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- EMDB-51346: Fusobacterium nucleatum adhesin CbpF -

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Basic information

Entry
Database: EMDB / ID: EMD-51346
TitleFusobacterium nucleatum adhesin CbpF
Map dataMain map file, sharpened with DeepEMhancer
Sample
  • Complex: Homotrimeric complex of CbpF, residues 25-274 resolved
    • Protein or peptide: Cell surface protein
Keywordsbacterial pathogenesis / adhesin / type V secretion system / trimeric autotransporter / CELL ADHESION
Function / homology
Function and homology information


cell outer membrane / protein transport / cell surface
Similarity search - Function
Trimeric autotransporter adhesin YadA-like, head domain / YadA head domain repeat (2 copies) / Trimeric autotransporter adhesin YadA-like, stalk domain / Coiled stalk of trimeric autotransporter adhesin / Trimeric autotransporter adhesin YadA-like, C-terminal membrane anchor domain / YadA-like membrane anchor domain / Pilin-like / Serralysin-like metalloprotease, C-terminal
Similarity search - Domain/homology
Cell surface protein
Similarity search - Component
Biological speciesFusobacterium nucleatum (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.8 Å
AuthorsRoderer D / Marongiu GL / Fink U
Funding support Germany, 1 items
OrganizationGrant numberCountry
Leibniz Association Germany
CitationJournal: Proc Natl Acad Sci U S A / Year: 2025
Title: Structural basis for immune cell binding of via the trimeric autotransporter adhesin CbpF.
Authors: Gian Luca Marongiu / Uwe Fink / Felix Schöpf / Andreas Oder / Jens Peter von Kries / Daniel Roderer /
Abstract: (Fn), a commensal in the human oral cavity, is overrepresented in the colon microbiota of colorectal cancer (CRC) patients and is linked to tumor chemoresistance, metastasis, and a poor therapeutic ... (Fn), a commensal in the human oral cavity, is overrepresented in the colon microbiota of colorectal cancer (CRC) patients and is linked to tumor chemoresistance, metastasis, and a poor therapeutic prognosis. Fn produces numerous adhesins that mediate tumor colonization and downregulation of the host's antitumor immune response. One of these, the trimeric autotransporter adhesin (TAA) CEACAM binding protein of (CbpF), targets CEACAM1 on T-cells and has been associated with immune evasion of Fn-colonized tumors. Whereas the role of CEACAM1 in homophilic and heterophilic cell interactions and immune evasion is well described, the mechanistic details of its interaction with fusobacterial CbpF remain unknown due to the lack of a high-resolution structure of the adhesin-receptor complex. Here, we present two structures of CbpF alone and in complex with CEACAM1, obtained by cryogenic electron microscopy and single particle analysis. They reveal that CbpF forms a stable homotrimeric complex whose N-terminal part of the extracellular domain comprises a 64 Å long β roll domain with a unique lateral loop extension. CEACAM1 binds to this loop with high affinity via its N-terminal IgV-like domain with a nanomolar dissociation constant as determined by surface plasmon resonance. This study provides a comprehensive structural description of a fusobacterial TAA, illustrates a yet undescribed CEACAM1 binding mode, and paves the way for rational drug design targeting Fn in CRC.
History
DepositionAug 15, 2024-
Header (metadata) releaseApr 2, 2025-
Map releaseApr 2, 2025-
UpdateApr 23, 2025-
Current statusApr 23, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_51346.png

Downloads & links

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Map

FileDownload / File: emd_51346.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationMain map file, sharpened with DeepEMhancer
Projections & slices

Image control

Size
Brightness
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Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 384 pix.
= 318.72 Å		0.83 Å/pix.
x 384 pix.
= 318.72 Å		0.83 Å/pix.
x 384 pix.
= 318.72 Å

Surface

Projections

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Slices (1/2)

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.83 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.16
Minimum - Maximum-0.0018210812 - 1.9818423
Average (Standard dev.)0.00044884766 (±0.017034844)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions384384384
Spacing384384384
CellA=B=C: 318.72 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_51346_msk_1.map
Projections & Slices
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Additional map: Non-sharpened full map

Fileemd_51346_additional_1.map
AnnotationNon-sharpened full map
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Half map: Half map A

Fileemd_51346_half_map_1.map
AnnotationHalf map A
Projections & Slices
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Half map: Half map B

Fileemd_51346_half_map_2.map
AnnotationHalf map B
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Sample components

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Entire : Homotrimeric complex of CbpF, residues 25-274 resolved

EntireName: Homotrimeric complex of CbpF, residues 25-274 resolved
Components
  • Complex: Homotrimeric complex of CbpF, residues 25-274 resolved
    • Protein or peptide: Cell surface protein

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Supramolecule #1: Homotrimeric complex of CbpF, residues 25-274 resolved

SupramoleculeName: Homotrimeric complex of CbpF, residues 25-274 resolved
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all / Details: nanodisc-embedded CbpF
Source (natural)Organism: Fusobacterium nucleatum (bacteria)
Molecular weightTheoretical: 160 KDa

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Macromolecule #1: Cell surface protein

MacromoleculeName: Cell surface protein / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Fusobacterium nucleatum (bacteria)
Molecular weightTheoretical: 51.827051 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MKKTAIAIAV ALAGFATVAQ ASAAPVIKAG TATDSTEAGV DNVANGVKSS AFGYDNKAIE KESSAFGTGN RATGEFSSAF GFHNIASKI HSSAFGSNNA ADGVNSSAFG FKNTVSGFNS SAFGSQYQVT GNFSGAFGMG EFNGQYQYKN EGNNSYMIGN K NKIASGSD ...String:
MKKTAIAIAV ALAGFATVAQ ASAAPVIKAG TATDSTEAGV DNVANGVKSS AFGYDNKAIE KESSAFGTGN RATGEFSSAF GFHNIASKI HSSAFGSNNA ADGVNSSAFG FKNTVSGFNS SAFGSQYQVT GNFSGAFGMG EFNGQYQYKN EGNNSYMIGN K NKIASGSD DNFILGNNVH IGGGINNSVA LGNNSTVSAS NTVSVGSSTL KRKIVNVGDG AISANSSDAV TGRQLYSGNG ID TAAWQNK LNVTRKNDYK DANDIDVNKW KAKLGVGSGG GGGAPVDAYT KSEADNKFAN KTDLNDYTKK DDYKDANGID VDK WKAKLG TGAGTADIEN LRNEVNEKID DVKDEVRTVG SLSAALAGLH PMQYDPKAPV QVMAALGHYR DKQSVAVGAS YYFN DRFMM STGIALSGEK RTKTMANVGF TLKLGKGSGV TYDETPQYVV QNEVKRLTVE NQELKERVRN LEEKLNMLLK NKRSS AWSH PQFEK

UniProtKB: Cell surface 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

BufferpH: 7
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 285 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Specialist opticsEnergy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 79.9 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.6 µm / Nominal defocus min: 1.4000000000000001 µm / Nominal magnification: 105000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 1054758
Startup modelType of model: NONE
Details: Initial model created from the data with ab initio reconstruction
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C3 (3 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.4.0) / Number images used: 46881
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.4.0)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.4.0)
Final 3D classificationNumber classes: 3 / Software - Name: cryoSPARC (ver. 4.4.0)
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelChain - Source name: AlphaFold / Chain - Initial model type: in silico model
RefinementSpace: REAL / Protocol: FLEXIBLE FIT
Output model

PDB-9gh4:
Fusobacterium nucleatum adhesin CbpF

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