8X7N | pdb_00008x7n

Cell-cell adhesion Nanobody/Antigen Pair


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.67 Å
  • R-Value Free: 
    0.285 (Depositor), 0.290 (DCC) 
  • R-Value Work: 
    0.260 (Depositor), 0.260 (DCC) 
  • R-Value Observed: 
    0.262 (Depositor) 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

A whole-cell platform for discovering synthetic cell adhesion molecules in bacteria.

Chen, P.Y.Chen, Y.C.Chen, P.P.Lin, K.T.Sargsyan, K.Hsu, C.P.Wang, W.L.Hsia, K.C.Ting, S.Y.

(2024) Nat Commun 15: 6568-6568

  • DOI: https://doi.org/10.1038/s41467-024-51017-1
  • Primary Citation of Related Structures:  
    8X7N

  • PubMed Abstract: 

    Developing programmable bacterial cell-cell adhesion is of significant interest due to its versatile applications. Current methods that rely on presenting cell adhesion molecules (CAMs) on bacterial surfaces are limited by the lack of a generalizable strategy to identify such molecules targeting bacterial membrane proteins in their natural states. Here, we introduce a whole-cell screening platform designed to discover CAMs targeting bacterial membrane proteins within a synthetic bacteria-displayed nanobody library. Leveraging the potency of the bacterial type IV secretion system-a contact-dependent DNA delivery nanomachine-we have established a positive feedback mechanism to selectively enrich for bacteria displaying nanobodies that target antigen-expressing cells. Our platform successfully identified functional CAMs capable of recognizing three distinct outer membrane proteins (TraN, OmpA, OmpC), demonstrating its efficacy in CAM discovery. This approach holds promise for engineering bacterial cell-cell adhesion, such as directing the antibacterial activity of programmed inhibitor cells toward target bacteria in mixed populations.


  • Organizational Affiliation
    • Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Conjugative transfer: aggregate stability
A, C, E, G, I
135Salmonella enterica subsp. enterica serovar Typhimurium str. LT2Mutation(s): 0 
Gene Names: traN
UniProt
Find proteins for Q93GM7 (Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720))
Explore Q93GM7 
Go to UniProtKB:  Q93GM7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ93GM7
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Nb-TraN
B, D, F, H, J
123synthetic constructMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.67 Å
  • R-Value Free:  0.285 (Depositor), 0.290 (DCC) 
  • R-Value Work:  0.260 (Depositor), 0.260 (DCC) 
  • R-Value Observed: 0.262 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 96.864α = 90
b = 153.263β = 90
c = 163.03γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data scaling
PHENIXphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Academia Sinica (Taiwan)TaiwanAS-IVA-112-L05

Revision History  (Full details and data files)

  • Version 1.0: 2024-07-17
    Type: Initial release
  • Version 1.1: 2024-11-20
    Changes: Structure summary
  • Version 1.2: 2026-01-28
    Changes: Database references