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- PDB-9u94: Cryo-EM structure of Fusobacterium nucleatum CbpF in complex with... -

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Basic information

Entry
Database: PDB / ID: 9u94
TitleCryo-EM structure of Fusobacterium nucleatum CbpF in complex with human CEACAM1
Components
  • Cell adhesion molecule CEACAM1
  • Fusobacterium nucleatum CbpF
KeywordsCELL ADHESION / Fusobacterium nucleatum / trimeric autotransporter adhesin / CbpF / CEACAM1
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)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.11 Å
AuthorsLi, L.J. / Shen, F. / Zhao, X. / Gao, G.F.
Funding support China, 1items
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, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Sep 3, 2025Provider: repository / Type: Initial release
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Revision 2.0Mar 18, 2026Data content type: EM metadata / Data content type: EM metadata / EM metadata / Group: Database references / Experimental summary / Data content type: EM metadata / EM metadata / EM metadata / Category: citation / citation_author / em_admin
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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
C: Fusobacterium nucleatum CbpF
F: Cell adhesion molecule CEACAM1
A: Fusobacterium nucleatum CbpF
E: Cell adhesion molecule CEACAM1
B: Fusobacterium nucleatum CbpF
D: Cell adhesion molecule CEACAM1


Theoretical massNumber of molelcules
Total (without water)155,3646
Polymers155,3646
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein Fusobacterium nucleatum CbpF


Mass: 35874.555 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Fusobacterium nucleatum (bacteria) / Production host: Escherichia coli (E. coli)
#2: Protein Cell adhesion molecule CEACAM1 / Biliary glycoprotein 1 / BGP-1 / Carcinoembryonic antigen-related cell adhesion molecule 1 / CEA ...Biliary glycoprotein 1 / BGP-1 / Carcinoembryonic antigen-related cell adhesion molecule 1 / CEA cell adhesion molecule 1


Mass: 15913.442 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CEACAM1, BGP, BGP1 / Production host: Escherichia coli (E. coli) / References: UniProt: P13688
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Fusobacterium nucleatum CbpF in complex with human CEACAM1
Type: COMPLEX / Entity ID: all / Source: MULTIPLE SOURCES
Source (natural)Organism: Fusobacterium nucleatum (bacteria)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 1800 nm / Nominal defocus min: 1200 nm
Image recordingElectron dose: 40 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k)

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Processing

EM softwareName: PHENIX / Version: 1.20.1_4487 / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.11 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 430775 / Symmetry type: POINT
RefinementHighest resolution: 2.11 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)

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