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 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

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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 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.

Macromolecule Content 

  • Total Structure Weight: 1,268.5 kDa 
  • Atom Count: 82,115 
  • Modeled Residue Count: 5,404 
  • Deposited Residue Count: 5,576 
  • Unique protein chains: 21
  • Unique nucleic acid chains: 2

Macromolecules


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Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
50S ribosomal protein L2277Bacillus subtilisMutation(s): 0 
Gene Names: rplB, B4122_1433, B4417_1509, CJ481_04175, D3797_021080, ETA10_00745, ETK61_00745, ETK71_00745, SC09_Contig26orf00064
UniProt
Find proteins for A0A063XCB6 (Bacillus subtilis)
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UniProt GroupA0A063XCB6
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Reference Sequence
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Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
50S ribosomal protein L3209Bacillus subtilisMutation(s): 0 
Gene Names: rplC, B4122_1436, B4417_1506, ETA10_00730, ETK61_00730, ETK71_00730, SC09_Contig26orf00060
UniProt
Find proteins for A0A063X745 (Bacillus subtilis)
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UniProt GroupA0A063X745
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Reference Sequence
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Entity ID: 5
MoleculeChains  Sequence LengthOrganismDetailsImage
50S ribosomal protein L4207Bacillus subtilisMutation(s): 0 
Gene Names: rplD, B4122_1435, B4417_1507, ETK71_00735, SC09_Contig26orf00061
UniProt
Find proteins for A0A063X8U6 (Bacillus subtilis)
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UniProt GroupA0A063X8U6
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Reference Sequence
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Entity ID: 6
MoleculeChains  Sequence LengthOrganismDetailsImage
50S ribosomal protein L6F [auth G]179Bacillus subtilisMutation(s): 0 
Gene Names: rplF, B4122_1422, B4417_1520, CJ481_04115, ETA10_00805, ETK61_00805, ETK71_00805, SC09_Contig26orf00076
UniProt
Find proteins for A0A063X781 (Bacillus subtilis)
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UniProt GroupA0A063X781
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Reference Sequence
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Entity ID: 7
MoleculeChains  Sequence LengthOrganismDetailsImage
50S ribosomal protein L13G [auth J]145Bacillus subtilisMutation(s): 0 
Gene Names: rplM, B4122_1403, B4417_1539, D3797_020925, ETA10_00900, ETK61_00900, ETK71_00900
UniProt
Find proteins for A0A063XCH0 (Bacillus subtilis)
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Reference Sequence
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Entity ID: 8
MoleculeChains  Sequence LengthOrganismDetailsImage
50S ribosomal protein L14H [auth K]122Bacillus subtilisMutation(s): 0 
Gene Names: rplN, B4122_1427, B4417_1515, CJ481_04140, D3797_021045, ETA10_00780, ETK61_00780, ETK71_00780, SC09_Contig26orf00070
UniProt
Find proteins for A0A063X754 (Bacillus subtilis)
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UniProt GroupA0A063X754
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Reference Sequence
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Entity ID: 9
MoleculeChains  Sequence LengthOrganismDetailsImage
50S ribosomal protein L15I [auth L]146Bacillus subtilisMutation(s): 0 
Gene Names: rplO, B4122_1418, B4417_1524, D3797_021000, ETA10_00825, ETK61_00825, ETK71_00825
UniProt
Find proteins for A0A063XCP1 (Bacillus subtilis)
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Entity ID: 10
MoleculeChains  Sequence LengthOrganismDetailsImage
50S ribosomal protein L17J [auth N]120Bacillus subtilisMutation(s): 0 
Gene Names: rplQ, B4122_1408, B4417_1534, CJ481_04045, D3797_020950, ETA10_00875, ETK61_00875, ETK71_00875, SC09_Contig26orf00091
UniProt
Find proteins for A0A063XCG5 (Bacillus subtilis)
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Reference Sequence
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Entity ID: 11
MoleculeChains  Sequence LengthOrganismDetailsImage
50S ribosomal protein L18K [auth O]120Bacillus subtilisMutation(s): 0 
Gene Names: rplR, B4122_1421, B4417_1521, ETA10_00810, ETK61_00810, ETK71_00810, SC09_Contig26orf00077
UniProt
Find proteins for F5HRS9 (Bacillus subtilis)
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Entity ID: 12
MoleculeChains  Sequence LengthOrganismDetailsImage
50S ribosomal protein L19L [auth P]115Bacillus subtilisMutation(s): 0 
Gene Names: rplS, B4122_2715, B4417_3551, CJ481_18820, D3797_012615, ETA10_08770, ETK61_09045, ETK71_08680, SC09_Contig19orf01139
UniProt
Find proteins for A0A063XHU6 (Bacillus subtilis)
