7OCJ | pdb_00007ocj

Crystal structure of E.coli LexA in complex with nanobody NbSOS2(Nb14509)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 
    0.260 (Depositor), 0.252 (DCC) 
  • R-Value Work: 
    0.228 (Depositor), 0.225 (DCC) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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This is version 1.3 of the entry. See complete history

Literature

Nanobodies targeting LexA autocleavage disclose a novel suppression strategy of SOS-response pathway.

Maso, L.Vascon, F.Chinellato, M.Goormaghtigh, F.Bellio, P.Campagnaro, E.Van Melderen, L.Ruzzene, M.Pardon, E.Angelini, A.Celenza, G.Steyaert, J.Tondi, D.Cendron, L.

(2022) Structure 30: 1479

  • DOI: https://doi.org/10.1016/j.str.2022.09.004
  • Primary Citation Related Structures: 
    7B5G, 7OCJ, 7ZRA

  • PubMed Abstract: 

    Antimicrobial resistance threatens the eradication of infectious diseases and impairs the efficacy of available therapeutics. The bacterial SOS pathway is a conserved response triggered by genotoxic stresses and represents one of the principal mechanisms that lead to resistance. The RecA recombinase acts as a DNA-damage sensor inducing the autoproteolysis of the transcriptional repressor LexA, thereby derepressing SOS genes that mediate DNA repair, survival to chemotherapy, and hypermutation. The inhibition of such pathway represents a promising strategy for delaying the evolution of antimicrobial resistance. We report the identification, via llama immunization and phage display, of nanobodies that bind LexA with sub-micromolar affinity and block autoproteolysis, repressing SOS response in Escherichia coli. Biophysical characterization of nanobody-LexA complexes revealed that they act by trapping LexA in an inactive conformation and interfering with RecA engagement. Our studies pave the way to the development of new-generation antibiotic adjuvants for the treatment of bacterial infections.


  • Organizational Affiliation
    • Dipartimento di Biologia, Università degli Studi di Padova, Via Ugo Bassi 58/b, 35131 Padova, Italy.

Macromolecule Content 

  • Total Structure Weight: 147.99 kDa 
  • Atom Count: 7,570 
  • Modeled Residue Count: 979 
  • Deposited Residue Count: 1,348 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
NbSOS2 (14509)A [auth G],
D [auth E],
E [auth B],
H
115Lama glamaMutation(s): 0 
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
LexA repressorB [auth A],
C,
F [auth D],
G [auth F]
222Escherichia coliMutation(s): 0 
Gene Names: lexAEAMG_02325
EC: 3.4.21.88

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
EDO

Query on EDO



Download:Ideal Coordinates CCD File
I [auth A]1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free:  0.260 (Depositor), 0.252 (DCC) 
  • R-Value Work:  0.228 (Depositor), 0.225 (DCC) 
Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 112.672α = 90
b = 112.672β = 90
c = 144.751γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
xia2data scaling
MOLREPphasing

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Italian Ministry of EducationItaly--

Revision History  (Full details and data files)

  • Version 1.0: 2022-10-26
    Type: Initial release
  • Version 1.1: 2022-11-16
    Changes: Database references
  • Version 1.2: 2024-01-31
    Changes: Data collection, Database references, Refinement description
  • Version 1.3: 2024-10-16
    Changes: Structure summary