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- PDB-9qks: B subtilis Type VIIb Core Unit (T7bCU) + DUF -

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Basic information

Entry
Database: PDB / ID: 9qks
TitleB subtilis Type VIIb Core Unit (T7bCU) + DUF
Components
  • ESX secretion system protein YukB,Green fluorescent protein
  • ESX secretion system protein YukC
  • ESX secretion system protein YukD
KeywordsPROTEIN TRANSPORT / T7SS / Type VII Secretion System / T7bCU
Function / homology
Function and homology information


bioluminescence / generation of precursor metabolites and energy / DNA binding / ATP binding / plasma membrane
Similarity search - Function
EsaB / Type VII secretion system EssB / Type VII secretion system EssB, C-terminal / WXG100 protein secretion system (Wss), protein YukC / Firmicutes EssC, N-terminal / Firmicutes EssC, C-terminal / DNA transporter / YukD-like / WXG100 protein secretion system (Wss), protein YukD / : ...EsaB / Type VII secretion system EssB / Type VII secretion system EssB, C-terminal / WXG100 protein secretion system (Wss), protein YukC / Firmicutes EssC, N-terminal / Firmicutes EssC, C-terminal / DNA transporter / YukD-like / WXG100 protein secretion system (Wss), protein YukD / : / FtsK domain / FtsK/SpoIIIE family / FtsK domain profile. / Green fluorescent protein, GFP / Green fluorescent protein-related / Green fluorescent protein / Green fluorescent protein / Ubiquitin-like domain superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
ESX secretion system protein YukB / Green fluorescent protein / ESX secretion system protein YukC / ESX secretion system protein YukD
Similarity search - Component
Biological speciesBacillus subtilis subsp. subtilis str. 168 (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.8 Å
AuthorsOka, G.U. / Fronzes, R.
Funding support France, 1items
OrganizationGrant numberCountry
Centre National de la Recherche Scientifique (CNRS) France
CitationJournal: Sci Adv / Year: 2025
Title: A ubiquitin-like protein controls assembly of a bacterial type VIIb secretion system.
Authors: Gabriel U Oka / Nathanaël Benoit / Axel Siroy / Francesca Gubellini / Esther Marza / Rémi Fronzes /
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 ...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 , 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.
History
DepositionMar 20, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 26, 2025Provider: repository / Type: Initial release
Revision 1.0Nov 26, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Nov 26, 2025Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Nov 26, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Nov 26, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Nov 26, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
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Revision 1.1Dec 3, 2025Group: Data collection / Database references / Category: citation / citation_author / em_admin
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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ESX secretion system protein YukD
C: ESX secretion system protein YukC
D: ESX secretion system protein YukC
G: ESX secretion system protein YukB,Green fluorescent protein
H: ESX secretion system protein YukB,Green fluorescent protein


Theoretical massNumber of molelcules
Total (without water)401,9465
Polymers401,9465
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

#1: Protein ESX secretion system protein YukD


Mass: 9277.689 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis subsp. subtilis str. 168 (bacteria)
Strain: 168 / Gene: yukD, BSU31900 / Plasmid: pGUO19.1WT / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P71071
#2: Protein ESX secretion system protein YukC


Mass: 53225.195 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: This sequence present a FLAG tag (DYKDDDDK) fused at the C-terminus
Source: (gene. exp.) Bacillus subtilis subsp. subtilis str. 168 (bacteria)
Strain: 168 / Gene: yukC, BSU31890 / Plasmid: pGUO19.1WT / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P71070
#3: Protein ESX secretion system protein YukB,Green fluorescent protein


Mass: 143109.125 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: YukB (1?973)?GAGG (linker)?LVPRGS (Thrombin site)?GGSGSV (linker)?msfGFP2 ...Details: YukB (1?973)?GAGG (linker)?LVPRGS (Thrombin site)?GGSGSV (linker)?msfGFP2 (DSTESLFTGVVPILVELDGDVNGHKFSVRGEGEGDATNGKLTLKFICTTGKLPVPWPTLVTTLTYGVQCFSRYPDHMKQHDFFKSAMPEGYVQERTITFKDDGTYKTRAEVKFEGDTLVNRIELKGIDFKEDGNILGHKLEYNYNSHNVYITADKQKNGIKANFKIRHNVEDGSVQLADHYQQNTPIGDGPVLLPDNHYLSTQSKLSKDPNEKRDHMVLLEFVTAAGITGGSGGS)?GSRGRSGSG (linker)?Twin-Strep tag (SAWSHPQFEKGGGSGGGSGGSAWSHPQFEKKG),YukB (1?973)?GAGG (linker)?LVPRGS (Thrombin site)?GGSGSV (linker)?msfGFP2 (DSTESLFTGVVPILVELDGDVNGHKFSVRGEGEGDATNGKLTLKFICTTGKLPVPWPTLVTTLTYGVQCFSRYPDHMKQHDFFKSAMPEGYVQERTITFKDDGTYKTRAEVKFEGDTLVNRIELKGIDFKEDGNILGHKLEYNYNSHNVYITADKQKNGIKANFKIRHNVEDGSVQLADHYQQNTPIGDGPVLLPDNHYLSTQSKLSKDPNEKRDHMVLLEFVTAAGITGGSGGS)?GSRGRSGSG (linker)?Twin-Strep tag (SAWSHPQFEKGGGSGGGSGGSAWSHPQFEKKG)
Source: (gene. exp.) Bacillus subtilis subsp. subtilis str. 168 (bacteria)
Strain: 168 / Gene: yukB, yukA, yukBA, BSU31875, BSU31880, GFP / Plasmid: pGUO19.1WT / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: C0SPA7, UniProt: P42212
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: T7bCU (Type VIIb Core Unit) / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Molecular weightValue: 0.4 MDa / Experimental value: NO
Source (natural)Organism: Bacillus subtilis subsp. subtilis str. 168 (bacteria)
Source (recombinant)Organism: Escherichia coli BL21(DE3) (bacteria) / Plasmid: pGUO19.1WT
Buffer solutionpH: 8
Buffer component
IDConc.NameFormulaBuffer-ID
150 mMTRIS HClC4H12ClNO31
2300 mMSodium ClorideNaCl1
30.03 mMLauryl Maltose Neopentyl GlycolC47H88O221
SpecimenConc.: 2 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES / Details: This sample was polidispese
Specimen supportGrid material: COPPER / Grid mesh size: 200 divisions/in. / Grid type: Quantifoil R2/2
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 278 K

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Electron microscopy imaging

Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company
MicroscopyModel: FEI TALOS ARCTICA
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 5000 nm / Nominal defocus min: 500 nm / C2 aperture diameter: 50 µm / Alignment procedure: BASIC
Image recordingElectron dose: 50.6 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

EM softwareName: PHENIX / Version: 1.21.1_5286: / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 303198 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00312209
ELECTRON MICROSCOPYf_angle_d0.50316487
ELECTRON MICROSCOPYf_dihedral_angle_d6.0631581
ELECTRON MICROSCOPYf_chiral_restr0.0421777
ELECTRON MICROSCOPYf_plane_restr0.0042137

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