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- EMDB-63959: Cryo-EM structure of Fusobacterium nucleatum CbpF in complex with... -

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Basic information

Entry
Database: EMDB / ID: EMD-63959
TitleCryo-EM structure of Fusobacterium nucleatum CbpF in complex with human CEACAM1
Map dataSharpen by DeepEMhancer
Sample
  • Complex: Fusobacterium nucleatum CbpF in complex with human CEACAM1
    • Protein or peptide: Fusobacterium nucleatum CbpF
    • Protein or peptide: Cell adhesion molecule CEACAM1
KeywordsFusobacterium nucleatum / trimeric autotransporter adhesin / CbpF / CEACAM1 / CELL ADHESION
Function / homology
Function and homology information


regulation of endothelial cell differentiation / insulin receptor internalization / negative regulation of cytotoxic T cell degranulation / granulocyte colony-stimulating factor signaling pathway / regulation of homophilic cell adhesion / Regulation of MITF-M dependent genes involved in invasion / negative regulation of hepatocyte proliferation / regulation of epidermal growth factor receptor signaling pathway / regulation of blood vessel remodeling / regulation of sprouting angiogenesis ...regulation of endothelial cell differentiation / insulin receptor internalization / negative regulation of cytotoxic T cell degranulation / granulocyte colony-stimulating factor signaling pathway / regulation of homophilic cell adhesion / Regulation of MITF-M dependent genes involved in invasion / negative regulation of hepatocyte proliferation / regulation of epidermal growth factor receptor signaling pathway / regulation of blood vessel remodeling / regulation of sprouting angiogenesis / filamin binding / negative regulation of natural killer cell mediated cytotoxicity directed against tumor cell target / negative regulation of lipid biosynthetic process / negative regulation of T cell mediated cytotoxicity / regulation of endothelial cell migration / insulin catabolic process / negative regulation of granulocyte differentiation / regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / common myeloid progenitor cell proliferation / negative regulation of interleukin-1 production / Fibronectin matrix formation / positive regulation of vasculogenesis / : / negative regulation of fatty acid biosynthetic process / negative regulation of platelet aggregation / bile acid transmembrane transporter activity / negative regulation of vascular permeability / regulation of immune system process / wound healing, spreading of cells / bile acid and bile salt transport / transport vesicle membrane / blood vessel development / microvillus membrane / homophilic cell-cell adhesion / tertiary granule membrane / lateral plasma membrane / negative regulation of T cell receptor signaling pathway / regulation of ERK1 and ERK2 cascade / negative regulation of protein kinase activity / specific granule membrane / regulation of cell migration / protein tyrosine kinase binding / basal plasma membrane / Cell surface interactions at the vascular wall / integrin-mediated signaling pathway / adherens junction / regulation of cell growth / kinase binding / cellular response to insulin stimulus / cell-cell junction / cell junction / cell migration / actin binding / angiogenesis / protein phosphatase binding / calmodulin binding / cell adhesion / protein dimerization activity / apical plasma membrane / Neutrophil degranulation / cell surface / signal transduction / protein homodimerization activity / extracellular exosome / membrane / identical protein binding / plasma membrane
Similarity search - Function
: / Immunoglobulin domain / Immunoglobulin / Immunoglobulin domain / Immunoglobulin domain / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype ...: / Immunoglobulin domain / Immunoglobulin / Immunoglobulin domain / Immunoglobulin domain / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
Cell adhesion molecule CEACAM1
Similarity search - Component
Biological speciesFusobacterium nucleatum (bacteria) / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.11 Å
AuthorsLi LJ / Shen F / Zhao X / Gao GF
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: Proc Natl Acad Sci U S A / Year: 2025
Title: Binding of autotransporter adhesin CbpF to human CEACAM1 and CEACAM5: A Velcro model for bacterium adhesion.
Authors: Fan Shen / Linjie Li / Dongchun Yang / Zhexiao Tang / Lu Zhang / Kefang Liu / Wenzhe Hou / Zhuozhuang Lu / Jing-Yuan Fang / Jianxun Qi / Xin Zhao / George F Gao /
Abstract: In eukaryotic systems, three major types of cell junctions have been well characterized. While bacterial adhesion mechanisms also exhibit remarkable diversity, the molecular processes that regulate ...In eukaryotic systems, three major types of cell junctions have been well characterized. While bacterial adhesion mechanisms also exhibit remarkable diversity, the molecular processes that regulate the dynamic modulation of binding strength between elongated bacterial cells and host cells remain poorly understood. () utilizes the surface adhesin CbpF to interact with the highly expressed host receptors CEACAM1 and CEACAM5 on cancer cells to facilitate tumor colonization. By elucidating the structural details of CbpF binding to human CEACAM1/CEACAM5 receptors, and through mechanistic investigations, we identified that the prominent EFNGQYQ loop on CbpF and the key Q78 residue of CEACAM1/CEACAM5 constitute the molecular linchpin of this pathogen-host interface. Furthermore, we found a distinct type of binding particle and proposed a Velcro-like adhesion model. In this model, CbpF mediates robust attachment through the simultaneous interaction of multiple binding sites, akin to the interlocking mechanism of Velcro. This multivalent interaction allows to dynamically switch between firm anchoring and easy detachment, adapting to varying physiological microenvironments. Our study elucidates the dynamic modulation of bacterial adhesion strength and lays the foundation for developing therapeutic interventions to disrupt the bacterium-host interface.
History
DepositionMar 27, 2025-
Header (metadata) releaseSep 3, 2025-
Map releaseSep 3, 2025-
UpdateMar 18, 2026-
Current statusMar 18, 2026Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_63959.png

