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- PDB-9u93: Cryo-EM structure of Fusobacterium nucleatum CbpF in complex with... -

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Basic information

Entry
Database: PDB / ID: 9u93
TitleCryo-EM structure of Fusobacterium nucleatum CbpF in complex with human CEACAM5
Components
  • Cell adhesion molecule CEACAM5
  • Fusobacterium nucleatum CbpF
KeywordsCELL ADHESION / Fusobacterium nucleatum / trimeric autotransporter adhesin / CbpF / CEACAM5
Function / homology
Function and homology information


GPI anchor binding / homotypic cell-cell adhesion / negative regulation of myotube differentiation / Post-translational modification: synthesis of GPI-anchored proteins / heterophilic cell-cell adhesion / homophilic cell-cell adhesion / negative regulation of anoikis / side of membrane / Cell surface interactions at the vascular wall / basolateral plasma membrane ...GPI anchor binding / homotypic cell-cell adhesion / negative regulation of myotube differentiation / Post-translational modification: synthesis of GPI-anchored proteins / heterophilic cell-cell adhesion / homophilic cell-cell adhesion / negative regulation of anoikis / side of membrane / Cell surface interactions at the vascular wall / basolateral plasma membrane / apical plasma membrane / apoptotic process / negative regulation of apoptotic process / cell surface / protein homodimerization activity / extracellular exosome / extracellular region / membrane / identical protein binding / plasma membrane
Similarity search - Function
: / 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 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 CEACAM5
Similarity search - Component
Biological speciesFusobacterium nucleatum (bacteria)
Homo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.4 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 CEACAM5
B: Fusobacterium nucleatum CbpF
D: Cell adhesion molecule CEACAM5
A: Fusobacterium nucleatum CbpF
E: Cell adhesion molecule CEACAM5


Theoretical massNumber of molelcules
Total (without water)156,8366
Polymers156,8366
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 CEACAM5 / Carcinoembryonic antigen / CEA / Carcinoembryonic antigen-related cell adhesion molecule 5 / CEA ...Carcinoembryonic antigen / CEA / Carcinoembryonic antigen-related cell adhesion molecule 5 / CEA cell adhesion molecule 5 / Meconium antigen 100


Mass: 16404.209 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CEACAM5, CEA / Production host: Escherichia coli (E. coli) / References: UniProt: P06731
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 CEACAM5
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 software
IDNameVersionCategory
1cryoSPARCparticle selection
2PHENIX1.20.1_4487model refinement
13cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 240256 / Symmetry type: POINT
RefinementHighest resolution: 2.4 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)

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