9BS0 image
Entry Detail
PDB ID:
9BS0
EMDB ID:
Keywords:
Title:
YphC-treated 45SYphC particle. Class 5
Biological Source:
PDB Version:
Deposition Date:
2024-05-12
Release Date:
2024-12-25
Method Details:
Experimental Method:
Resolution:
3.30 Å
Aggregation State:
PARTICLE
Reconstruction Method:
SINGLE PARTICLE
Macromolecular Entities
Polymer Type:polyribonucleotide
Description:23S rRNA
Chain IDs:A
Chain Length:2927
Number of Molecules:1
Biological Source:Bacillus subtilis subsp. subtilis str. 168
Polymer Type:polyribonucleotide
Description:5S rRNA
Chain IDs:B
Chain Length:119
Number of Molecules:1
Biological Source:Bacillus subtilis subsp. subtilis str. 168
Polymer Type:polypeptide(L)
Description:Large ribosomal subunit protein uL2
Chain IDs:C
Chain Length:277
Number of Molecules:1
Biological Source:Bacillus subtilis subsp. subtilis str. 168
Polymer Type:polypeptide(L)
Description:Large ribosomal subunit protein uL3
Chain IDs:D
Chain Length:209
Number of Molecules:1
Biological Source:Bacillus subtilis subsp. subtilis str. 168
Polymer Type:polypeptide(L)
Description:Large ribosomal subunit protein uL4
Chain IDs:E
Chain Length:207
Number of Molecules:1
Biological Source:Bacillus subtilis subsp. subtilis str. 168
Polymer Type:polypeptide(L)
Description:Large ribosomal subunit protein uL6
Chain IDs:F
Chain Length:179
Number of Molecules:1
Biological Source:Bacillus subtilis subsp. subtilis str. 168
Polymer Type:polypeptide(L)
Description:Large ribosomal subunit protein uL13
Chain IDs:G
Chain Length:145
Number of Molecules:1
Biological Source:Bacillus subtilis subsp. subtilis str. 168
Polymer Type:polypeptide(L)
Description:Large ribosomal subunit protein uL14
Chain IDs:H
Chain Length:122
Number of Molecules:1
Biological Source:Bacillus subtilis subsp. subtilis str. 168
Polymer Type:polypeptide(L)
Description:Large ribosomal subunit protein uL15
Chain IDs:I
Chain Length:146
Number of Molecules:1
Biological Source:Bacillus subtilis subsp. subtilis str. 168
Polymer Type:polypeptide(L)
Description:Large ribosomal subunit protein bL17
Chain IDs:J
Chain Length:120
Number of Molecules:1
Biological Source:Bacillus subtilis subsp. subtilis str. 168
Polymer Type:polypeptide(L)
Description:Large ribosomal subunit protein bL19
Chain IDs:K
Chain Length:115
Number of Molecules:1
Biological Source:Bacillus subtilis subsp. subtilis str. 168
Polymer Type:polypeptide(L)
Description:Large ribosomal subunit protein bL20
Chain IDs:L
Chain Length:118
Number of Molecules:1
Biological Source:Bacillus subtilis subsp. subtilis str. 168
Polymer Type:polypeptide(L)
Description:Large ribosomal subunit protein bL21
Chain IDs:M
Chain Length:102
Number of Molecules:1
Biological Source:Bacillus subtilis subsp. subtilis str. 168
Polymer Type:polypeptide(L)
Description:Large ribosomal subunit protein uL22
Chain IDs:N
Chain Length:113
Number of Molecules:1
Biological Source:Bacillus subtilis subsp. subtilis str. 168
Polymer Type:polypeptide(L)
Description:Large ribosomal subunit protein uL23
Chain IDs:O
Chain Length:95
Number of Molecules:1
Biological Source:Bacillus subtilis subsp. subtilis str. 168
Polymer Type:polypeptide(L)
Description:Large ribosomal subunit protein uL24
Chain IDs:P
Chain Length:103
Number of Molecules:1
Biological Source:Bacillus subtilis subsp. subtilis str. 168
Polymer Type:polypeptide(L)
Description:Large ribosomal subunit protein bL27
Chain IDs:Q
Chain Length:94
Number of Molecules:1
Biological Source:Bacillus subtilis subsp. subtilis str. 168
Polymer Type:polypeptide(L)
Description:Large ribosomal subunit protein uL29
Chain IDs:R
Chain Length:66
Number of Molecules:1
Biological Source:Bacillus subtilis subsp. subtilis str. 168
Polymer Type:polypeptide(L)
Description:Large ribosomal subunit protein uL30
Chain IDs:S
Chain Length:59
Number of Molecules:1
Biological Source:Bacillus subtilis subsp. subtilis str. 168
Polymer Type:polypeptide(L)
Description:Large ribosomal subunit protein bL32
Chain IDs:T
Chain Length:59
Number of Molecules:1
Biological Source:Bacillus subtilis subsp. subtilis str. 168
Polymer Type:polypeptide(L)
Description:Large ribosomal subunit protein bL34
Chain IDs:U
Chain Length:44
Number of Molecules:1
Biological Source:Bacillus subtilis subsp. subtilis str. 168
Polymer Type:polypeptide(L)
Description:Large ribosomal subunit protein uL18
Chain IDs:V
Chain Length:120
Number of Molecules:1
Biological Source:Bacillus subtilis subsp. subtilis str. 168
Polymer Type:polypeptide(L)
Description:GTPase Der
Chain IDs:W
Chain Length:436
Number of Molecules:1
Biological Source:Bacillus subtilis subsp. subtilis str. 168
Polymer Type:polypeptide(L)
Description:Large ribosomal subunit protein uL1
Chain IDs:Y
Chain Length:232
Number of Molecules:1
Biological Source:Bacillus subtilis subsp. subtilis str. 168
Polymer Type:polypeptide(L)
Description:Large ribosomal subunit protein bL33A
Chain IDs:X (auth: Z)
Chain Length:49
Number of Molecules:1
Biological Source:Bacillus subtilis subsp. subtilis str. 168
Ligand Molecules
Primary Citation
The binding of RbgA to a critical 50S assembly intermediate facilitates YphC function in bacterial ribosomal assembly.
Nucleic Acids Res. 53 ? ? (2025)
PMID: 39658043 DOI: 10.1093/nar/gkae1197

Abstact

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.

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Primary Citation of related structures