5ZKP

Crystal structure of the human platelet-activating factor receptor in complex with SR 27417


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.81 Å
  • R-Value Free: 0.259 
  • R-Value Work: 0.222 
  • R-Value Observed: 0.224 

wwPDB Validation 3D Report Full Report



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:  
    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 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

    CAS Center for Excellence in Biomacromolecules, Chinese Academy of Sciences, Beijing, China. beiliwu@simm.ac.cn.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Platelet-activating factor receptor,Flavodoxin,Platelet-activating factor receptorA466Homo sapiensDesulfovibrio vulgaris str. HildenboroughMutation(s): 7 
Gene Names: PTAFRPAFR
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 P00323 (Desulfovibrio vulgaris (strain Hildenborough / ATCC 29579 / DSM 644 / NCIMB 8303))
Explore P00323 
Go to UniProtKB:  P00323
Find proteins for P25105 (Homo sapiens)
Explore P25105 
Go to UniProtKB:  P25105
NIH Common Fund Data Resources
PHAROS  P25105
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
9ER
Query on 9ER

Download CCD File 
A
N1,N1-dimethyl-N2-[(pyridin-3-yl)methyl]-N2-{4-[2,4,6-tri(propan-2-yl)phenyl]-1,3-thiazol-2-yl}ethane-1,2-diamine
C28 H40 N4 S
VVBFISAUNSXQGZ-UHFFFAOYSA-N
 Ligand Interaction
FMN
Query on FMN

Download CCD File 
A
FLAVIN MONONUCLEOTIDE
C17 H21 N4 O9 P
FVTCRASFADXXNN-SCRDCRAPSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.81 Å
  • R-Value Free: 0.259 
  • R-Value Work: 0.222 
  • R-Value Observed: 0.224 
  • Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 67.05α = 90
b = 67.05β = 90
c = 280.25γ = 120
Software Package:
Software NamePurpose
BUSTERrefinement
XDSdata reduction
SCALAdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



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