9QKS | pdb_00009qks

B subtilis Type VIIb Core Unit (T7bCU) + DUF


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.80 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

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This is version 1.1 of the entry. See complete history

Literature

A ubiquitin-like protein controls assembly of a bacterial type VIIb secretion system.

Oka, G.U.Benoit, N.Siroy, A.Gubellini, F.Marza, E.Fronzes, R.

(2025) Sci Adv 11: eady9587-eady9587

  • DOI: https://doi.org/10.1126/sciadv.ady9587
  • Primary Citation Related Structures: 
    9QKS

  • PubMed Abstract: 

    Type VII secretion systems (T7SS) are protein translocation machines crucial for virulence and bacterial competition in Gram-positive bacteria. Despite their importance, the structural basis for assembly of type VIIb secretion systems (T7SSb), a widely distributed variant in Firmicutes, remains poorly understood. We present the cryo-electron microscopy structure of the T7SSb core complex from Bacillus subtilis , revealing how the ubiquitin-like protein YukD, coordinates assembly of the secretion machinery. YukD interacts extensively with the central channel component YukB and facilitates its association with the pseudokinase YukC, forming a stable building block for channel assembly. Time-lapse microscopy and competition assays demonstrate that YukD is essential for proper T7SSb complex formation and contact-dependent bacterial killing. Our findings reveal how bacteria have adapted a ubiquitin-like protein as a structural regulator for assembling a large secretion complex.


  • Organizational Affiliation
    • CNRS UMR 5234 Microbiologie Fondamentale et Pathogénicité, Institut Européen de Chimie et Biologie, University of Bordeaux, 33600 Pessac, France.

Macromolecule Content 

  • Total Structure Weight: 401.95 kDa 
  • Atom Count: 11,940 
  • Modeled Residue Count: 1,441 
  • Deposited Residue Count: 3,529 
  • Unique protein chains: 3

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
ESX secretion system protein YukD81Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
Gene Names: yukDBSU31900
UniProt
Find proteins for P71071 (Bacillus subtilis (strain 168))
Explore P71071 
Go to UniProtKB:  P71071
Entity Groups
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UniProt GroupP71071
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
ESX secretion system protein YukCB [auth C],
C [auth D]
459Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
Gene Names: yukCBSU31890
UniProt
Find proteins for P71070 (Bacillus subtilis (strain 168))
Explore P71070 
Go to UniProtKB:  P71070
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP71070
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
ESX secretion system protein YukB,Green fluorescent proteinD [auth G],
E [auth H]
1,265Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
Gene Names: yukByukAyukBABSU31875BSU31880GFP
UniProt
Find proteins for C0SPA7 (Bacillus subtilis (strain 168))
Explore C0SPA7 
Go to UniProtKB:  C0SPA7
Find proteins for P42212 (Aequorea victoria)
Explore P42212 
Go to UniProtKB:  P42212
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupsP42212C0SPA7
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.80 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.21.1_5286:

Structure Validation

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Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Centre National de la Recherche Scientifique (CNRS)France--

Revision History  (Full details and data files)

  • Version 1.0: 2025-11-26
    Type: Initial release
  • Version 1.1: 2025-12-03
    Changes: Data collection, Database references