+Open data
-Basic information
Entry | Database: PDB / ID: 6ppf | |||||||||
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Title | Bacterial 45SRbgA ribosomal particle class B | |||||||||
Components |
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Keywords | RIBOSOME / Ribosome assembly / 50S subunit / RbgA / YlqF | |||||||||
Function / homology | Function and homology information positive regulation of rRNA processing / nucleoid / rRNA processing / large ribosomal subunit / ribosomal large subunit assembly / transferase activity / large ribosomal subunit rRNA binding / 5S rRNA binding / cytoplasmic translation / cytosolic large ribosomal subunit ...positive regulation of rRNA processing / nucleoid / rRNA processing / large ribosomal subunit / ribosomal large subunit assembly / transferase activity / large ribosomal subunit rRNA binding / 5S rRNA binding / cytoplasmic translation / cytosolic large ribosomal subunit / negative regulation of translation / rRNA binding / ribosome / structural constituent of ribosome / ribonucleoprotein complex / translation / mRNA binding / DNA binding / RNA binding / cytoplasm Similarity search - Function | |||||||||
Biological species | Bacillus subtilis (bacteria) | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.4 Å | |||||||||
Authors | Ortega, J. / Seffouh, A. / Jain, N. / Jahagirdar, D. / Basu, K. / Razi, A. / Ni, X. / Guarne, A. / Britton, R.A. | |||||||||
Funding support | Canada, United States, 2items
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Citation | Journal: Nucleic Acids Res / Year: 2019 Title: Structural consequences of the interaction of RbgA with a 50S ribosomal subunit assembly intermediate. Authors: Amal Seffouh / Nikhil Jain / Dushyant Jahagirdar / Kaustuv Basu / Aida Razi / Xiaodan Ni / Alba Guarné / Robert A Britton / Joaquin Ortega / Abstract: Bacteria harbor a number GTPases that function in the assembly of the ribosome and are essential for growth. RbgA is one of these GTPases and is required for the assembly of the 50S subunit in most ...Bacteria harbor a number GTPases that function in the assembly of the ribosome and are essential for growth. RbgA is one of these GTPases and is required for the assembly of the 50S subunit in most bacteria. Homologs of this protein are also implicated in the assembly of the large subunit of the mitochondrial and eukaryotic ribosome. We present here the cryo-electron microscopy structure of RbgA bound to a Bacillus subtilis 50S subunit assembly intermediate (45SRbgA particle) that accumulates in cells upon RbgA depletion. Binding of RbgA at the P site of the immature particle stabilizes functionally important rRNA helices in the A and P-sites, prior to the completion of the maturation process of the subunit. The structure also reveals the location of the highly conserved N-terminal end of RbgA containing the catalytic residue Histidine 9. The derived model supports a mechanism of GTP hydrolysis, and it shows that upon interaction of RbgA with the 45SRbgA particle, Histidine 9 positions itself near the nucleotide potentially acting as the catalytic residue with minimal rearrangements. This structure represents the first visualization of the conformational changes induced by an assembly factor in a bacterial subunit intermediate. | |||||||||
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 | 6ppf.cif.gz | 1.6 MB | Display | PDBx/mmCIF format |
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PDB format | pdb6ppf.ent.gz | 1.2 MB | Display | PDB format |
PDBx/mmJSON format | 6ppf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6ppf_validation.pdf.gz | 1 MB | Display | wwPDB validaton report |
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Full document | 6ppf_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | 6ppf_validation.xml.gz | 122.7 KB | Display | |
Data in CIF | 6ppf_validation.cif.gz | 199.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pp/6ppf ftp://data.pdbj.org/pub/pdb/validation_reports/pp/6ppf | HTTPS FTP |
-Related structure data
Related structure data | 20435MC 6ppkC 6pvkC 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
-RNA chain , 2 types, 2 molecules AB
#1: RNA chain | Mass: 949340.125 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bacillus subtilis (bacteria) / References: GenBank: 723796434 |
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#2: RNA chain | Mass: 38423.863 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bacillus subtilis (bacteria) / References: GenBank: 1012899741 |
-50S ribosomal protein ... , 19 types, 19 molecules CDEJKLNOPQRSTUVZbYd
#3: Protein | Mass: 30335.125 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bacillus subtilis (bacteria) / References: UniProt: A0A063XCB6, UniProt: P42919*PLUS |
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#4: Protein | Mass: 22723.348 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bacillus subtilis (bacteria) / References: UniProt: A0A063X745, UniProt: P42920*PLUS |
