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- EMDB-53220: B subtilis Type VIIb Core Unit (T7bCU) + DUF -

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Basic information

Entry
Database: EMDB / ID: EMD-53220
TitleB subtilis Type VIIb Core Unit (T7bCU) + DUF
Map data
Sample
  • Complex: T7bCU (Type VIIb Core Unit)
    • Protein or peptide: ESX secretion system protein YukD
    • Protein or peptide: ESX secretion system protein YukC
    • Protein or peptide: ESX secretion system protein YukB,Green fluorescent protein
KeywordsT7SS / Type VII Secretion System / T7bCU / PROTEIN TRANSPORT
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)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.8 Å
AuthorsOka GU / Fronzes R
Funding support France, 1 items
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, 2025-
Header (metadata) releaseNov 26, 2025-
Map releaseNov 26, 2025-
UpdateDec 3, 2025-
Current statusDec 3, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_53220.png

Downloads & links

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Map

FileDownload / File: emd_53220.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.2 Å/pix.
x 300 pix.
= 360. Å		1.2 Å/pix.
x 300 pix.
= 360. Å		1.2 Å/pix.
x 300 pix.
= 360. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.2 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.2
Minimum - Maximum-0.24671671 - 0.59588295
Average (Standard dev.)-0.00024894098 (±0.0164447)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 360.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_53220_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_53220_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : T7bCU (Type VIIb Core Unit)

EntireName: T7bCU (Type VIIb Core Unit)
Components
  • Complex: T7bCU (Type VIIb Core Unit)
    • Protein or peptide: ESX secretion system protein YukD
    • Protein or peptide: ESX secretion system protein YukC
    • Protein or peptide: ESX secretion system protein YukB,Green fluorescent protein

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Supramolecule #1: T7bCU (Type VIIb Core Unit)

SupramoleculeName: T7bCU (Type VIIb Core Unit) / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Bacillus subtilis subsp. subtilis str. 168 (bacteria)
Molecular weightTheoretical: 400 KDa

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Macromolecule #1: ESX secretion system protein YukD

MacromoleculeName: ESX secretion system protein YukD / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Bacillus subtilis subsp. subtilis str. 168 (bacteria)
Strain: 168
Molecular weightTheoretical: 9.277689 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString:
MGMYIDITID LKHYNGSVFD LRLSDYHPVK KVIDIAWQAQ SVSMPPREGH WIRVVNKDKV FSGECKLSDC GITNGDRLEI L

UniProtKB: ESX secretion system protein YukD

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Macromolecule #2: ESX secretion system protein YukC

MacromoleculeName: ESX secretion system protein YukC / type: protein_or_peptide / ID: 2
Details: This sequence present a FLAG tag (DYKDDDDK) fused at the C-terminus
Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Bacillus subtilis subsp. subtilis str. 168 (bacteria)
Strain: 168
Molecular weightTheoretical: 53.225195 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MSGEQKSYLE NQLEAVAEKT DAGYTFTFQR EKIKLLDGLE ANVIKDINPF FHKEIDVTDD EVIITIQPPS SYKAFRFMKA KDKKSKWQF AYQLVQAVQQ HNLSRLNLIV APENIVFDKG LTPYFLHYGV KESIPPYERD EERVWQELKA AAALAVDGAF A FEDYLKFN ...String:
MSGEQKSYLE NQLEAVAEKT DAGYTFTFQR EKIKLLDGLE ANVIKDINPF FHKEIDVTDD EVIITIQPPS SYKAFRFMKA KDKKSKWQF AYQLVQAVQQ HNLSRLNLIV APENIVFDKG LTPYFLHYGV KESIPPYERD EERVWQELKA AAALAVDGAF A FEDYLKFN ETLTFSAEAK AILDAESYDD LLELIQTHID ELEAKAKTYI HIPRKKWNIQ RYIGLGLIVL LVPALIYSMY AL FFAQPKH QAIVDSNRAF LNKQYSEVIS TLSKYDAESL PESVQYQLAT SYVEVENLGS AKTKNIENNL VTLQSDPQHF LYW IDYGRG EYKEAISIGR KLEYNDYIYF ALAKYKQQLL SEDTNDEDIQ KELDSVNSEL EKAQKERQEN KQSNSETSLV DTSE EQTQT DEEKQAEEKA AEEKAAAEEK AKKEEQKEKE DEKKETEKKD EKKDDKDYKD DDDK

UniProtKB: ESX secretion system protein YukC

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Macromolecule #3: ESX secretion system protein YukB,Green fluorescent protein

