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- PDB-9bs0: YphC-treated 45SYphC particle. Class 5 -

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Basic information

Entry
Database: PDB / ID: 9bs0
TitleYphC-treated 45SYphC particle. Class 5
Components
  • (Large ribosomal subunit protein ...) x 22
  • 23S rRNA
  • 5S rRNA
  • GTPase Der
KeywordsRIBOSOME / ribosome assembly / YphC
Function / homology
Function and homology information


positive regulation of rRNA processing / nucleoid / rRNA processing / regulation of translation / ribosome biogenesis / large ribosomal subunit / transferase activity / ribosome binding / 5S rRNA binding / ribosomal large subunit assembly ...positive regulation of rRNA processing / nucleoid / rRNA processing / regulation of translation / ribosome biogenesis / large ribosomal subunit / transferase activity / ribosome binding / 5S rRNA binding / ribosomal large subunit assembly / large ribosomal subunit rRNA binding / cytosolic large ribosomal subunit / cytoplasmic translation / tRNA binding / negative regulation of translation / rRNA binding / ribosome / structural constituent of ribosome / translation / ribonucleoprotein complex / mRNA binding / GTP binding / DNA binding / RNA binding / cytoplasm
Similarity search - Function
EngA-type guanine nucleotide-binding (G) domain / EngA-type guanine nucleotide-binding (G) domain profile. / GTP-binding protein EngA / GTPase Der, C-terminal KH-domain-like / KH-domain-like of EngA bacterial GTPase enzymes, C-terminal / 50S ribosome-binding GTPase / Ribosomal protein L1, bacterial-type / GTP binding domain / Ribosomal protein L1, conserved site / Ribosomal protein L1 signature. ...EngA-type guanine nucleotide-binding (G) domain / EngA-type guanine nucleotide-binding (G) domain profile. / GTP-binding protein EngA / GTPase Der, C-terminal KH-domain-like / KH-domain-like of EngA bacterial GTPase enzymes, C-terminal / 50S ribosome-binding GTPase / Ribosomal protein L1, bacterial-type / GTP binding domain / Ribosomal protein L1, conserved site / Ribosomal protein L1 signature. / Ribosomal protein L1 / Ribosomal protein L1, 3-layer alpha/beta-sandwich / Ribosomal protein L1-like / Ribosomal protein L1/ribosomal biogenesis protein / Ribosomal protein L1p/L10e family / Ribosomal protein L21, conserved site / Ribosomal protein L21 signature. / Ribosomal protein L6, conserved site / Ribosomal protein L6 signature 1. / : / Ribosomal protein L17 signature. / Ribosomal protein L32p, bacterial type / Ribosomal protein L33, conserved site / Ribosomal protein L33 signature. / : / Ribosomal protein L18, bacterial-type / : / Ribosomal protein L6, bacterial-type / Ribosomal protein L19, conserved site / Ribosomal protein L19 signature. / Ribosomal protein L27, conserved site / Ribosomal protein L27 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 L2, bacterial/organellar-type / Ribosomal protein L33 / Ribosomal protein L33 / Ribosomal protein L33 superfamily / Ribosomal protein L18 / Ribosomal L18 of archaea, bacteria, mitoch. and chloroplast / Ribosomal protein L30, bacterial-type / : / Ribosomal protein L27 / Ribosomal L27 protein / Ribosomal protein L20 / Ribosomal L32p protein family / Ribosomal protein L19 / Ribosomal protein L19 / Ribosomal protein L20 / Ribosomal protein L20, C-terminal / Ribosomal protein L19 superfamily / Ribosomal protein L21 / Ribosomal protein L32p / Ribosomal protein L17 / Ribosomal protein L17 superfamily / Ribosomal protein L17 / Ribosomal proteins 50S L24/mitochondrial 39S L24 / Ribosomal protein L21-like / L21-like superfamily / Ribosomal prokaryotic L21 protein / Ribosomal protein L34 / Ribosomal protein L34 / Ribosomal protein L24 / Ribosomal protein L13, bacterial-type / Ribosomal protein L3, bacterial/organelle-type / Ribosomal protein L15, bacterial-type / 50S ribosomal protein uL4 / Ribosomal protein L23/L25, conserved site / Ribosomal protein L23 signature. / Ribosomal protein L30, conserved site / Ribosomal protein L30 signature. / Ribosomal protein L2 signature. / Ribosomal protein L29, conserved site / Ribosomal protein L29 signature. / Ribosomal protein L2, conserved site / Ribosomal protein L15, conserved site / Ribosomal protein L15 signature. / Ribosomal protein L6, alpha-beta domain / Ribosomal protein L6 / Ribosomal protein L6 / Small GTP-binding protein domain / Ribosomal protein L6, alpha-beta domain superfamily / Ribosomal protein L13 signature. / Ribosomal protein L2, domain 3 / Ribosomal protein L13, conserved site / K homology domain-like, alpha/beta / 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 Proteins L2, C-terminal domain / Ribosomal protein L2, C-terminal / Ribosomal Proteins L2, C-terminal domain / Ribosomal Proteins L2, RNA binding domain
Similarity search - Domain/homology
PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER / : / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Large ribosomal subunit protein bL19 / Large ribosomal subunit protein bL32 / Large ribosomal subunit protein bL34 ...PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER / : / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Large ribosomal subunit protein bL19 / Large ribosomal subunit protein bL32 / Large ribosomal subunit protein bL34 / Large ribosomal subunit protein bL27 / Large ribosomal subunit protein uL24 / Large ribosomal subunit protein uL29 / Large ribosomal subunit protein uL14 / Large ribosomal subunit protein uL15 / Large ribosomal subunit protein uL30 / Large ribosomal subunit protein bL17 / Large ribosomal subunit protein bL21 / Large ribosomal subunit protein uL22 / Large ribosomal subunit protein uL2 / Large ribosomal subunit protein uL3 / Large ribosomal subunit protein uL4 / Large ribosomal subunit protein uL23 / Large ribosomal subunit protein uL6 / Large ribosomal subunit protein uL18 / GTPase Der / Large ribosomal subunit protein bL20 / Large ribosomal subunit protein bL33A / Large ribosomal subunit protein uL13 / Large ribosomal subunit protein uL1
Similarity search - Component
Biological speciesBacillus subtilis subsp. subtilis str. 168 (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.3 Å
AuthorsArpin, D. / Ortega, J.
Funding support Canada, 1items
OrganizationGrant numberCountry
Natural Sciences and Engineering Research Council (NSERC, Canada) Canada
CitationJournal: Nucleic Acids Res / Year: 2025
Title: The binding of RbgA to a critical 50S assembly intermediate facilitates YphC function in bacterial ribosomal assembly.
Authors: Dominic Arpin / Armando Palacios / Kaustuv Basu / Joaquin Ortega /
Abstract: The intricate process of 50S ribosomal subunit assembly in Bacillus subtilis involves multiple parallel pathways converging into a crucial intermediate known as the 45S particle. RbgA and YphC, play ...The intricate process of 50S ribosomal subunit assembly in Bacillus subtilis involves multiple parallel pathways converging into a crucial intermediate known as the 45S particle. RbgA and YphC, play pivotal roles in completing the maturation of the functional sites in the 45S particle. In this work, we found that RbgA and YphC can independently bind the 45S particle with high affinity, but when RbgA binds first to the particle, it significantly increases the binding affinity of YphC. Using cryo-electron microscopy, we determined that the changes exerted by RbgA and YphC when binding independently closely resemble those observed when the two factors bind to the 45S particle simultaneously. However, the structural analysis revealed that RbgA binding causes a conformational change that uncovers the binding site for YphC, thus increasing its binding affinity. We concluded that the functional interplay between RbgA and YphC primarily revolves around one factor promoting the binding of the other, rather than the binding of the two factors inducing entirely new conformational changes compared with those induced by the factors individually. These results highlight the synergic mechanism between two essential assembly factors, underscoring the intricate mechanism bacteria use to maximize the efficiency of the ribosome assembly process.
History
DepositionMay 12, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 25, 2024Provider: repository / Type: Initial release
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Revision 1.1Jan 29, 2025Group: Data collection / Database references / Category: citation / em_admin
Item: _citation.journal_volume / _citation.year / _em_admin.last_update
Revision 1.2May 14, 2025Group: Data collection / Category: em_admin / em_software / Item: _em_admin.last_update / _em_software.name
Revision 1.1May 14, 2025Data content type: EM metadata / Data content type: EM metadata / EM metadata / Group: Data processing / Experimental summary / Data content type: EM metadata / EM metadata / Category: em_admin / em_software / Data content type: EM metadata / EM metadata / Item: _em_admin.last_update / _em_software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 23S rRNA
B: 5S rRNA
C: Large ribosomal subunit protein uL2
D: Large ribosomal subunit protein uL3
E: Large ribosomal subunit protein uL4
F: Large ribosomal subunit protein uL6
G: Large ribosomal subunit protein uL13
H: Large ribosomal subunit protein uL14
I: Large ribosomal subunit protein uL15
J: Large ribosomal subunit protein bL17
K: Large ribosomal subunit protein bL19
L: Large ribosomal subunit protein bL20
M: Large ribosomal subunit protein bL21
N: Large ribosomal subunit protein uL22
O: Large ribosomal subunit protein uL23
P: Large ribosomal subunit protein uL24
Q: Large ribosomal subunit protein bL27
R: Large ribosomal subunit protein uL29
S: Large ribosomal subunit protein uL30
T: Large ribosomal subunit protein bL32
U: Large ribosomal subunit protein bL34
V: Large ribosomal subunit protein uL18
W: GTPase Der
Z: Large ribosomal subunit protein bL33A
Y: Large ribosomal subunit protein uL1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,345,01127
Polymers1,343,96625
Non-polymers1,0442
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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RNA chain , 2 types, 2 molecules AB

