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- EMDB-53314: 3D cryoEM map of the BSAP-1 and B1RS complex -

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Basic information

Entry
Database: EMDB / ID: EMD-53314
Title3D cryoEM map of the BSAP-1 and B1RS complex
Map dataElectron density map of the BSAP-1 B1RS complex.
Sample
  • Complex: Complex of the pore forming toxin BSAP-1 bound the the receptor B1RS
    • Protein or peptide: BSAP-1
    • Protein or peptide: B1RS
KeywordsComplex / Pore forming toxin / Bacteroidales / MACPF / MEMBRANE PROTEIN
Function / homology: / : / MACPF protein, D2 domain / MACPF protein, D3 domain / Membrane attack complex/perforin (MACPF) domain profile. / Membrane attack complex component/perforin (MACPF) domain / Prokaryotic membrane lipoprotein lipid attachment site profile. / Conserved hypothetical exported protein / MACPF domain-containing protein
Function and homology information
Biological speciesBacteroides fragilis (bacteria) / Bacteroides thetaiotaomicron VPI-5482 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.3 Å
AuthorsPasveer EL / Remaut HK
Funding support Belgium, 4 items
OrganizationGrant numberCountry
Research Foundation - Flanders (FWO)1S60723N Belgium
Research Foundation - Flanders (FWO)1S60721N Belgium
Fonds de la Recherche Scientifique (FNRS)1B.274.22F Belgium
Fonds National de la Recherche Scientifique (FNRS)ANR-20-PAMR-0010 Belgium
CitationJournal: J Biol Chem / Year: 2025
Title: Identification of receptor-binding domains of Bacteroidales antibacterial pore-forming toxins.
Authors: Sofia Borgini / Edwin Pasveer / Chloé Petre / Bogdan I Iorga / Didier Vertommen / Han Remaut / Jean-François Collet / Frédéric Lauber /
Abstract: Bacteroidales are abundant Gram-negative bacteria present in the gut microbiota of most animals, including humans, where they carry out vital functions for host health. To thrive in this competitive ...Bacteroidales are abundant Gram-negative bacteria present in the gut microbiota of most animals, including humans, where they carry out vital functions for host health. To thrive in this competitive environment, Bacteroidales use sophisticated weapons to outmatch competitors. Among these, BSAPs (Bacteroidales Secreted Antimicrobial Proteins) represent a novel class of bactericidal pore-forming toxins that are highly specific to their receptor, typically targeting only a single membrane protein or lipopolysaccharide. The molecular determinants conferring this high selectivity remain unknown. In this study, we therefore investigated the model protein BSAP-1 and determined which of its domains is involved in providing receptor specificity. We demonstrate that receptor recognition is entirely driven by the C-terminal domain (CTD) of BSAP-1 using a combination of in vivo competition assays, in vitro protein binding studies and mutational analysis. Specifically, we show that deletion of the CTD abrogates BSAP-1 bactericidal activity by preventing receptor binding, while grafting the CTD to unrelated carrier proteins enables CTD-driven interaction with the BSAP-1 receptor. Combining structural investigation of a BSAP-1-receptor complex with mutational analysis, we unveil that this interaction is driven by electrostatic interactions. Building upon this discovery, we show that BSAPs can be categorized according to the structure of their CTD, suggesting a strong CTD structure/receptor type correlation. In summary, our research demonstrates that BSAP receptor recognition is driven by their CTD and paves the way for future applications.
History
DepositionApr 2, 2025-
Header (metadata) releaseJan 14, 2026-
Map releaseJan 14, 2026-
UpdateJan 14, 2026-
Current statusJan 14, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_53314.png

Downloads & links

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Map

FileDownload / File: emd_53314.map.gz / Format: CCP4 / Size: 40.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationElectron density map of the BSAP-1 B1RS complex.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.75 Å/pix.
x 220 pix.
= 165.66 Å		0.75 Å/pix.
x 220 pix.
= 165.66 Å		0.75 Å/pix.
x 220 pix.
= 165.66 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.753 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.00485
Minimum - Maximum-0.006101853 - 0.022657217
Average (Standard dev.)0.00005684214 (±0.00066129694)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions220220220
Spacing220220220
CellA=B=C: 165.66 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: half map 1

Fileemd_53314_half_map_1.map
Annotationhalf map 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map 2

Fileemd_53314_half_map_2.map
Annotationhalf map 2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Complex of the pore forming toxin BSAP-1 bound the the receptor B1RS

EntireName: Complex of the pore forming toxin BSAP-1 bound the the receptor B1RS
Components
  • Complex: Complex of the pore forming toxin BSAP-1 bound the the receptor B1RS
    • Protein or peptide: BSAP-1
    • Protein or peptide: B1RS

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Supramolecule #1: Complex of the pore forming toxin BSAP-1 bound the the receptor B1RS

SupramoleculeName: Complex of the pore forming toxin BSAP-1 bound the the receptor B1RS
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all / Details: Purified BSAP-1
Source (natural)Organism: Bacteroides fragilis (bacteria)
Molecular weightTheoretical: 125 KDa

