5X33

Leukotriene B4 receptor BLT1 in complex with BIIL260


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.7 Å
  • R-Value Free: 0.296 
  • R-Value Work: 0.248 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Na+-mimicking ligands stabilize the inactive state of leukotriene B4receptor BLT1.

Hori, T.Okuno, T.Hirata, K.Yamashita, K.Kawano, Y.Yamamoto, M.Hato, M.Nakamura, M.Shimizu, T.Yokomizo, T.Miyano, M.Yokoyama, S.

(2018) Nat. Chem. Biol. 14: 262-269

  • DOI: 10.1038/nchembio.2547

  • PubMed Abstract: 
  • Most G-protein-coupled receptors (GPCRs) are stabilized in common in the inactive state by the formation of the sodium ion-centered water cluster with the conserved Asp <sup>2.50 </sup> inside the seven-transmembrane domain. We determined the crystal ...

    Most G-protein-coupled receptors (GPCRs) are stabilized in common in the inactive state by the formation of the sodium ion-centered water cluster with the conserved Asp 2.50 inside the seven-transmembrane domain. We determined the crystal structure of the leukotriene B 4 (LTB 4 ) receptor BLT1 bound with BIIL260, a chemical bearing a benzamidine moiety. Surprisingly, the amidine group occupies the sodium ion and water locations, interacts with D66 2.50 , and mimics the entire sodium ion-centered water cluster. Thus, BLT1 is fixed in the inactive state, and the transmembrane helices cannot change their conformations to form the active state. Moreover, the benzamidine molecule alone serves as a negative allosteric modulator for BLT1. As the residues involved in the benzamidine binding are widely conserved among GPCRs, the unprecedented inverse-agonist mechanism by the benzamidine moiety could be adapted to other GPCRs. Consequently, the present structure will enable the rational development of inverse agonists specific for each GPCR.


    Organizational Affiliation

    Japan Science and Technology Agency, Precursory Research for Embryonic Science and Technology (PRESTO), Kawaguchi, Saitama, Japan.,Department of Chemistry and Biological Science, College of Science and Engineering, Aoyama Gakuin University, Chuo-ku, Sagamihara, Kanagawa, Japan.,RIKEN Structural Biology Laboratory, Tsurumi-ku, Yokohama, Kanagawa, Japan.,Division of Structural and Synthetic Biology, RIKEN Center for Life Science Technologies, Tsurumi-ku, Yokohama, Japan.,Department of Biochemistry and Molecular Biology, Faculty of Medicine, The University of Tokyo, Bunkyo-ku, Tokyo, Japan.,RIKEN SPring-8 Center, Sayo, Hyogo, Japan.,Department of Lipid Signaling, National Center for Global Health and Medicine, Shinjuku, Tokyo, Japan.,Department of Life Science, Faculty of Science, Okayama University of Science, Kita-ku, Okayama, Japan.,Department of Biochemistry, Juntendo University School of Medicine, Bunkyo-ku, Tokyo, Japan.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
LTB4 receptor,Lysozyme,LTB4 receptor
A
523Enterobacteria phage RB55Cavia porcellus
This entity is chimeric
Mutation(s): 6 
Gene Names: e, Ltb4r
EC: 3.2.1.17
Membrane protein
mpstruct
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
G Protein-Coupled Receptors (GPCRs)
Protein: 
Leukotriene B4 receptor BLT1 with bound antagonist BIIL260, inactive state
Find proteins for A0A097J792 (Enterobacteria phage RB55)
Go to UniProtKB:  A0A097J792
Find proteins for Q9WTK1 (Cavia porcellus)
Go to UniProtKB:  Q9WTK1
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
7Y9
Query on 7Y9

Download SDF File 
Download CCD File 
A
4-[[3-[[4-[2-(4-hydroxyphenyl)propan-2-yl]phenoxy]methyl]phenyl]methoxy]benzenecarboximidamide
C30 H30 N2 O3
MBLJFKQACMILLC-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.7 Å
  • R-Value Free: 0.296 
  • R-Value Work: 0.248 
  • Space Group: P 2 21 21
Unit Cell:
Length (Å)Angle (°)
a = 69.560α = 90.00
b = 77.620β = 90.00
c = 135.530γ = 90.00
Software Package:
Software NamePurpose
XDSdata processing
XDSdata scaling
PHENIXphasing
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2018-01-03
    Type: Initial release
  • Version 1.1: 2018-02-07
    Type: Database references
  • Version 1.2: 2018-04-04
    Type: Data collection, Database references