6DBF

Crystal Structure of VHH R303 in complex with InlB-LRR


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.55 Å
  • R-Value Free: 0.163 
  • R-Value Work: 0.138 
  • R-Value Observed: 0.139 

wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

Structural basis of VHH-mediated neutralization of the food-borne pathogenListeria monocytogenes.

King, M.T.Huh, I.Shenai, A.Brooks, T.M.Brooks, C.L.

(2018) J Biol Chem 293: 13626-13635

  • DOI: https://doi.org/10.1074/jbc.RA118.003888
  • Primary Citation of Related Structures:  
    6DBA, 6DBD, 6DBE, 6DBF, 6DBG

  • PubMed Abstract: 

    Listeria monocytogenes causes listeriosis, a potentially fatal food-borne disease. The condition is especially harmful to pregnant women. Listeria outbreaks can originate from diverse foods, highlighting the need for novel strategies to improve food safety. The first step in Listeria invasion is internalization of the bacteria, which is mediated by the interaction of the internalin family of virulence factors with host cell receptors. A crucial interaction for Listeria invasion of the placenta, and thus a target for therapeutic intervention, is between internalin B (InlB) and the receptor c-Met. Single-domain antibodies (V H H, also called nanobodies, or sdAbs) from camel heavy-chain antibodies are a novel solution for preventing Listeria infections. The V H H R303, R330, and R326 all bind InlB with high affinity; however, the molecular mechanism behind their mode of action was unknown. We demonstrate that despite a high degree of sequence and structural diversity, the V H H bind a single epitope on InlB. A combination of gentamicin protection assays and florescent microscopy establish that InlB-specific V H H inhibit Listeria invasion of HeLa cells. A high-resolution X-ray structure of V H H R303 in complex with InlB showed that the V H H binds at the c-Met interaction site on InlB, thereby acting as a competitive inhibitor preventing bacterial invasion. These results point to the potential of V H H as a novel class of therapeutics for the prevention of listeriosis.


  • Organizational Affiliation

    From the Department of Chemistry, California State University, Fresno, California 93740.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Listeria virulence factor InlB229Listeria monocytogenesMutation(s): 0 
UniProt
Find proteins for P0DQD3 (Listeria monocytogenes serotype 1/2a (strain EGD / Mackaness))
Explore P0DQD3 
Go to UniProtKB:  P0DQD3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0DQD3
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
InlB specific VHH R303142Camelus dromedariusMutation(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: 1.55 Å
  • R-Value Free: 0.163 
  • R-Value Work: 0.138 
  • R-Value Observed: 0.139 
  • Space Group: P 43
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 82.964α = 90
b = 82.964β = 90
c = 64.216γ = 90
Software Package:
Software NamePurpose
xia2data scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
xia2data reduction
PHENIXphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesSC3GM112532

Revision History  (Full details and data files)

  • Version 1.0: 2018-07-18
    Type: Initial release
  • Version 1.1: 2018-07-25
    Changes: Data collection, Database references
  • Version 1.2: 2018-09-12
    Changes: Data collection, Database references, Source and taxonomy
  • Version 1.3: 2020-01-01
    Changes: Author supporting evidence
  • Version 1.4: 2023-10-04
    Changes: Data collection, Database references, Refinement description