MacromoleculeName: ESX secretion system protein YukB,Green fluorescent protein
type: protein_or_peptide / ID: 3
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)
Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Bacillus subtilis subsp. subtilis str. 168 (bacteria)
Strain: 168
Molecular weightTheoretical: 143.109125 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MLPFGRKGVR HLSLLWVFYQ NNVQKLNLSN LPSSHPVTIG PDVKDSVTIS TIPFNSGVIS LKRKESGGQY EVFLGNDCLG TIETDISFT LQTDQQDIRL ILTGSEPEKS VYFTGNRDEI VCSSEKTNAD IYLNPQDFAF AEQSTFSLLR AGGSWSVRPE S GTIFLNGE ...String:
MLPFGRKGVR HLSLLWVFYQ NNVQKLNLSN LPSSHPVTIG PDVKDSVTIS TIPFNSGVIS LKRKESGGQY EVFLGNDCLG TIETDISFT LQTDQQDIRL ILTGSEPEKS VYFTGNRDEI VCSSEKTNAD IYLNPQDFAF AEQSTFSLLR AGGSWSVRPE S GTIFLNGE KINANTPLKP GDEIFWNFTQ MRVTEQDLLE IVHYAQFETA LTETVKPSTE MQKKYPQYRR TPRMVYDLPD DR VSFSFPS QESDQTNRGL WLVILPPLVM LIVMGVVAII QPRGIFILVS LAMFMMTLIT STVQYFRDKN QRKKREEKRE RVY KLYLDN KRKELQALAE KQKQVLEFHF PSFEQMKYLT SEISDRIWEK SLESKDYLQL RLGTGTVPSS YEINMSGGDL ANRD IDDLM EKSQHMQRVY KDIRNAPVTV DLAEGPMGLV GKSQIVKNEI HQLIGQLSFF NSYHDLRFVF IFHEEEYKDW EWMKW LPQF QMPHIYAKGF IYNEQTRDQL LSSLYELIRE RDLEDDKEKL QFKPHFVFVI TNQQLISEHV ILEYLEGQHE HLGIST IVA AETKESLSEN ITTLVRYINE HEGDILIQKK KAVRIPFRLD HHQREDNERF SRTLRTLNHQ VGITNSIPET VSFLELF HA KEVKEIGIQQ RWLTSESSKS LSVPIGYKGK DDIVYLNLHE KAHGPHGLLA GTTGSGKSEF LQTYILSLAV HFHPHEAA F LLIDYKGGGM AQPFRNIPHL LGTITNIEGS KNFSMRALAS IKSELKKRQR LFDQYQVNHI NDYTKLYKQG KAEVAMPHL FLISDEFAEL KSEEPDFIRE LVSAARIGRS LGVHLILATQ KPGGIIDDQI WSNSRFKVAL KVQDATDSKE ILKNSDAANI TVTGRGYLQ VGNNEVYELF QSAWSGAPYL EEVYGTEDEI AIVTDTGLIP LSEVDTEDNA KKDVQTEIEA VVDEIERIQD E MGIEKLPS PWLPPGAGGL VPRGSGGSGS VDSTESLFTG VVPILVELDG DVNGHKFSVR GEGEGDATNG KLTLKFICTT GK LPVPWPT LVTTLTYGVQ CFSRYPDHMK QHDFFKSAMP EGYVQERTIT FKDDGTYKTR AEVKFEGDTL VNRIELKGID FKE DGNILG HKLEYNYNSH NVYITADKQK NGIKANFKIR HNVEDGSVQL ADHYQQNTPI GDGPVLLPDN HYLSTQSKLS KDPN EKRDH MVLLEFVTAA GITGGSGGSG SRGRSGSGSA WSHPQFEKGG GSGGGSGGSA WSHPQFEKKG

UniProtKB: ESX secretion system protein YukB, Green fluorescent protein

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration2 mg/mL
BufferpH: 8
Component:
ConcentrationFormulaName
50.0 mMC4H12ClNO3TRIS HCl
300.0 mMNaClSodium Cloride
0.03 mMC47H88O22Lauryl Maltose Neopentyl Glycol
GridModel: Quantifoil R2/2 / Material: COPPER / Mesh: 200 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec.
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 278 K / Instrument: FEI VITROBOT MARK IV
DetailsThis sample was polidispese

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Electron microscopy

MicroscopeFEI TALOS ARCTICA
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average electron dose: 50.6 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 5.0 µm / Nominal defocus min: 0.5 µm
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 303198
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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