6PVK

Bacterial 45SRbgA ribosomal particle class A


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.40 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structural consequences of the interaction of RbgA with a 50S ribosomal subunit assembly intermediate.

Seffouh, A.Jain, N.Jahagirdar, D.Basu, K.Razi, A.Ni, X.Guarne, A.Britton, R.A.Ortega, J.

(2019) Nucleic Acids Res 47: 10414-10425

  • DOI: 10.1093/nar/gkz770
  • Primary Citation of Related Structures:  
    6PPF, 6PPK, 6PVK

  • PubMed 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. Homologs of this protein are also implicated in the assembly of the large subunit of the mitochondrial and eukaryotic ribosome ...

    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.


    Organizational Affiliation

    Department of Anatomy and Cell Biology, McGill University, Montreal, Quebec H3A 0C7, Canada.



Macromolecules

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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L2B [auth C]277Bacillus subtilisMutation(s): 0 
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Find proteins for P42919 (Bacillus subtilis (strain 168))
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L3C [auth D]209Bacillus subtilisMutation(s): 0 
UniProt
Find proteins for P42920 (Bacillus subtilis (strain 168))
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L4D [auth E]207Bacillus subtilisMutation(s): 0 
UniProt
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L13E [auth J]145Bacillus subtilisMutation(s): 0 
UniProt
Find proteins for P70974 (Bacillus subtilis (strain 168))
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L14F [auth K]122Bacillus subtilisMutation(s): 0 
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L15G [auth L]145Bacillus subtilisMutation(s): 0 
UniProt
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Entity ID: 8
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50S ribosomal protein L17H [auth N]120Bacillus subtilisMutation(s): 0 
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L19I [auth P]115Bacillus subtilisMutation(s): 0 
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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L20J [auth Q]118Bacillus subtilisMutation(s): 0 
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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L21K [auth R]102Bacillus subtilisMutation(s): 0 
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Find proteins for P26908 (Bacillus subtilis (strain 168))
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Entity ID: 12
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50S ribosomal protein L22L [auth S]113Bacillus subtilisMutation(s): 0 
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Entity ID: 13
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L23M [auth T]95Bacillus subtilisMutation(s): 0 
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Entity ID: 14
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50S ribosomal protein L24N [auth U]103Bacillus subtilisMutation(s): 0 
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Entity ID: 15
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50S ribosomal protein L32O [auth b]59Bacillus subtilisMutation(s): 0 
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Find proteins for O34687 (Bacillus subtilis (strain 168))
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Entity ID: 16
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L29P [auth Y]66Bacillus subtilisMutation(s): 0 
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Entity ID: 17
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L34Q [auth d]44Bacillus subtilisMutation(s): 0 
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Find proteins for P05647 (Bacillus subtilis (strain 168))
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  • Reference Sequence
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Entity ID: 1
MoleculeChainsLengthOrganismImage
23S rRNAA2927Bacillus subtilis
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Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.40 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Canadian Institutes of Health Research (CIHR)CanadaPJT-153044
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesR01GM110248

Revision History  (Full details and data files)

  • Version 1.0: 2019-09-18
    Type: Initial release
  • Version 1.1: 2019-12-18
    Changes: Author supporting evidence
  • Version 1.2: 2021-02-03
    Changes: Database references