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Entity ID: 13
MoleculeChains  Sequence LengthOrganismDetailsImage
50S ribosomal protein L20M [auth Q]118Bacillus subtilisMutation(s): 0 
Gene Names: rplT, B4122_3557, B4122_3823, B4417_0515, CJ481_11505, D3797_006720, ETA10_14785, ETK61_15815, ETK71_14810, SC09_Contig17orf00528
UniProt
Find proteins for A0A063XFC1 (Bacillus subtilis)
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Reference Sequence
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Entity ID: 14
MoleculeChains  Sequence LengthOrganismDetailsImage
50S ribosomal protein L21N [auth R]102Bacillus subtilisMutation(s): 0 
Gene Names: rplU, B4122_3686, B4417_0614, D3797_007210, ETA10_14315, ETK61_15045, ETK71_14340, SC09_Contig17orf00255
UniProt
Find proteins for A0A063XIS2 (Bacillus subtilis)
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Reference Sequence
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Entity ID: 15
MoleculeChains  Sequence LengthOrganismDetailsImage
50S ribosomal protein L22O [auth S]113Bacillus subtilisMutation(s): 0 
Gene Names: rplV, B4122_1432, B4417_1510, CJ481_04165, D3797_021070, ETA10_00755, ETK61_00755, ETK71_00755, KS08_00695, SC09_Contig26orf00065
UniProt
Find proteins for F5HRT3 (Bacillus subtilis)
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Reference Sequence
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Entity ID: 16
MoleculeChains  Sequence LengthOrganismDetailsImage
50S ribosomal protein L23P [auth T]95Bacillus subtilisMutation(s): 0 
Gene Names: rplW, B4122_1434, B4417_1508, ETA10_00740, ETK61_00740, ETK71_00740, KS08_00680, SC09_Contig26orf00062
UniProt
Find proteins for A0A063XB36 (Bacillus subtilis)
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Reference Sequence
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Entity ID: 17
MoleculeChains  Sequence LengthOrganismDetailsImage
50S ribosomal protein L24Q [auth U]103Bacillus subtilisMutation(s): 0 
Gene Names: rplX, B4122_1426, B4417_1516, CJ481_04135, D3797_021040, ETA10_00785, ETK61_00785, ETK71_00785, SC09_Contig26orf00072
UniProt
Find proteins for F5HRS7 (Bacillus subtilis)
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Reference Sequence
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Entity ID: 18
MoleculeChains  Sequence LengthOrganismDetailsImage
50S ribosomal protein L27R [auth V]94Bacillus subtilisMutation(s): 0 
Gene Names: rpmA, B4122_3684, B4417_0616, CJ481_12025, D3797_007220, ETA10_14305, ETK61_15035, ETK71_14330, SC09_Contig17orf00253
UniProt
Find proteins for A0A063XF22 (Bacillus subtilis)
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UniProt GroupA0A063XF22
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Reference Sequence
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Entity ID: 19
MoleculeChains  Sequence LengthOrganismDetailsImage
50S ribosomal protein L29S [auth Y]66Bacillus subtilisMutation(s): 0 
Gene Names: rpmC, B4122_1429, B4417_1513, CJ481_04150, D3797_021055, ETA10_00770, ETK61_00770, ETK71_00770, KS08_00710, SC09_Contig26orf00068
UniProt
Find proteins for F5HRV8 (Bacillus subtilis)
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Entity ID: 20
MoleculeChains  Sequence LengthOrganismDetailsImage
50S ribosomal protein L30T [auth Z]59Bacillus subtilisMutation(s): 0 
Gene Names: rpmD, B4122_1419, B4417_1523, CJ481_04100, D3797_021005, ETA10_00820, ETK61_00820, ETK71_00820, KS08_00760, SC09_Contig26orf00079
UniProt
Find proteins for F5HRU6 (Bacillus subtilis)
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UniProt GroupF5HRU6
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Reference Sequence
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Entity ID: 21
MoleculeChains  Sequence LengthOrganismDetailsImage
50S ribosomal protein L32U [auth b]59Bacillus subtilisMutation(s): 0 
Gene Names: rpmF, CJ481_19300, D3797_013100, ETA10_08290, ETK61_08565, ETK71_08200, KS08_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: rpmH, CJ481_04925, D3797_000040, ETA10_21790, ETK61_22795, ETK71_21425, KS08_20020
UniProt
Find proteins for A0A063XCT1 (Bacillus subtilis)
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Reference Sequence
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Entity ID: 23
MoleculeChains  Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein bL36W [auth f]37Bacillus subtilisMutation(s): 0 
Gene Names: rpmJ, B4122_1412, J5227_17960, P5633_02205, QL281_13020, SC09_Contig26orf00087
UniProt
Find proteins for A0A063XCR0 (Bacillus subtilis)
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UniProt GroupA0A063XCR0
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Reference Sequence
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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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Reference Sequence

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