9U93 | pdb_00009u93

Cryo-EM structure of Fusobacterium nucleatum CbpF in complex with human CEACAM5


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.40 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Binding of Fusobacterium nucleatum autotransporter adhesin CbpF to human CEACAM1 and CEACAM5: A Velcro model for bacterium adhesion.

Shen, F.Li, L.Yang, D.Tang, Z.Zhang, L.Liu, K.Hou, W.Lu, Z.Fang, J.Y.Qi, J.Zhao, X.Gao, G.F.

(2025) Proc Natl Acad Sci U S A 122: e2516574122-e2516574122

  • DOI: https://doi.org/10.1073/pnas.2516574122
  • Primary Citation Related Structures: 
    9U93, 9U94

  • PubMed 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 the dynamic modulation of binding strength between elongated bacterial cells and host cells remain poorly understood. Fusobacterium nucleatum ( F. nucleatum ) 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 F. nucleatum 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.


  • Organizational Affiliation
    • Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Fusobacterium nucleatum CbpFA [auth C],
C [auth B],
E [auth A]
342Fusobacterium nucleatumMutation(s): 0 
UniProt
Find proteins for A0A0M4S4Q9 (Fusobacterium nucleatum subsp. nucleatum)
Explore A0A0M4S4Q9 
Go to UniProtKB:  A0A0M4S4Q9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A0M4S4Q9
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Cell adhesion molecule CEACAM5B [auth F],
D,
F [auth E]
148Homo sapiensMutation(s): 0 
Gene Names: CEACAM5CEA
UniProt & NIH Common Fund Data Resources
Find proteins for P06731 (Homo sapiens)
Explore P06731 
Go to UniProtKB:  P06731
PHAROS:  P06731
GTEx:  ENSG00000105388 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP06731
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.40 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.20.1_4487
RECONSTRUCTIONcryoSPARC

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China--

Revision History  (Full details and data files)

  • Version 1.0: 2025-09-03
    Type: Initial release
  • Version 1.1: 2026-03-18
    Changes: Data collection, Database references