#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 subsp. subtilis str. 168 (bacteria)
Production host: Bacillus subtilis subsp. subtilis str. 168 (bacteria)
References: GenBank: 1775206404
#2: RNA chain 5S rRNA


Mass: 38423.863 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis subsp. subtilis str. 168 (bacteria)
Production host: Bacillus subtilis subsp. subtilis str. 168 (bacteria)
References: GenBank: 2592576696

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Large ribosomal subunit protein ... , 22 types, 22 molecules CDEFGHIJKLMNOPQRSTUVZY

#3: Protein Large ribosomal subunit protein uL2 / 50S ribosomal protein L2 / BL2


Mass: 30335.125 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis subsp. subtilis str. 168 (bacteria)
Gene: rplB, BSU01190
Production host: Bacillus subtilis subsp. subtilis str. 168 (bacteria)
References: UniProt: P42919
#4: Protein Large ribosomal subunit protein uL3 / 50S ribosomal protein L3 / BL3


Mass: 22723.348 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis subsp. subtilis str. 168 (bacteria)
Gene: rplC, BSU01160
Production host: Bacillus subtilis subsp. subtilis str. 168 (bacteria)
References: UniProt: P42920
#5: Protein Large ribosomal subunit protein uL4 / 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 subsp. subtilis str. 168 (bacteria)
Gene: rplD, BSU01170
Production host: Bacillus subtilis subsp. subtilis str. 168 (bacteria)
References: UniProt: P42921
#6: Protein Large ribosomal subunit protein uL6 / 50S ribosomal protein L6 / BL10


Mass: 19543.389 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis subsp. subtilis str. 168 (bacteria)
Gene: rplF, BSU01310
Production host: Bacillus subtilis subsp. subtilis str. 168 (bacteria)
References: UniProt: P46898
#7: Protein Large ribosomal subunit protein uL13 / 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 subsp. subtilis str. 168 (bacteria)
Gene: rplM, BSU01490
Production host: Bacillus subtilis subsp. subtilis str. 168 (bacteria)
References: UniProt: P70974
#8: Protein Large ribosomal subunit protein uL14 / 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 subsp. subtilis str. 168 (bacteria)
Gene: rplN, BSU01260
Production host: Bacillus subtilis subsp. subtilis str. 168 (bacteria)
References: UniProt: P12875
#9: Protein Large ribosomal subunit protein uL15 / 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 subsp. subtilis str. 168 (bacteria)
Gene: rplO, BSU01350
Production host: Bacillus subtilis subsp. subtilis str. 168 (bacteria)
References: UniProt: P19946
#10: Protein Large ribosomal subunit protein bL17 / 50S ribosomal protein L17 / BL15 / BL21


Mass: 13774.806 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis subsp. subtilis str. 168 (bacteria)
Gene: rplQ, BSU01440
Production host: Bacillus subtilis subsp. subtilis str. 168 (bacteria)
References: UniProt: P20277
#11: Protein Large ribosomal subunit protein bL19 / 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 subsp. subtilis str. 168 (bacteria)
Gene: rplS, BSU16040
Production host: Bacillus subtilis subsp. subtilis str. 168 (bacteria)
References: UniProt: O31742
#12: Protein Large ribosomal subunit protein bL20 / 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 subsp. subtilis str. 168 (bacteria)
Gene: rplT, BSU28850
Production host: Bacillus subtilis subsp. subtilis str. 168 (bacteria)
References: UniProt: P55873
#13: Protein Large ribosomal subunit protein bL21 / 50S ribosomal protein L21 / BL20


