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: 49.32 kDa 
• Atom Count: 3446 
• Residue Count: 433 
• Unique protein chains: 2

6LW5

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

• DOI: 10.2210/pdb6LW5/pdb

• Classification: MEMBRANE PROTEIN
• Organism(s): Escherichia coli, Homo sapiens, synthetic construct
• Expression System: Mammalian expression vector Flag-MCS-pcDNA3.1
• Mutation(s): Yes 


• Deposited: 2020-02-07 Released: 2020-03-25 
• Deposition Author(s): Chen, T., Zong, X., Zhang, H., Wang, M., Zhao, Q., Wu, B.
• Funding Organization(s): National Science Foundation (NSF, China), Ministry of Science and Technology (MoST, China)

---

Experimental Data Snapshot

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

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

• PubMed: 32139677 
• 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 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. [e-mail].

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Soluble cytochrome b562,N-formyl peptide receptor 2	A	427	Escherichia coli, Homo sapiens This entity is chimeric	Mutation(s): 4  Gene Names: cybC, FPR2, FPRH1, FPRL1, LXA4R
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 GTEx:  ENSG00000171049

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
TRP-LYS-TYR-MET-VAL-QXV	B	6	synthetic construct	Mutation(s): 0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CLR	A	CHOLESTEROL C27 H46 O HVYWMOMLDIMFJA-DPAQBDIFSA-N

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 = 66.28	α = 90
b = 66.28	β = 90
c = 244.9	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XDS	data scaling
PHENIX	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Deposited Date: 2020-02-07 
• Released Date: 2020-03-25 
Deposition Author(s): Chen, T., Zong, X., Zhang, H., Wang, M., Zhao, Q., Wu, B.

---

Funding Organization	Location	Grant Number
National Science Foundation (NSF, China)	China	31825010
Ministry of Science and Technology (MoST, China)	China	2018YFA0507000
National Science Foundation (NSF, China)	China	31730027
National Science Foundation (NSF, China)	China	81525024

Revision History 

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