8X7N | pdb_00008x7n

Cell-cell adhesion Nanobody/Antigen Pair

• PDB DOI: https://doi.org/10.2210/pdb8X7N/pdb

• Classification: ANTIMICROBIAL PROTEIN
• Organism(s): Salmonella enterica subsp. enterica serovar Typhimurium str. LT2, synthetic construct
• Expression System: Escherichia coli BL21(DE3), Escherichia coli
• Mutation(s): No 


• Deposited: 2023-11-24 Released: 2024-07-17 
• Deposition Author(s): Chen, P.-P., Hsia, K.-C., Ting, S.-Y., Chen, Y.-C.
• Funding Organization(s): Academia Sinica (Taiwan)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.67 Å
• R-Value Free: 
  0.285 (Depositor), 0.261 (DCC) 
• R-Value Work: 
  0.260 (Depositor) 
• R-Value Observed: 
  0.262 (Depositor) 

Starting Model: experimental

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

• PubMed: 39095377 
• DOI: https://doi.org/10.1038/s41467-024-51017-1
• Primary Citation 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.

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Organizational Affiliation: 
• Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan.
Molecular and Cell Biology, Taiwan International Graduate Program, Academia Sinica and National Defense Medical Center, Taipei, Taiwan.
Institute of Biochemistry and Molecular Biology, College of Life Sciences, National Yang Ming Chiao Tung University, Taipei, Taiwan.
Program in Molecular Medicine, National Yang-Ming Chao-Tung University and Academia Sinica, Taipei, Taiwan.
Institute of Chemistry, Academia Sinica, Taipei, Taiwan.
Physics Division, National Center for Theoretical Sciences, Taipei, Taiwan.
Genome and Systems Biology Degree Program, National Taiwan University, Taipei, Taiwan.
Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan. [e-mail].
Molecular and Cell Biology, Taiwan International Graduate Program, Academia Sinica and National Defense Medical Center, Taipei, Taiwan. [e-mail].
Genome and Systems Biology Degree Program, National Taiwan University, Taipei, Taiwan. [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: isothermal titration calorimetry

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 2 assigned by authors.

Biological Assembly 3  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 3 assigned by authors.

Biological Assembly 4  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 4 assigned by authors.

Biological Assembly 5  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 5 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 139.05 kDa 
• Atom Count: 8,930 
• Modeled Residue Count: 1,190 
• Deposited Residue Count: 1,290 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Conjugative transfer: aggregate stability	A, C, E, G, I	135	Salmonella enterica subsp. enterica serovar Typhimurium str. LT2	Mutation(s): 0  Gene Names: traN
UniProt
Find proteins for Q93GM7 (Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720)) Explore Q93GM7  Go to UniProtKB:  Q93GM7

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Nb-TraN	B, D, F, H, J	123	synthetic construct	Mutation(s): 0

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.67 Å
• R-Value Free:  0.285 (Depositor), 0.261 (DCC) 
• R-Value Work:  0.260 (Depositor) 
• R-Value Observed: 0.262 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 96.864	α = 90
b = 153.263	β = 90
c = 163.03	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data scaling
PHENIX	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2024-07-17 
Deposition Author(s): Chen, P.-P., Hsia, K.-C., Ting, S.-Y., Chen, Y.-C.

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Funding Organization	Location	Grant Number
Academia Sinica (Taiwan)	Taiwan	AS-IVA-112-L05

Revision History  

• 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