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- PDB-9p38: YsxC-GMPPNP treated 44.5SYsxC particles. Class 1. -

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Basic information

Entry
Database: PDB / ID: 9p38
TitleYsxC-GMPPNP treated 44.5SYsxC particles. Class 1.
Components
  • (50S ribosomal protein ...) x 16
  • 23S rRNA
  • Probable GTP-binding protein EngB
KeywordsRIBOSOME / 44.5S particle / YsxC
Function / homology
Function and homology information


division septum assembly / large ribosomal subunit / ribosomal large subunit assembly / large ribosomal subunit rRNA binding / cytosolic large ribosomal subunit / negative regulation of translation / rRNA binding / structural constituent of ribosome / ribosome / translation ...division septum assembly / large ribosomal subunit / ribosomal large subunit assembly / large ribosomal subunit rRNA binding / cytosolic large ribosomal subunit / negative regulation of translation / rRNA binding / structural constituent of ribosome / ribosome / translation / ribonucleoprotein complex / mRNA binding / GTP binding / metal ion binding / cytoplasm / cytosol
Similarity search - Function
GTP-binding protein, ribosome biogenesis, YsxC / EngB-type guanine nucleotide-binding (G) domain profile. / EngB-type guanine nucleotide-binding (G) domain / 50S ribosome-binding GTPase / GTP binding domain / Ribosomal protein L21, conserved site / Ribosomal protein L21 signature. / : / Ribosomal protein L17 signature. / Ribosomal protein L32p, bacterial type ...GTP-binding protein, ribosome biogenesis, YsxC / EngB-type guanine nucleotide-binding (G) domain profile. / EngB-type guanine nucleotide-binding (G) domain / 50S ribosome-binding GTPase / GTP binding domain / Ribosomal protein L21, conserved site / Ribosomal protein L21 signature. / : / Ribosomal protein L17 signature. / Ribosomal protein L32p, bacterial type / : / : / Ribosomal protein L19, conserved site / Ribosomal protein L19 signature. / Ribosomal protein L20 signature. / Ribosomal protein L22, bacterial/chloroplast-type / Ribosomal protein L14P, bacterial-type / Ribosomal protein L34, conserved site / Ribosomal protein L34 signature. / Ribosomal protein L30, bacterial-type / : / Ribosomal protein L20 / Ribosomal L32p protein family / Ribosomal protein L19 / Ribosomal protein L20 / Ribosomal protein L20, C-terminal / Ribosomal protein L19 / Ribosomal protein L19 superfamily / Ribosomal protein L21 / Ribosomal protein L32p / Large ribosomal subunit protein uL24, C-terminal domain / Ribosomal protein L17 / Ribosomal protein L17 superfamily / Ribosomal protein L17 / Ribosomal protein L21-like / L21-like superfamily / Ribosomal prokaryotic L21 protein / Ribosomal protein L34 / Ribosomal protein L34 / Ribosomal protein L24 / Ribosomal protein L3, bacterial/organelle-type / Ribosomal protein L15, bacterial-type / 50S ribosomal protein uL4 / Ribosomal protein L13, bacterial-type / Ribosomal protein L23/L25, conserved site / Ribosomal protein L23 signature. / Ribosomal protein L30, conserved site / Ribosomal protein L30 signature. / Ribosomal protein L29, conserved site / Ribosomal protein L29 signature. / Ribosomal protein L15, conserved site / Ribosomal protein L15 signature. / Small GTP-binding protein domain / Ribosomal protein L13 signature. / Ribosomal protein L13, conserved site / Ribosomal protein L22/L17, conserved site / Ribosomal protein L22 signature. / Ribosomal protein L14P, conserved site / Ribosomal protein L14 signature. / Ribosomal L29 protein / Ribosomal protein L29/L35 / Ribosomal protein L29/L35 superfamily / Ribosomal protein L24 signature. / Ribosomal protein L24/L26, conserved site / KOW (Kyprides, Ouzounis, Woese) motif. / Ribosomal protein L23 / Ribosomal protein L13 / Ribosomal protein L13 / Ribosomal protein L13 superfamily / Ribosomal protein L30, ferredoxin-like fold domain / Ribosomal protein L30p/L7e / Ribosomal protein L25/L23 / Ribosomal protein L30, ferredoxin-like fold domain superfamily / Ribosomal protein L15 / Ribosomal proteins 50S-L15, 50S-L18e, 60S-L27A / Ribosomal protein L14p/L23e / Ribosomal protein L14P / Ribosomal protein L14 superfamily / Ribosomal protein L14p/L23e / Ribosomal protein L22/L17 / Ribosomal protein L22p/L17e / Ribosomal protein L22/L17 superfamily / Ribosomal protein L26/L24, KOW domain / Ribosomal protein L3, conserved site / Ribosomal protein L3 signature. / Ribosomal protein L3 / Ribosomal protein L3 / Ribosomal protein L18e/L15P / Ribosomal L18e/L15P superfamily / Ribosomal protein L4/L1e / Ribosomal protein L4 domain superfamily / Ribosomal protein L4/L1 family / Translation protein SH3-like domain superfamily / Ribosomal protein L23/L15e core domain superfamily / Zinc-binding ribosomal protein / KOW motif / KOW / Translation protein, beta-barrel domain superfamily / Ribosomal protein L2, domain 2 / Nucleotide-binding alpha-beta plait domain superfamily
Similarity search - Domain/homology
: / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Large ribosomal subunit protein uL3 / Large ribosomal subunit protein uL14 / Large ribosomal subunit protein uL4 / Large ribosomal subunit protein uL23 / Large ribosomal subunit protein bL17 ...: / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Large ribosomal subunit protein uL3 / Large ribosomal subunit protein uL14 / Large ribosomal subunit protein uL4 / Large ribosomal subunit protein uL23 / Large ribosomal subunit protein bL17 / Large ribosomal subunit protein uL13 / Large ribosomal subunit protein uL15 / Large ribosomal subunit protein bL34 / Probable GTP-binding protein EngB / Large ribosomal subunit protein bL20 / Large ribosomal subunit protein bL19 / Large ribosomal subunit protein bL21 / Large ribosomal subunit protein bL32 / Large ribosomal subunit protein uL24 / Large ribosomal subunit protein uL22 / Large ribosomal subunit protein uL30 / Large ribosomal subunit protein uL29
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.5 Å
AuthorsOrtega, J. / Seffouh, A.
Funding support Canada, 1items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR) Canada
CitationJournal: Nucleic Acids Res / Year: 2025
Title: YsxC is a placeholder for ribosomal protein uL2 during 50S ribosomal subunit assembly.
Authors: Amal Seffouh / Dominic Arpin / Kaustuv Basu / Joaquin Ortega /
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 ...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.
History
DepositionJun 13, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 12, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 23S rRNA
D: 50S ribosomal protein L3
E: 50S ribosomal protein L4
J: 50S ribosomal protein L13
K: 50S ribosomal protein L14
L: 50S ribosomal protein L15
N: 50S ribosomal protein L17
P: 50S ribosomal protein L19
Q: 50S ribosomal protein L20
R: 50S ribosomal protein L21
S: 50S ribosomal protein L22
T: 50S ribosomal protein L23
U: 50S ribosomal protein L24
Z: 50S ribosomal protein L30
b: 50S ribosomal protein L32
Y: 50S ribosomal protein L29
d: 50S ribosomal protein L34
B: Probable GTP-binding protein EngB