Mass: 11296.081 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis subsp. subtilis str. 168 (bacteria)
Gene: rplU, BSU27960
Production host: Bacillus subtilis subsp. subtilis str. 168 (bacteria)
References: UniProt: P26908
#14: Protein Large ribosomal subunit protein uL22 / 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 subsp. subtilis str. 168 (bacteria)
Gene: rplV, BSU01210
Production host: Bacillus subtilis subsp. subtilis str. 168 (bacteria)
References: UniProt: P42060
#15: Protein Large ribosomal subunit protein uL23 / 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 subsp. subtilis str. 168 (bacteria)
Gene: rplW, BSU01180
Production host: Bacillus subtilis subsp. subtilis str. 168 (bacteria)
References: UniProt: P42924
#16: Protein Large ribosomal subunit protein uL24 / 12 kDa DNA-binding protein / 50S ribosomal protein L24 / BL23 / HPB12


Mass: 11166.120 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis subsp. subtilis str. 168 (bacteria)
Gene: rplX, BSU01270
Production host: Bacillus subtilis subsp. subtilis str. 168 (bacteria)
References: UniProt: P0CI78
#17: Protein Large ribosomal subunit protein bL27 / 50S ribosomal protein L27 / BL24 / BL30


Mass: 10391.855 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis subsp. subtilis str. 168 (bacteria)
Gene: rpmA, BSU27940
Production host: Bacillus subtilis subsp. subtilis str. 168 (bacteria)
References: UniProt: P05657
#18: Protein Large ribosomal subunit protein uL29 / 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 subsp. subtilis str. 168 (bacteria)
Gene: rpmC, BSU01240
Production host: Bacillus subtilis subsp. subtilis str. 168 (bacteria)
References: UniProt: P12873
#19: Protein Large ribosomal subunit protein uL30 / 50S ribosomal protein L30 / BL27


Mass: 6650.795 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis subsp. subtilis str. 168 (bacteria)
Gene: rpmD, BSU01340
Production host: Bacillus subtilis subsp. subtilis str. 168 (bacteria)
References: UniProt: P19947
#20: Protein Large ribosomal subunit protein bL32 / 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 subsp. subtilis str. 168 (bacteria)
Gene: rpmF, BSU15080
Production host: Bacillus subtilis subsp. subtilis str. 168 (bacteria)
References: UniProt: O34687
#21: Protein/peptide Large ribosomal subunit protein bL34 / 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 subsp. subtilis str. 168 (bacteria)
Gene: rpmH, BSU41060
Production host: Bacillus subtilis subsp. subtilis str. 168 (bacteria)
References: UniProt: P05647
#22: Protein Large ribosomal subunit protein uL18 / 50S ribosomal protein L18 / BL16


Mass: 12993.829 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis subsp. subtilis str. 168 (bacteria)
Gene: rplR, BSU01320
Production host: Bacillus subtilis subsp. subtilis str. 168 (bacteria)
References: UniProt: P46899
#24: Protein/peptide Large ribosomal subunit protein bL33A / 50S ribosomal protein L33 1


Mass: 5915.875 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis subsp. subtilis str. 168 (bacteria)
Gene: rpmGA, rpmG1, BSU24900
Production host: Bacillus subtilis subsp. subtilis str. 168 (bacteria)
References: UniProt: P56849
#25: Protein Large ribosomal subunit protein uL1 / 50S ribosomal protein L1 / BL1


Mass: 25026.887 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis subsp. subtilis str. 168 (bacteria)
Gene: rplA, BSU01030
Production host: Bacillus subtilis subsp. subtilis str. 168 (bacteria)
References: UniProt: Q06797

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Protein / Non-polymers , 2 types, 3 molecules W

#23: Protein GTPase Der / GTP-binding protein EngA


Mass: 48846.547 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis subsp. subtilis str. 168 (bacteria)
Gene: der, engA, yphC, BSU22840
Production host: Bacillus subtilis subsp. subtilis str. 168 (bacteria)
References: UniProt: P50743
#26: Chemical ChemComp-GNP / PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER


Mass: 522.196 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H17N6O13P3
Comment: GppNHp, GMPPNP, energy-carrying molecule analogue*YM

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Details

Has ligand of interestN
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: 50S assembly intermediate 45SYphC Class 1 / Type: RIBOSOME / Source: NATURAL
Molecular weightExperimental value: NO
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: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2750 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 softwareName: PHENIX / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 18086 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00589455
ELECTRON MICROSCOPYf_angle_d0.694134652
ELECTRON MICROSCOPYf_dihedral_angle_d19.76436537
ELECTRON MICROSCOPYf_chiral_restr0.03817355
ELECTRON MICROSCOPYf_plane_restr0.0056649

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