6BCS

LilrB2 D1D2 domains complexed with benzamidine


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.233 
  • R-Value Work: 0.182 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history

Literature

Inhibiting amyloid-beta cytotoxicity through its interaction with the cell surface receptor LilrB2 by structure-based design.

Cao, Q.Shin, W.S.Chan, H.Vuong, C.K.Dubois, B.Li, B.Murray, K.A.Sawaya, M.R.Feigon, J.Black, D.L.Eisenberg, D.S.Jiang, L.

(2018) Nat Chem 10: 1213-1221

  • DOI: 10.1038/s41557-018-0147-z

  • PubMed Abstract: 
  • Inhibiting the interaction between amyloid-β (Aβ) and a neuronal cell surface receptor, LilrB2, has been suggested as a potential route for treating Alzheimer's disease. Supporting this approach, Alzheimer's-like symptoms are reduced in mouse models ...

    Inhibiting the interaction between amyloid-β (Aβ) and a neuronal cell surface receptor, LilrB2, has been suggested as a potential route for treating Alzheimer's disease. Supporting this approach, Alzheimer's-like symptoms are reduced in mouse models following genetic depletion of the LilrB2 homologue. In its pathogenic, oligomeric state, Aβ binds to LilrB2, triggering a pathway to synaptic loss. Here we identify the LilrB2 binding moieties of Aβ ( 16 KLVFFA 21 ) and identify its binding site on LilrB2 from a crystal structure of LilrB2 immunoglobulin domains D1D2 complexed to small molecules that mimic phenylalanine residues. In this structure, we observed two pockets that can accommodate the phenylalanine side chains of KLVFFA. These pockets were confirmed to be 16 KLVFFA 21 binding sites by mutagenesis. Rosetta docking revealed a plausible geometry for the Aβ-LilrB2 complex and assisted with the structure-guided selection of small molecule inhibitors. These molecules inhibit Aβ-LilrB2 interactions in vitro and on the cell surface and reduce Aβ cytotoxicity, which suggests these inhibitors are potential therapeutic leads against Alzheimer's disease.


    Organizational Affiliation

    Systems Neurobiology Laboratory, The Salk Institute for Biological Studies, La Jolla, CA, USA.,Departments of Chemistry and Biochemistry and Biological Chemistry, UCLA-DOE Institute and Howard Hughes Medical Institute, UCLA, Los Angeles, CA, USA. david@mbi.ucla.edu.,Department of Neurology, Molecular Biology Institute and Brain Research Institute, UCLA, Los Angeles, CA, USA. jianglin@ucla.edu.,Department of Microbiology, Immunology and Molecular Genetics, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA.,Division of Applied Mathematics, Brown University, Providence, RI, USA.,Departments of Chemistry and Biochemistry and Biological Chemistry, UCLA-DOE Institute and Howard Hughes Medical Institute, UCLA, Los Angeles, CA, USA.,Department of Chemistry and Biochemistry, UCLA, Los Angeles, CA, USA.,Department of Neurology, Molecular Biology Institute and Brain Research Institute, UCLA, Los Angeles, CA, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Leukocyte immunoglobulin-like receptor subfamily B member 2
A
198Homo sapiensMutation(s): 0 
Gene Names: LILRB2 (ILT4, LIR2, MIR10)
Find proteins for Q8N423 (Homo sapiens)
Go to Gene View: LILRB2
Go to UniProtKB:  Q8N423
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CL
Query on CL

Download SDF File 
Download CCD File 
A
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
DMS
Query on DMS

Download SDF File 
Download CCD File 
A
DIMETHYL SULFOXIDE
C2 H6 O S
IAZDPXIOMUYVGZ-UHFFFAOYSA-N
 Ligand Interaction
BEN
Query on BEN

Download SDF File 
Download CCD File 
A
BENZAMIDINE
C7 H8 N2
PXXJHWLDUBFPOL-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.233 
  • R-Value Work: 0.182 
  • Space Group: P 41 21 2
Unit Cell:
Length (Å)Angle (°)
a = 57.050α = 90.00
b = 57.050β = 90.00
c = 101.180γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
XSCALEdata scaling
PHENIXrefinement
Cootmodel building
PDB_EXTRACTdata extraction
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute on Aging (NIH/NIA)United StatesNIH AG054022

Revision History 

  • Version 1.0: 2018-09-05
    Type: Initial release
  • Version 1.1: 2018-10-24
    Type: Data collection, Database references, Source and taxonomy
  • Version 1.2: 2018-12-05
    Type: Data collection, Database references
  • Version 1.3: 2019-02-20
    Type: Author supporting evidence, Data collection
  • Version 1.4: 2019-12-18
    Type: Author supporting evidence