Theoretical massNumber of molelcules
Total (without water)1,174,54918
Polymers1,174,54918
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

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50S ribosomal protein ... , 16 types, 16 molecules DEJKLNPQRSTUZbYd

#2: Protein 50S ribosomal protein L3


Mass: 22723.348 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria)
Gene: rplC, B4122_1436, B4417_1506, ETA10_00730, ETK61_00730, ETK71_00730, SC09_Contig26orf00060
Production host: Bacillus subtilis (bacteria) / References: UniProt: A0A063X745
#3: Protein 50S ribosomal protein L4


Mass: 22424.951 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria)
Gene: rplD, B4122_1435, B4417_1507, ETK71_00735, SC09_Contig26orf00061
Production host: Bacillus subtilis (bacteria) / References: UniProt: A0A063X8U6
#4: Protein 50S ribosomal protein L13


Mass: 16407.104 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria)
Gene: rplM, B4122_1403, B4417_1539, D3797_020925, ETA10_00900, ETK61_00900, ETK71_00900
Production host: Bacillus subtilis (bacteria) / References: UniProt: A0A063XCH0
#5: Protein 50S ribosomal protein L14


Mass: 13175.288 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria)
Gene: rplN, B4122_1427, B4417_1515, CJ481_04140, D3797_021045, ETA10_00780, ETK61_00780, ETK71_00780, SC09_Contig26orf00070
Production host: Bacillus subtilis (bacteria) / References: UniProt: A0A063X754
#6: Protein 50S ribosomal protein L15


Mass: 15410.694 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria)
Gene: rplO, B4122_1418, B4417_1524, D3797_021000, ETA10_00825, ETK61_00825, ETK71_00825
Production host: Bacillus subtilis (bacteria) / References: UniProt: A0A063XCP1
#7: Protein 50S ribosomal protein L17


Mass: 13774.806 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria)
Gene: rplQ, B4122_1408, B4417_1534, CJ481_04045, D3797_020950, ETA10_00875, ETK61_00875, ETK71_00875, SC09_Contig26orf00091
Production host: Bacillus subtilis (bacteria) / References: UniProt: A0A063XCG5
#8: Protein 50S ribosomal protein L19


