8H64

Crystal structure of Internalin A from Listeria monocytogenes with nanobody VHH24 bound


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.35 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.188 
  • R-Value Observed: 0.190 

wwPDB Validation   3D Report Full Report


This is version 1.1 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 Biol Chem 299: 105254-105254

  • DOI: https://doi.org/10.1016/j.jbc.2023.105254
  • Primary Citation of 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.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Internalin A
A, C, E, G
462Listeria monocytogenes EGD-eMutation(s): 0 
Gene Names: inlAlmo0433
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:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Anti-internalin A VHH24
B, D, F, H
123Lama glamaMutation(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: 2.35 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.188 
  • R-Value Observed: 0.190 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 129.73α = 90
b = 141.12β = 90
c = 198.61γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
MOSFLMdata reduction
SCALAdata 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