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- EMDB-53218: Focused Cryo-EM Map of the Dimeric Type VIIb Core Unit (T7bCU) -

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Basic information

Entry
Database: EMDB / ID: EMD-53218
TitleFocused Cryo-EM Map of the Dimeric Type VIIb Core Unit (T7bCU)
Map data
Sample
  • Complex: Dimer of T7bCU (Type VIIb Core Unit) + DUF
    • Protein or peptide: YukD
    • Protein or peptide: YukC
    • Protein or peptide: YukB(1973)-GFP-Twin-Strep-Tag
KeywordsT7SSb / Type VII Secretion System / T7bCU / Type VII b Core Unity / PROTEIN TRANSPORT
Function / homology
Function and homology information


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. / Ubiquitin-like domain superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
ESX secretion system protein YukB / 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: 6.9 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_53218.png

Downloads & links

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Map

FileDownload / File: emd_53218.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: 0.1
Minimum - Maximum-0.19889088 - 0.5005161
Average (Standard dev.)-0.00024002221 (±0.018379016)
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: #1

Fileemd_53218_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_53218_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 : Dimer of T7bCU (Type VIIb Core Unit) + DUF

EntireName: Dimer of T7bCU (Type VIIb Core Unit) + DUF
Components
  • Complex: Dimer of T7bCU (Type VIIb Core Unit) + DUF
    • Protein or peptide: YukD
    • Protein or peptide: YukC
    • Protein or peptide: YukB(1973)-GFP-Twin-Strep-Tag

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Supramolecule #1: Dimer of T7bCU (Type VIIb Core Unit) + DUF

SupramoleculeName: Dimer of T7bCU (Type VIIb Core Unit) + DUF / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Bacillus subtilis subsp. subtilis str. 168 (bacteria)
Molecular weightTheoretical: 650 KDa

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Macromolecule #1: YukD

MacromoleculeName: YukD / type: protein_or_peptide / ID: 1 / Details: YukD / Enantiomer: LEVO
Source (natural)Organism: Bacillus subtilis subsp. subtilis str. 168 (bacteria)
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: YukC

MacromoleculeName: YukC / type: protein_or_peptide / ID: 2 / Details: YukD-FLAG / Enantiomer: LEVO
Source (natural)Organism: Bacillus subtilis subsp. subtilis str. 168 (bacteria)
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MSGEQKSYLE NQLEAVAEKT DAGYTFTFQR EKIKLLDGLE ANVIKDINPF FHKEIDVTDD EVIITIQPPS SYKAFRFMKA KDKKSKWQFA YQLVQAVQQH NLSRLNLIVA PENIVFDKGL TPYFLHYGVK ESIPPYERDE ERVWQELKAA AALAVDGAFA FEDYLKFNET ...String:
MSGEQKSYLE NQLEAVAEKT DAGYTFTFQR EKIKLLDGLE ANVIKDINPF FHKEIDVTDD EVIITIQPPS SYKAFRFMKA KDKKSKWQFA YQLVQAVQQH NLSRLNLIVA PENIVFDKGL TPYFLHYGVK ESIPPYERDE ERVWQELKAA AALAVDGAFA FEDYLKFNET LTFSAEAKAI LDAESYDDLL ELIQTHIDEL EAKAKTYIHI PRKKWNIQRY IGLGLIVLLV PALIYSMYAL FFAQPKHQAI VDSNRAFLNK QYSEVISTLS KYDAESLPES VQYQLATSYV EVENLGSAKT KNIENNLVTL QSDPQHFLYW IDYGRGEYKE AISIGRKLEY NDYIYFALAK YKQQLLSEDT NDEDIQKELD SVNSELEKAQ KERQENKQSN SETSLVDTSE EQTQTDEEKQ AEEKAAEEKA AAEEKAKKEE QKEKEDEKKE TEKKDEKKDD KDYKDDDDK

