6LW5

Crystal structure of the human formyl peptide receptor 2 in complex with WKYMVm


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.289 
  • R-Value Work: 0.258 

wwPDB Validation   3D Report Full Report



Literature

Structural basis of ligand binding modes at the human formyl peptide receptor 2.

Chen, T.Xiong, M.Zong, X.Ge, Y.Zhang, H.Wang, M.Won Han, G.Yi, C.Ma, L.Ye, R.D.Xu, Y.Zhao, Q.Wu, B.

(2020) Nat Commun 11: 1208-1208

  • DOI: 10.1038/s41467-020-15009-1
  • Primary Citation of Related Structures:  
    6LW5

  • PubMed Abstract: 
  • The human formyl peptide receptor 2 (FPR2) plays a crucial role in host defense and inflammation, and has been considered as a drug target for chronic inflammatory diseases. A variety of peptides with different structures and origins have been characteri ...

    The human formyl peptide receptor 2 (FPR2) plays a crucial role in host defense and inflammation, and has been considered as a drug target for chronic inflammatory diseases. A variety of peptides with different structures and origins have been characterized as FPR2 ligands. However, the ligand-binding modes of FPR2 remain elusive, thereby limiting the development of potential drugs. Here we report the crystal structure of FPR2 bound to the potent peptide agonist WKYMVm at 2.8 Å resolution. The structure adopts an active conformation and exhibits a deep ligand-binding pocket. Combined with mutagenesis, ligand binding and signaling studies, key interactions between the agonist and FPR2 that govern ligand recognition and receptor activation are identified. Furthermore, molecular docking and functional assays reveal key factors that may define binding affinity and agonist potency of formyl peptides. These findings deepen our understanding about ligand recognition and selectivity mechanisms of the formyl peptide receptor family.


    Organizational Affiliation

    School of Life Science and Technology, ShanghaiTech University, 393 Hua Xia Zhong Road, 201210, Shanghai, China. beiliwu@simm.ac.cn.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Soluble cytochrome b562,N-formyl peptide receptor 2 A427Escherichia coliHomo sapiens
This entity is chimeric
Mutation(s): 4 
Gene Names: cybCFPR2FPRH1FPRL1LXA4R
Membrane protein
Mpstruc
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
G Protein-Coupled Receptors: Class A
Protein: 
Formylpeptide receptor FPR2 with bound peptide agonist WKYMVm
Find proteins for P0ABE7 (Escherichia coli)
Explore P0ABE7 
Go to UniProtKB:  P0ABE7
Find proteins for P25090 (Homo sapiens)
Explore P25090 
Go to UniProtKB:  P25090
NIH Common Fund Data Resources
PHAROS:  P25090
Protein Feature View
Expand
  • Reference Sequence
  • Find similar proteins by:  Sequence   |   Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
TRP-LYS-TYR-MET-VAL-QXV B6synthetic constructMutation(s): 0 
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CLR
Query on CLR

Download Ideal Coordinates CCD File 
A
CHOLESTEROL
C27 H46 O
HVYWMOMLDIMFJA-DPAQBDIFSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.289 
  • R-Value Work: 0.258 
  • Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 66.28α = 90
b = 66.28β = 90
c = 244.9γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XDSdata scaling
PHENIXphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Science Foundation (NSF, China)China31825010
Ministry of Science and Technology (MoST, China)China2018YFA0507000
National Science Foundation (NSF, China)China31730027
National Science Foundation (NSF, China)China81525024

Revision History 

  • Version 1.0: 2020-03-25
    Type: Initial release