8H62 | pdb_00008h62

Crystal structure of Internalin A from Listeria monocytogenes with human E-cadherin EC12


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.91 Å
  • R-Value Free: 
    0.210 (Depositor), 0.214 (DCC) 
  • R-Value Work: 
    0.176 (Depositor), 0.184 (DCC) 
  • R-Value Observed: 
    0.178 (Depositor) 

Starting Models: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 8H62

This is version 1.2 of the entry. See complete history

Literature

Anti-InlA single-domain antibodies that inhibit the cell invasion of Listeria monocytogenes.

Yamazaki, T.Nagatoishi, S.Yamawaki, T.Nozawa, T.Matsunaga, R.Nakakido, M.Caaveiro, J.M.M.Nakagawa, I.Tsumoto, K.

(2023) J Biological Chem 299: 105254-105254

  • DOI: https://doi.org/10.1016/j.jbc.2023.105254
  • Primary Citation Related Structures: 
    8H62, 8H63, 8H64

  • PubMed Abstract: 

    Listeriosis, caused by infection with Listeria monocytogenes, is a severe disease with a high mortality rate. The L. monocytogenes virulence factor, internalin family protein InlA, which binds to the host receptor E-cadherin, is necessary to invade host cells. Here, we isolated two single-domain antibodies (V H Hs) that bind to InlA with picomolar affinities from an alpaca immune library using the phage display method. These InlA-specific V H Hs inhibited the binding of InlA to the extracellular domains of E-cadherin in vitro as shown by biophysical interaction analysis. Furthermore, we determined that the V H Hs inhibited the invasion of L. monocytogenes into host cells in culture. High-resolution X-ray structure analyses of the complexes of V H Hs with InlA revealed that the V H Hs bind to the same binding site as E-cadherin against InlA. We conclude that these V H Hs have the potential for use as drugs to treat listeriosis.


  • Organizational Affiliation
    • Department of Bioengineering, School of Engineering, The University of Tokyo, Tokyo, Japan.

Macromolecule Content 

  • Total Structure Weight: 73.27 kDa 
  • Atom Count: 5,815 
  • Modeled Residue Count: 675 
  • Deposited Residue Count: 675 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Internalin A462Listeria monocytogenes EGD-eMutation(s): 0 
Gene Names: inlAlmo0433intlA
UniProt
Find proteins for P0DJM0 (Listeria monocytogenes serovar 1/2a (strain ATCC BAA-679 / EGD-e))
Explore P0DJM0 
Go to UniProtKB:  P0DJM0
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0DJM0
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Cadherin-1213Homo sapiensMutation(s): 1 
Gene Names: CDH1CDHEUVO
UniProt & NIH Common Fund Data Resources
Find proteins for P12830 (Homo sapiens)
Explore P12830 
Go to UniProtKB:  P12830
PHAROS:  P12830
GTEx:  ENSG00000039068 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP12830
Sequence Annotations
Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.91 Å
  • R-Value Free:  0.210 (Depositor), 0.214 (DCC) 
  • R-Value Work:  0.176 (Depositor), 0.184 (DCC) 
  • R-Value Observed: 0.178 (Depositor) 
Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 55.35α = 101.48
b = 69.58β = 97.77
c = 72.49γ = 105.99
Software Package:
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
MOSFLMdata reduction
Aimlessdata scaling
MOLREPphasing

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Japan Society for the Promotion of Science (JSPS)JapanJP16H02420

Revision History  (Full details and data files)

  • Version 1.0: 2023-10-04
    Type: Initial release
  • Version 1.1: 2023-10-25
    Changes: Database references
  • Version 1.2: 2026-03-04
    Changes: Refinement description, Structure summary