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Macromolecule #1: BSAP-1

MacromoleculeName: BSAP-1 / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Bacteroides thetaiotaomicron VPI-5482 (bacteria)
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MKKLFISLCI ILFTISCTNE EETNNYTPVD NQSNSTSEII LQERNSSLPR VWSKKTAQRV TTRASFTDAT DFLGCSYAVE NGTSIIGDFA NAKYPVVNMK KLLERYPSYI NPKELRTTET KALSYSDFDR LEKNKTFTKT VKSGFSLNLG PFKFGRQKTI KETFVHNTDD ...String:
MKKLFISLCI ILFTISCTNE EETNNYTPVD NQSNSTSEII LQERNSSLPR VWSKKTAQRV TTRASFTDAT DFLGCSYAVE NGTSIIGDFA NAKYPVVNMK KLLERYPSYI NPKELRTTET KALSYSDFDR LEKNKTFTKT VKSGFSLNLG PFKFGRQKTI KETFVHNTDD SEKVVHGELS IEVVNGMLNL QTAPSALRKI AADYLDELFV DALYNSSMVE LMQSYGEFVL TGYYTGGRAS ALFYGVDTNS IQFDSKEKDM DVAINASYEW KNKKPTAPSD TIHSASGNLS IGTKRENSET ITNKFSALSY SIKTLGGAYG YSISTPPYDI TNYSIDLTPW LQSLNDPKTH TMIDLQDGGL YPISDFILEE NFKQRYNDTH MDFQYQESLE EPYIEIIKMY IRKSNSGEKL YDIVPVLNTR QGDKLIFSNP DAASQSDEEL KANSIPATFL TKSNAIKDEK SKYYQLKIKA DPNKTINPII QTTLSFQINN VDEKGMYKFK NANTNIWYIY NPTSMYCFAY YDDDYIPDAY GILDWVNGIP IKAVTMTTLY QRYKIYGL

UniProtKB: MACPF domain-containing protein

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Macromolecule #2: B1RS

MacromoleculeName: B1RS / type: protein_or_peptide / ID: 2 / Enantiomer: LEVO
Source (natural)Organism: Bacteroides fragilis (bacteria)
SequenceString: MKKIITLATL GLLVAAAPIS AQTVYDAAKI TGKDLNGTAR FVGMGGAMGA LGGDISTIGT NPAGIGIYRS NDFMTSFGFS SYGTESKYLG DKFKSDKIQG SFDNLGFVFA SKIGNETSLR YVNFGFNYHK AKSFYKNMNM KGGLGNSSQT YQMAQQASGI TKWGDYPYDD ...String:
MKKIITLATL GLLVAAAPIS AQTVYDAAKI TGKDLNGTAR FVGMGGAMGA LGGDISTIGT NPAGIGIYRS NDFMTSFGFS SYGTESKYLG DKFKSDKIQG SFDNLGFVFA SKIGNETSLR YVNFGFNYHK AKSFYKNMNM KGGLGNSSQT YQMAQQASGI TKWGDYPYDD PEIGWLSILG YDGWLISDIT TDKMNAAGKP NSPYVDKDGN QRYDANGKPL YTTPGNYYGM YDDGVANFHS QERGGIDQYD FNVAFNFNDR FYLGLTLGAY AVDYSKYTYY SEAYTGANAP QNYNLRSWNK VRGSGFDLKL GTIIRPFENS PFRIGLAIHT PTFYNLDYKT SARVESDVLN VETGKIDQWS VDTRDKLPGN GDMVREFRLQ TPWTYNVSLG YTIGTSLALG AEYEYQDYST MKFRGPTGSS SEFTFENSTR PMMKGVNTLR LGLEYKVIPQ FALRAGYNYT SAIFHGDAFK DLPYYSIQTD TDWANTKALS NYTLGIGYRG SVFYADLAYK FSTYNEDFYP FVNKYEENNA TTVLTPETTK VTNTRSQVLF TLGLRF

UniProtKB: Conserved hypothetical exported 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

Concentration1 mg/mL
BufferpH: 7.5 / Details: 50mM HEPES, 150mM NaCl, 1mM DTT, 0.03% DDM
GridModel: Quantifoil R2/1 / Material: COPPER / Mesh: 300 / Support film - Material: GRAPHENE OXIDE / Support film - topology: CONTINUOUS / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 40 sec. / Pretreatment - Atmosphere: OTHER / Pretreatment - Pressure: 0.004 kPa
VitrificationCryogen name: ETHANE / Chamber humidity: 90 % / Chamber temperature: 298 K / Instrument: GATAN CRYOPLUNGE 3

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Electron microscopy

MicroscopeJEOL CRYO ARM 300
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Digitization - Dimensions - Width: 5760 pixel / Digitization - Dimensions - Height: 4092 pixel / Number grids imaged: 1 / Number real images: 31383 / Average exposure time: 3.036 sec. / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 100.0 µm / Illumination mode: OTHER / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.4 µm / Nominal defocus min: 0.8 µm
Sample stageSpecimen holder model: JEOL 3200FSC CRYOHOLDER / Cooling holder cryogen: NITROGEN

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Image processing

CTF correctionSoftware - Name: cryoSPARC / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.3 Å / Resolution method: FSC 0.33 CUT-OFF / Software - Name: RELION / Number images used: 23000
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final 3D classificationSoftware - Name: cryoSPARC
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelChain - Source name: AlphaFold / Chain - Initial model type: in silico model
DetailsPredictAndBuild
RefinementProtocol: OTHER

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