UniProtKB: ESX secretion system protein YukC

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Macromolecule #3: YukB(1973)-GFP-Twin-Strep-Tag

MacromoleculeName: YukB(1973)-GFP-Twin-Strep-Tag / type: protein_or_peptide / ID: 3 / Enantiomer: LEVO
Source (natural)Organism: Bacillus subtilis subsp. subtilis str. 168 (bacteria)
SequenceString: MLPFGRKGVR HLSLLWVFYQ NNVQKLNLSN LPSSHPVTIG PDVKDSVTIS TIPFNSGVIS LKRKESGGQY EVFLGNDCLG TIETDISFTL QTDQQDIRLI LTGSEPEKSV YFTGNRDEIV CSSEKTNADI YLNPQDFAFA EQSTFSLLRA GGSWSVRPES GTIFLNGEKI ...String:
MLPFGRKGVR HLSLLWVFYQ NNVQKLNLSN LPSSHPVTIG PDVKDSVTIS TIPFNSGVIS LKRKESGGQY EVFLGNDCLG TIETDISFTL QTDQQDIRLI LTGSEPEKSV YFTGNRDEIV CSSEKTNADI YLNPQDFAFA EQSTFSLLRA GGSWSVRPES GTIFLNGEKI NANTPLKPGD EIFWNFTQMR VTEQDLLEIV HYAQFETALT ETVKPSTEMQ KKYPQYRRTP RMVYDLPDDR VSFSFPSQES DQTNRGLWLV ILPPLVMLIV MGVVAIIQPR GIFILVSLAM FMMTLITSTV QYFRDKNQRK KREEKRERVY KLYLDNKRKE LQALAEKQKQ VLEFHFPSFE QMKYLTSEIS DRIWEKSLES KDYLQLRLGT GTVPSSYEIN MSGGDLANRD IDDLMEKSQH MQRVYKDIRN APVTVDLAEG PMGLVGKSQI VKNEIHQLIG QLSFFNSYHD LRFVFIFHEE EYKDWEWMKW LPQFQMPHIY AKGFIYNEQT RDQLLSSLYE LIRERDLEDD KEKLQFKPHF VFVITNQQLI SEHVILEYLE GQHEHLGIST IVAAETKESL SENITTLVRY INEHEGDILI QKKKAVRIPF RLDHHQREDN ERFSRTLRTL NHQVGITNSI PETVSFLELF HAKEVKEIGI QQRWLTSESS KSLSVPIGYK GKDDIVYLNL HEKAHGPHGL LAGTTGSGKS EFLQTYILSL AVHFHPHEAA FLLIDYKGGG MAQPFRNIPH LLGTITNIEG SKNFSMRALA SIKSELKKRQ RLFDQYQVNH INDYTKLYKQ GKAEVAMPHL FLISDEFAEL KSEEPDFIRE LVSAARIGRS LGVHLILATQ KPGGIIDDQI WSNSRFKVAL KVQDATDSKE ILKNSDAANI TVTGRGYLQV GNNEVYELFQ SAWSGAPYLE EVYGTEDEIA IVTDTGLIPL SEVDTEDNAK KDVQTEIEAV VDEIERIQDE MGIEKLPSPW LPPGAGGLVP RGSGGSGSVD STESLFTGVV PILVELDGDV NGHKFSVRGE GEGDATNGKL TLKFICTTGK LPVPWPTLVT TLTYGVQCFS RYPDHMKQHD FFKSAMPEGY VQERTITFKD DGTYKTRAEV KFEGDTLVNR IELKGIDFKE DGNILGHKLE YNYNSHNVYI TADKQKNGIK ANFKIRHNVE DGSVQLADHY QQNTPIGDGP VLLPDNHYLS TQSKLSKDPN EKRDHMVLLE FVTAAGITGG SGGSGSRGRS GSGSAWSHPQ FEKGGGSGGG SGGSAWSHPQ FEKKG

UniProtKB: ESX secretion system protein YukB

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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
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: 6.9 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 94509
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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