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 9XUZ | pdb_00009xuz

Solution structure of Site2 dimer of Ler


Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 100 
  • Conformers Submitted: 20 
  • Selection Criteria: structures with the lowest energy 

wwPDB Validation 3D Report Full Report

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This is version 1.0 of the entry. See complete history. 

Literature

Structural basis of the oligomerization of anti-silencer Ler from enterohemorrhagic E. coli (EHEC).

Wang, G., Duan, B., Xia, B.

(2026) Struct Dyn 13: 024702-024702

  • DOI: https://doi.org/10.1063/4.0001203
  • Primary Citation Related Structures: 
    9XUZ

  • PubMed Abstract: 

    The locus of enterocyte effacement-encoded regulator (Ler) is a master transcriptional activator essential for the virulence of enterohemorrhagic and enteropathogenic Escherichia coli . Although Ler shares homology with the global silencer H-NS, it functions uniquely as an anti-silencer, a role strictly dependent on its oligomerization state. However, the structural mechanism governing Ler assembly remains poorly understood. In this study, we have characterized the N-terminal oligomerization domain (Ler 1-74 ) of Ler using solution NMR spectroscopy and biophysical assays, and found that Ler 1-74 shows concentration-dependent oligomerization. We demonstrate that Ler oligomerization is driven by two distinct interfaces with contrasting dynamic properties. We determined the solution structure of the Ler 18-74 dimer, revealing a stable, anti-parallel "tail-to-tail" interface (dimer Site-2, residues 35-66) stabilized by a hydrophobic core. In contrast, the N-terminal interface (dimer Site-1, residues 12-33) forms a highly dynamic "head-to-head" dimer, which undergoes significant conformational exchange and exhibits concentration- and temperature-dependent dimerization. Based on these findings, we propose a structural model wherein Ler forms supramolecular assemblies through the propagation of alternating stable (Site-2) and dynamic (Site-1) interactions. This architecture, while reminiscent of H-NS, displays distinct stability features that may underlie Ler's specific anti-silencing function in bacterial pathogenesis.

Macromolecule Content 

  • Total Structure Weight: 13.94 kDa 
  • Atom Count: 978 
  • Modeled Residue Count: 122 
  • Deposited Residue Count: 122 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Transcription regulator Ler
A, B
61Escherichia coliMutation(s): 0 
Gene Names: ler, HVV39_11365, NCTC10279_01062
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 100 
  • Conformers Submitted: 20 
  • Selection Criteria: structures with the lowest energy 

Structure Validation

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Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Basic Research Program of China (973 Program)China--

Revision History  (Full details and data files)

  • Version 1.0: 2026-09-30
    Type: Initial release