Downloads & links

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Map

FileDownload / File: emd_63959.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSharpen by DeepEMhancer
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
0.76 Å/pix.
x 320 pix.
= 243.2 Å		0.76 Å/pix.
x 320 pix.
= 243.2 Å		0.76 Å/pix.
x 320 pix.
= 243.2 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.76 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.08
Minimum - Maximum-0.0017590832 - 1.8480554
Average (Standard dev.)0.0011608448 (±0.024186818)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 243.2 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_63959_msk_1.map
Projections & Slices
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Additional map: Map before sharpening

Fileemd_63959_additional_1.map
AnnotationMap before sharpening
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Half map: Half-A map

Fileemd_63959_half_map_1.map
AnnotationHalf-A map
Projections & Slices
AxesZYX

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Histogram

Histogram (log scale)

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Half map: Half-B map

Fileemd_63959_half_map_2.map
AnnotationHalf-B map
Projections & Slices
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Sample components

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Entire : Fusobacterium nucleatum CbpF in complex with human CEACAM1

EntireName: Fusobacterium nucleatum CbpF in complex with human CEACAM1
Components
  • Complex: Fusobacterium nucleatum CbpF in complex with human CEACAM1
    • Protein or peptide: Fusobacterium nucleatum CbpF
    • Protein or peptide: Cell adhesion molecule CEACAM1

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Supramolecule #1: Fusobacterium nucleatum CbpF in complex with human CEACAM1

SupramoleculeName: Fusobacterium nucleatum CbpF in complex with human CEACAM1
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Fusobacterium nucleatum (bacteria)

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Macromolecule #1: Fusobacterium nucleatum CbpF

MacromoleculeName: Fusobacterium nucleatum CbpF / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Fusobacterium nucleatum (bacteria)
Molecular weightTheoretical: 35.874555 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MVSFSAPVFQ AGTGTDSTVA GVNNEANGEK SSAFGYENKA KEKLSSAFGY KNIANGIEGS AFGISNLAKG QYSSAFGFRN VANKRHSSA FGSGNEANGE QSSAFGFKNT VSGFNSSAFG SQYEVTGNFS GAFGMGEFNG QYQYKNEGNN SYMIGNKNKI A SGSNDNFI ...String:
MVSFSAPVFQ AGTGTDSTVA GVNNEANGEK SSAFGYENKA KEKLSSAFGY KNIANGIEGS AFGISNLAKG QYSSAFGFRN VANKRHSSA FGSGNEANGE QSSAFGFKNT VSGFNSSAFG SQYEVTGNFS GAFGMGEFNG QYQYKNEGNN SYMIGNKNKI A SGSNDNFI LGNNVHIGGG INNSVALGNN STVSASNTVS VGSSTLKRKI VNVGDGAISA NSSDAVTGRQ LYSGNGIDTA AW QNKLNVT RKNDYKDAND IDVNKWKAKL GVGSGGGGGT ADIENLRNEV NEKIDDVKDE VRENLYFQGS AWSHPQFEKG GGS GGGSGG SAWSHPQFEK HHHHHH

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Macromolecule #2: Cell adhesion molecule CEACAM1

MacromoleculeName: Cell adhesion molecule CEACAM1 / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 15.913442 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MQLTTESMPF NVAEGKEVLL LVHNLPQQLF GYSWYKGERV DGNRQIVGYA IGTQQATPGP ANSGRETIYP NASLLIQNVT QNDTGFYTL QVIKSDLVNE EATGQFHVYE NLYFQGSAWS HPQFEKGGGS GGGSGGSAWS HPQFEK

UniProtKB: Cell adhesion molecule CEACAM1

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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: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.8 µm / Nominal defocus min: 1.2 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.11 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 430775
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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