9P38 | pdb_00009p38

YsxC-GMPPNP treated 44.5SYsxC particles. Class 1.


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.50 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


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Literature

YsxC is a placeholder for ribosomal protein uL2 during 50S ribosomal subunit assembly.

Seffouh, A.Arpin, D.Basu, K.Ortega, J.

(2025) Nucleic Acids Res 53

  • DOI: https://doi.org/10.1093/nar/gkaf1071
  • Primary Citation of Related Structures:  
    9P38, 9P4I

  • PubMed Abstract: 

    The maturation of the functional core of the 50S ribosomal subunit in Bacillus subtilis is assisted by assembly factors that enhance the efficiency of the process. Two essential assembly factors, the GTPases RbgA and YphC, bind at or near the functional sites of the 50S subunit to promote the folding of ribosomal RNA helices that play key functional roles. YsxC is another GTPase involved in the maturation of the 50S subunit, whose function remains unknown. We demonstrate that YsxC aids 50S assembly through a drastically different mechanism. YsxC binds in the body of the 44.5S large ribosome assembly intermediate, occupying the site where uL2 binds and controls the timing in the folding of rRNA helices forming the binding site for uL2. It creates a "primordial" binding site that includes six out of the eleven rRNA helices forming the uL2 mature binding site. Once YsxC is released, uL2 binds to this "primordial" binding site, and the remaining helices that stabilize uL2 fold, and the entire region adopts the mature conformation. This role of YsxC functioning as a placeholder factor for ribosomal protein uL2 provides the first example of such a factor's involvement in the ribosome assembly process in bacteria.


  • Organizational Affiliation
    • Department of Anatomy and Cell Biology, McGill University, 3640 Rue University, Montreal, Quebec H3A 0C7, Canada.

Macromolecules

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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L3B [auth D]209Bacillus subtilisMutation(s): 0 
Gene Names: rplCB4122_1436B4417_1506ETA10_00730ETK61_00730ETK71_00730SC09_Contig26orf00060
UniProt
Find proteins for A0A063X745 (Bacillus subtilis)
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UniProt GroupA0A063X745
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L4C [auth E]207Bacillus subtilisMutation(s): 0 
Gene Names: rplDB4122_1435B4417_1507ETK71_00735SC09_Contig26orf00061
UniProt
Find proteins for A0A063X8U6 (Bacillus subtilis)
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UniProt GroupA0A063X8U6
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L13D [auth J]145Bacillus subtilisMutation(s): 0 
Gene Names: rplMB4122_1403B4417_1539D3797_020925ETA10_00900ETK61_00900ETK71_00900
UniProt
Find proteins for A0A063XCH0 (Bacillus subtilis)
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UniProt GroupA0A063XCH0
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L14E [auth K]122Bacillus subtilisMutation(s): 0 
Gene Names: rplNB4122_1427B4417_1515CJ481_04140D3797_021045ETA10_00780ETK61_00780ETK71_00780SC09_Contig26orf00070
UniProt
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L15F [auth L]146Bacillus subtilisMutation(s): 0 
Gene Names: rplOB4122_1418B4417_1524D3797_021000ETA10_00825ETK61_00825ETK71_00825
UniProt
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L17G [auth N]120Bacillus subtilisMutation(s): 0 
Gene Names: rplQB4122_1408B4417_1534CJ481_04045D3797_020950ETA10_00875ETK61_00875ETK71_00875SC09_Contig26orf00091
UniProt
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L19H [auth P]115Bacillus subtilisMutation(s): 0 
Gene Names: rplSB4122_2715B4417_3551CJ481_18820D3797_012615ETA10_08770ETK61_09045ETK71_08680SC09_Contig19orf01139
UniProt
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L20I [auth Q]118Bacillus subtilisMutation(s): 0 
Gene Names: rplTB4122_3557B4122_3823B4417_0515CJ481_11505D3797_006720ETA10_14785ETK61_15815ETK71_14810SC09_Contig17orf00528
UniProt
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L21J [auth R]102Bacillus subtilisMutation(s): 0 
Gene Names: rplUB4122_3686B4417_0614D3797_007210ETA10_14315ETK61_15045ETK71_14340SC09_Contig17orf00255
UniProt
Find proteins for A0A063XIS2 (Bacillus subtilis)
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L22K [auth S]113Bacillus subtilisMutation(s): 0 
Gene Names: rplVB4122_1432B4417_1510CJ481_04165D3797_021070ETA10_00755ETK61_00755ETK71_00755KS08_00695SC09_Contig26orf00065
UniProt
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L23L [auth T]95Bacillus subtilisMutation(s): 0 
Gene Names: rplWB4122_1434B4417_1508ETA10_00740ETK61_00740ETK71_00740KS08_00680SC09_Contig26orf00062
UniProt
Find proteins for A0A063XB36 (Bacillus subtilis)
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L24M [auth U]103Bacillus subtilisMutation(s): 0 
Gene Names: rplXB4122_1426B4417_1516CJ481_04135D3797_021040ETA10_00785ETK61_00785ETK71_00785SC09_Contig26orf00072
UniProt
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L30N [auth Z]59Bacillus subtilisMutation(s): 0 
Gene Names: rpmDB4122_1419B4417_1523CJ481_04100D3797_021005ETA10_00820ETK61_00820ETK71_00820KS08_00760SC09_Contig26orf00079
UniProt
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L32O [auth b]59Bacillus subtilisMutation(s): 0 
Gene Names: rpmFCJ481_19300D3797_013100ETA10_08290ETK61_08565ETK71_08200KS08_07655
UniProt
Find proteins for A0A3A5I502 (Bacillus subtilis)
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L29P [auth Y]66Bacillus subtilisMutation(s): 0 
Gene Names: rpmCB4122_1429B4417_1513CJ481_04150D3797_021055ETA10_00770ETK61_00770ETK71_00770KS08_00710SC09_Contig26orf00068
UniProt
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L34Q [auth d]44Bacillus subtilisMutation(s): 0 
Gene Names: rpmHCJ481_04925D3797_000040ETA10_21790ETK61_22795ETK71_21425KS08_20020
UniProt
Find proteins for A0A063XCT1 (Bacillus subtilis)
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
Probable GTP-binding protein EngBR [auth B]195Bacillus subtilisMutation(s): 0 
Gene Names: yihAengBB4122_3751J5227_02435P5633_09985SC09_Contig17orf00345
UniProt
Find proteins for A0A063XEZ9 (Bacillus subtilis)
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Entity ID: 1
MoleculeChains LengthOrganismImage
23S rRNA2,927Bacillus subtilis
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Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.50 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.21.2_5419
RECONSTRUCTIONcryoSPARC

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Canadian Institutes of Health Research (CIHR)Canada--

Revision History  (Full details and data files)

  • Version 1.0: 2025-11-12
    Type: Initial release