Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 22.77 kDa 
• Atom Count: 1592 
• Modelled Residue Count: 196 
• Deposited Residue Count: 198 
• Unique protein chains: 1

6BCS

LilrB2 D1D2 domains complexed with benzamidine

• PDB DOI: 10.2210/pdb6BCS/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2017-10-20 Released: 2018-09-05 
• Deposition Author(s): Cao, Q., Sawaya, M.R., Eisenberg, D.S.
• Funding Organization(s): National Institutes of Health/National Institute on Aging (NIH/NIA)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.233 
• R-Value Work: 0.182 
• R-Value Observed: 0.187 

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

• PubMed: 30297750 
• DOI: 10.1038/s41557-018-0147-z
• Primary Citation of Related Structures:  
  6BCS


• 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 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.

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Organizational Affiliation: 

Department of Neurology, Molecular Biology Institute and Brain Research Institute, UCLA, Los Angeles, CA, USA. [e-mail].

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Leukocyte immunoglobulin-like receptor subfamily B member 2	A	198	Homo sapiens	Mutation(s): 0  Gene Names: LILRB2, ILT4, LIR2, MIR10
UniProt & NIH Common Fund Data Resources
Find proteins for Q8N423 (Homo sapiens) Explore Q8N423  Go to UniProtKB:  Q8N423
PHAROS:  Q8N423

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
BEN	B [auth A], C [auth A], D [auth A], E [auth A]	BENZAMIDINE C7 H8 N2 PXXJHWLDUBFPOL-UHFFFAOYSA-N
DMS	H [auth A], I [auth A]	DIMETHYL SULFOXIDE C2 H6 O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N
CL	F [auth A], G [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.233 
• R-Value Work: 0.182 
• R-Value Observed: 0.187 
• Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 57.05	α = 90
b = 57.05	β = 90
c = 101.18	γ = 90

Software Package:

Software Name	Purpose
XSCALE	data scaling
PHASER	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction
Coot	model building
XDS	data reduction

Structure Validation

Entry History & Funding Information

Deposition Data

• Deposited Date: 2017-10-20 
• Released Date: 2018-09-05 
Deposition Author(s): Cao, Q., Sawaya, M.R., Eisenberg, D.S.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute on Aging (NIH/NIA)	United States	NIH AG054022

Revision History  

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