 59000 X / Calibrated magnification: 100719 X |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Electron dose: 40 e/Å2 / Detector mode: INTEGRATING / Film or detector model: FEI FALCON III (4k x 4k) |
-Processing
EM software |
| ||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
CTF correction | Details: On the fly in RELION / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||||||||||||||
3D reconstruction | Resolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 104838 / Algorithm: FOURIER SPACE / Symmetry type: POINT | ||||||||||||||||||||||||
Atomic model building | Protocol: OTHER Details: Starting models of ribosomal proteins of the T. brucei mitochondrial ribosomal small subunit were taken from PDB 6HIW. Mitchondrial ribosomal small subunit assembly factors were built de novo. |