9P4I | pdb_00009p4i

YsxC-GTP treated 44.5SYsxC particles. Class 5.


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.80 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


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: 3
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L2277Bacillus subtilisMutation(s): 0 
Gene Names: rplBB4122_1433B4417_1509CJ481_04175D3797_021080ETA10_00745ETK61_00745ETK71_00745SC09_Contig26orf00064
UniProt
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UniProt GroupA0A063XCB6
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L3209Bacillus subtilisMutation(s): 0 
Gene Names: rplCB4122_1436B4417_1506ETA10_00730ETK61_00730ETK71_00730SC09_Contig26orf00060
UniProt
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UniProt GroupA0A063X745
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L4207Bacillus subtilisMutation(s): 0 
Gene Names: rplDB4122_1435B4417_1507ETK71_00735SC09_Contig26orf00061
UniProt
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UniProt GroupA0A063X8U6
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L6F [auth G]179Bacillus subtilisMutation(s): 0 
Gene Names: rplFB4122_1422B4417_1520CJ481_04115ETA10_00805ETK61_00805ETK71_00805SC09_Contig26orf00076
UniProt
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UniProt GroupA0A063X781
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L13G [auth J]145Bacillus subtilisMutation(s): 0 
Gene Names: rplMB4122_1403B4417_1539D3797_020925ETA10_00900ETK61_00900ETK71_00900
UniProt
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L14H [auth K]122Bacillus subtilisMutation(s): 0 
Gene Names: rplNB4122_1427B4417_1515CJ481_04140D3797_021045ETA10_00780ETK61_00780ETK71_00780SC09_Contig26orf00070
UniProt
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L15I [auth L]146Bacillus subtilisMutation(s): 0 
Gene Names: rplOB4122_1418B4417_1524D3797_021000ETA10_00825ETK61_00825ETK71_00825
UniProt
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L17J [auth N]120Bacillus subtilisMutation(s): 0 
Gene Names: rplQB4122_1408B4417_1534CJ481_04045D3797_020950ETA10_00875ETK61_00875ETK71_00875SC09_Contig26orf00091
UniProt
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L18K [auth O]120Bacillus subtilisMutation(s): 0 
Gene Names: rplRB4122_1421B4417_1521ETA10_00810ETK61_00810ETK71_00810SC09_Contig26orf00077
UniProt
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L19L [auth P]115Bacillus subtilisMutation(s): 0 
Gene Names: rplSB4122_2715B4417_3551CJ481_18820D3797_012615ETA10_08770ETK61_09045ETK71_08680SC09_Contig19orf01139
UniProt
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L20M [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: 14
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L21N [auth R]102Bacillus subtilisMutation(s): 0 
Gene Names: rplUB4122_3686B4417_0614D3797_007210ETA10_14315ETK61_15045ETK71_14340SC09_Contig17orf00255
UniProt
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L22O [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: 16
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L23P [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: 17
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L24Q [auth U]103Bacillus subtilisMutation(s): 0 
Gene Names: rplXB4122_1426B4417_1516CJ481_04135D3797_021040ETA10_00785ETK61_00785ETK71_00785SC09_Contig26orf00072
UniProt
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L27R [auth V]94Bacillus subtilisMutation(s): 0 
Gene Names: rpmAB4122_3684B4417_0616CJ481_12025D3797_007220ETA10_14305ETK61_15035ETK71_14330SC09_Contig17orf00253
UniProt
Find proteins for A0A063XF22 (Bacillus subtilis)
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L29S [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: 20
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L30T [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: 21
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L32U [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: 22
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L34V [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: 23
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein bL36W [auth f]37Bacillus subtilisMutation(s): 0 
Gene Names: rpmJB4122_1412J5227_17960P5633_02205QL281_13020SC09_Contig26orf00087
UniProt
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Entity ID: 1
MoleculeChains LengthOrganismImage
23S rRNA2,927Bacillus subtilis
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Entity ID: 2
MoleculeChains LengthOrganismImage
5S rRNA119Bacillus subtilis
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Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.80 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