Mass: 13416.853 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria)
Gene: rplS, B4122_2715, B4417_3551, CJ481_18820, D3797_012615, ETA10_08770, ETK61_09045, ETK71_08680, SC09_Contig19orf01139
Production host: Bacillus subtilis (bacteria) / References: UniProt: A0A063XHU6
#9: Protein 50S ribosomal protein L20


Mass: 13537.993 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria)
Gene: rplT, B4122_3557, B4122_3823, B4417_0515, CJ481_11505, D3797_006720, ETA10_14785, ETK61_15815, ETK71_14810, SC09_Contig17orf00528
Production host: Bacillus subtilis (bacteria) / References: UniProt: A0A063XFC1
#10: Protein 50S ribosomal protein L21


Mass: 11296.081 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria)
Gene: rplU, B4122_3686, B4417_0614, D3797_007210, ETA10_14315, ETK61_15045, ETK71_14340, SC09_Contig17orf00255
Production host: Bacillus subtilis (bacteria) / References: UniProt: A0A063XIS2
#11: Protein 50S ribosomal protein L22


Mass: 12481.608 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria)
Gene: rplV, B4122_1432, B4417_1510, CJ481_04165, D3797_021070, ETA10_00755, ETK61_00755, ETK71_00755, KS08_00695, SC09_Contig26orf00065
Production host: Bacillus subtilis (bacteria) / References: UniProt: F5HRT3
#12: Protein 50S ribosomal protein L23


Mass: 10978.813 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria)
Gene: rplW, B4122_1434, B4417_1508, ETA10_00740, ETK61_00740, ETK71_00740, KS08_00680, SC09_Contig26orf00062
Production host: Bacillus subtilis (bacteria) / References: UniProt: A0A063XB36
#13: Protein 50S ribosomal protein L24


Mass: 11166.120 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria)
Gene: rplX, B4122_1426, B4417_1516, CJ481_04135, D3797_021040, ETA10_00785, ETK61_00785, ETK71_00785, SC09_Contig26orf00072
Production host: Bacillus subtilis (bacteria) / References: UniProt: F5HRS7
#14: Protein 50S ribosomal protein L30


Mass: 6650.795 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria)
Gene: rpmD, B4122_1419, B4417_1523, CJ481_04100, D3797_021005, ETA10_00820, ETK61_00820, ETK71_00820, KS08_00760, SC09_Contig26orf00079
Production host: Bacillus subtilis (bacteria) / References: UniProt: F5HRU6
#15: Protein 50S ribosomal protein L32


Mass: 6745.073 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria)
Gene: rpmF, CJ481_19300, D3797_013100, ETA10_08290, ETK61_08565, ETK71_08200, KS08_07655
Production host: Bacillus subtilis (bacteria) / References: UniProt: A0A3A5I502
#16: Protein 50S ribosomal protein L29


Mass: 7728.029 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria)
Gene: rpmC, B4122_1429, B4417_1513, CJ481_04150, D3797_021055, ETA10_00770, ETK61_00770, ETK71_00770, KS08_00710, SC09_Contig26orf00068
Production host: Bacillus subtilis (bacteria) / References: UniProt: F5HRV8
#17: Protein/peptide 50S ribosomal protein L34


Mass: 5271.332 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria)
Gene: rpmH, CJ481_04925, D3797_000040, ETA10_21790, ETK61_22795, ETK71_21425, KS08_20020
Production host: Bacillus subtilis (bacteria) / References: UniProt: A0A063XCT1

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RNA chain / Protein , 2 types, 2 molecules AB

#18: Protein Probable GTP-binding protein EngB


Mass: 22060.414 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria)
Gene: yihA, engB, B4122_3751, J5227_02435, P5633_09985, SC09_Contig17orf00345
Production host: Bacillus subtilis (bacteria) / References: UniProt: A0A063XEZ9
#1: RNA chain 23S rRNA


Mass: 949300.062 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Production host: Bacillus subtilis (bacteria) / References: GenBank: 2210155072

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Details

Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: YsxC-GMPPNP treated 44.5SYsxC particles. Class 1. / Type: RIBOSOME / Entity ID: all / Source: NATURAL
Source (natural)Organism: Bacillus subtilis (bacteria)
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2500 nm / Nominal defocus min: 1000 nm
Image recordingElectron dose: 40 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

EM software
IDNameVersionCategory
1cryoSPARCparticle selection
2PHENIX1.21.2_5419model refinement
13cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 873768 / Symmetry type: POINT
RefinementHighest resolution: 2.5 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00566341
ELECTRON MICROSCOPYf_angle_d0.694100118
ELECTRON MICROSCOPYf_dihedral_angle_d24.24233365
ELECTRON MICROSCOPYf_chiral_restr0.04112938
ELECTRON MICROSCOPYf_plane_restr0.0054737

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