#5: Protein | Mass: 22424.951 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bacillus subtilis (bacteria) / References: UniProt: A0A063X8U6, UniProt: P42921*PLUS |
#6: Protein | Mass: 16407.104 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bacillus subtilis (bacteria) / References: UniProt: A0A063XCH0, UniProt: P70974*PLUS |
#7: Protein | Mass: 13175.288 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bacillus subtilis (bacteria) / References: UniProt: A0A063X754, UniProt: P12875*PLUS |
#8: Protein | Mass: 15297.536 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bacillus subtilis (bacteria) / References: UniProt: A0A063XCP1, UniProt: P19946*PLUS |
#9: Protein | Mass: 13774.806 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bacillus subtilis (bacteria) / References: UniProt: A0A063XCG5, UniProt: P20277*PLUS |
#10: Protein | Mass: 12993.829 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bacillus subtilis (bacteria) / References: UniProt: F5HRS9, UniProt: P46899*PLUS |
#11: Protein | Mass: 13416.853 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bacillus subtilis (bacteria) / References: UniProt: A0A063XHU6, UniProt: O31742*PLUS |
#12: Protein | Mass: 13537.993 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bacillus subtilis (bacteria) / References: UniProt: A0A063XFC1, UniProt: P55873*PLUS |
#13: Protein | Mass: 11296.081 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bacillus subtilis (bacteria) / References: UniProt: A0A063XIS2, UniProt: P26908*PLUS |
#14: Protein | Mass: 12481.608 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bacillus subtilis (bacteria) / References: UniProt: F5HRT3, UniProt: P42060*PLUS |
#15: Protein | Mass: 10978.813 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bacillus subtilis (bacteria) / References: UniProt: A0A063XB36, UniProt: P42924*PLUS |
#16: Protein | Mass: 11166.120 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bacillus subtilis (bacteria) / References: UniProt: F5HRS7, UniProt: P0CI78*PLUS |
#17: Protein | Mass: 10391.855 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bacillus subtilis (bacteria) / References: UniProt: A0A063XF22, UniProt: P05657*PLUS |
#18: Protein | Mass: 6650.795 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bacillus subtilis (bacteria) / References: UniProt: F5HRU6, UniProt: P19947*PLUS |
#19: Protein | Mass: 6745.073 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bacillus subtilis (bacteria) / References: UniProt: A0A3A5I502, UniProt: O34687*PLUS |
#20: Protein | Mass: 7728.029 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bacillus subtilis (bacteria) / References: UniProt: F5HRV8, UniProt: P12873*PLUS |
#21: Protein/peptide | Mass: 5271.332 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bacillus subtilis (bacteria) / References: UniProt: A0A063XCT1, UniProt: P05647*PLUS |
-Non-polymers , 1 types, 13 molecules
#22: Water | ChemComp-HOH / |
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-Details
Has ligand of interest | N |
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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: 45SRbgA ribosomal assembly intermediate / Type: RIBOSOME Details: 50S subunit assembly intermediate generated by RbgA depletion in cells. Entity ID: #1-#21 / Source: NATURAL |
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Molecular weight | Experimental value: NO |
Source (natural) | Organism: Bacillus subtilis (bacteria) / Strain: JH642 |
Buffer solution | pH: 7.5 Details: 20mM Tris-HCl pH 7.5, 10mM MgCl2, 50mM NH4Cl, 1mM DTT |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Grid material: COPPER / Grid mesh size: 200 divisions/in. / Grid type: C-flat-2/2 |
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % Details: Cryo-EM grids were prepared by applying a 3.6 microliters volume of the diluted samples to holey carbon grids (c-flat CF-2/2-2C-T) with a freshly applied additional layer of continuous thin ...Details: Cryo-EM grids were prepared by applying a 3.6 microliters volume of the diluted samples to holey carbon grids (c-flat CF-2/2-2C-T) with a freshly applied additional layer of continuous thin carbon (5-10nm). Grids were blotted for 3 seconds and with a blot force +1 |
-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 |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Average exposure time: 1 sec. / Electron dose: 40 e/Å2 / Detector mode: INTEGRATING / Film or detector model: FEI FALCON II (4k x 4k) / Num. of real images: 8950 |
-Processing
Software | Name: PHENIX / Version: 1.14_3260: / Classification: refinement | |||||||||||||||||||||
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EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | |||||||||||||||||||||
Particle selection | Num. of particles selected: 1339712 | |||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | |||||||||||||||||||||
3D reconstruction | Resolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 546297 / Symmetry type: POINT |