5ZKQ

Crystal structure of the human platelet-activating factor receptor in complex with ABT-491


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.9 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.203 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Structural basis for signal recognition and transduction by platelet-activating-factor receptor.

Cao, C.Tan, Q.Xu, C.He, L.Yang, L.Zhou, Y.Zhou, Y.Qiao, A.Lu, M.Yi, C.Han, G.W.Wang, X.Li, X.Yang, H.Rao, Z.Jiang, H.Zhao, Y.Liu, J.Stevens, R.C.Zhao, Q.Zhang, X.C.Wu, B.

(2018) Nat. Struct. Mol. Biol. 25: 488-495

  • DOI: 10.1038/s41594-018-0068-y
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Platelet-activating-factor receptor (PAFR) responds to platelet-activating factor (PAF), a phospholipid mediator of cell-to-cell communication that exhibits diverse physiological effects. PAFR is considered an important drug target for treating asthm ...

    Platelet-activating-factor receptor (PAFR) responds to platelet-activating factor (PAF), a phospholipid mediator of cell-to-cell communication that exhibits diverse physiological effects. PAFR is considered an important drug target for treating asthma, inflammation and cardiovascular diseases. Here we report crystal structures of human PAFR in complex with the antagonist SR 27417 and the inverse agonist ABT-491 at 2.8-Å and 2.9-Å resolution, respectively. The structures, supported by molecular docking of PAF, provide insights into the signal-recognition mechanisms of PAFR. The PAFR-SR 27417 structure reveals an unusual conformation showing that the intracellular tips of helices II and IV shift outward by 13 Å and 4 Å, respectively, and helix VIII adopts an inward conformation. The PAFR structures, combined with single-molecule FRET and cell-based functional assays, suggest that the conformational change in the helical bundle is ligand dependent and plays a critical role in PAFR activation, thus greatly extending knowledge about signaling by G-protein-coupled receptors.


    Organizational Affiliation

    State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China.,University of Chinese Academy of Sciences, Beijing, China.,National Laboratory of Biomacromolecules, National Center of Protein Science-Beijing, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China. zhangc@ibp.ac.cn.,Department of Chemistry, Bridge Institute, University of Southern California, Los Angeles, CA, USA.,Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China.,iHuman Institute, ShanghaiTech University, Shanghai, China.,School of Life Science and Technology, ShanghaiTech University, Shanghai, China.,CAS Center for Excellence in Biomacromolecules, Chinese Academy of Sciences, Beijing, China.,CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China. beiliwu@simm.ac.cn.,School of Life Science and Technology, ShanghaiTech University, Shanghai, China. beiliwu@simm.ac.cn.,University of Chinese Academy of Sciences, Beijing, China. zhangc@ibp.ac.cn.,CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China.,University of Chinese Academy of Sciences, Beijing, China. beiliwu@simm.ac.cn.,College of Life Science and Technology, Collaborative Innovation Center for Genetics and Development, and Key Laboratory of Molecular Biophysics of the Ministry of Education, Huazhong University of Science and Technology, Wuhan, China.,Department of Pharmacology, School of Basic Medical Sciences, Zhengzhou University, Zhengzhou, China.,CAS Center for Excellence in Biomacromolecules, Chinese Academy of Sciences, Beijing, China. beiliwu@simm.ac.cn.,National Laboratory of Biomacromolecules, National Center of Protein Science-Beijing, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Platelet-activating factor receptor,Endolysin,Endolysin,Platelet-activating factor receptor
A, B
438Enterobacteria phage T4Homo sapiens
This entity is chimeric
Mutation(s): 7 
Gene Names: E, PTAFR (PAFR)
EC: 3.2.1.17
Find proteins for P00720 (Enterobacteria phage T4)
Go to UniProtKB:  P00720
Find proteins for P25105 (Homo sapiens)
Go to Gene View: PTAFR
Go to UniProtKB:  P25105
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
OLC
Query on OLC

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Download CCD File 
A, B
(2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate
1-Oleoyl-R-glycerol
C21 H40 O4
RZRNAYUHWVFMIP-GDCKJWNLSA-N
 Ligand Interaction
ZN
Query on ZN

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Download CCD File 
A, B
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
SO4
Query on SO4

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Download CCD File 
B
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
9EU
Query on 9EU

Download SDF File 
Download CCD File 
A, B
4-ethynyl-3-{3-fluoro-4-[(2-methyl-1H-imidazo[4,5-c]pyridin-1-yl)methyl]benzene-1-carbonyl}-N,N-dimethyl-1H-indole-1-carboxamide
C28 H22 F N5 O2
GDLNHSUSOZEAOR-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.9 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.203 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 86.220α = 90.00
b = 166.540β = 100.00
c = 100.310γ = 90.00
Software Package:
Software NamePurpose
BUSTERrefinement
PHASERphasing
XDSdata reduction
XDSdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Science Foundation (China)China81525024
Ministry of Education (China)ChinaB08029

Revision History 

  • Version 1.0: 2018-06-20
    Type: Initial release