Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

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

Macromolecule Content

• Total Structure Weight: 104.42 kDa 
• Atom Count: 5568 
• Residue Count: 678 
• Unique protein chains: 1

5ZKQ

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

• DOI: 10.2210/pdb5ZKQ/pdb

• Classification: SIGNALING PROTEIN
• Organism(s): Homo sapiens, Escherichia virus T4
• Expression System: Spodoptera frugiperda
• Mutation(s): Yes 


• Deposited: 2018-03-25 Released: 2018-06-20 
• Deposition Author(s): Cao, C., Zhao, Q., Zhang, X.C., Wu, B.
• Funding Organization(s): National Science Foundation (China), Ministry of Education (China)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.90 Å
• R-Value Free: 0.235 
• R-Value Work: 0.203 
• R-Value Observed: 0.204 

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

• PubMed: 29808000 
• DOI: 10.1038/s41594-018-0068-y
• Primary Citation of Related Structures:  
  5ZKQ, 5ZKP


• 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 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.

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Organizational Affiliation: 

CAS Center for Excellence in Biomacromolecules, Chinese Academy of Sciences, Beijing, China. [e-mail].

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Platelet-activating factor receptor,Endolysin,Endolysin,Platelet-activating factor receptor	A, B	438	Homo sapiens, Escherichia virus T4	Mutation(s): 7  Gene Names: PTAFR, PAFR EC: 3.2.1.17
Membrane protein Mpstruc	Group:  TRANSMEMBRANE PROTEINS: ALPHA-HELICAL		Sub Group:  G Protein-Coupled Receptors (GPCRs): Class A	Protein:  Platelet activating factor complex with bound antagonist SR 27417
Find proteins for P00720 (Enterobacteria phage T4) Explore P00720  Go to UniProtKB:  P00720
Find proteins for P25105 (Homo sapiens) Explore P25105  Go to UniProtKB:  P25105
NIH Common Fund Data Resources
PHAROS  P25105 GTEx  ENSG00000169403

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
9EU	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
OLC	A, B	(2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate C21 H40 O4 RZRNAYUHWVFMIP-GDCKJWNLSA-N
SO4	B	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
ZN	A, B	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.90 Å
• R-Value Free: 0.235 
• R-Value Work: 0.203 
• R-Value Observed: 0.204 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 86.22	α = 90
b = 166.54	β = 100
c = 100.31	γ = 90

Software Package:

Software Name	Purpose
BUSTER	refinement
XDS	data reduction
XDS	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Deposited Date: 2018-03-25 
• Released Date: 2018-06-20 
Deposition Author(s): Cao, C., Zhao, Q., Zhang, X.C., Wu, B.

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Funding Organization	Location	Grant Number
National Science Foundation (China)	China	81525024
Ministry of Education (China)	China	B08029

Revision History 

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