Biological Assembly 1  

 3D View: Structure | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 6-mer - A1B1C1D1E1F1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 156.99 kDa 
• Atom Count: 9134 
• Residue Count: 1142 
• Unique protein chains: 6

6OMM

Cryo-EM structure of formyl peptide receptor 2/lipoxin A4 receptor in complex with Gi

• DOI: 10.2210/pdb6OMM/pdb
• EMDataResource: EMD-20126

• Classification: SIGNALING PROTEIN
• Organism(s): Homo sapiens, synthetic construct
• Expression System: Spodoptera frugiperda, Escherichia coli
• Mutation(s): Yes 


• Deposited: 2019-04-19 Released: 2020-02-26 
• Deposition Author(s): Zhuang, Y., Liu, H., de Waal, P.W., Zhou, X.E., Wang, L., Meng, X., Zhao, G., Kang, Y., Melcher, K., Xu, H.E., Zhang, C.
• Funding Organization(s): National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.17 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Structure of formylpeptide receptor 2-Gicomplex reveals insights into ligand recognition and signaling.

Zhuang, Y., Liu, H., Edward Zhou, X., Kumar Verma, R., de Waal, P.W., Jang, W., Xu, T.H., Wang, L., Meng, X., Zhao, G., Kang, Y., Melcher, K., Fan, H., Lambert, N.A., Eric Xu, H., Zhang, C.

(2020) Nat Commun 11: 885-885

• PubMed: 32060286 
• DOI: 10.1038/s41467-020-14728-9
• Primary Citation of Related Structures:  
  6OMM


• PubMed Abstract: 
  

Formylpeptide receptors (FPRs) as G protein-coupled receptors (GPCRs) can recognize formylpeptides derived from pathogens or host cells to function in host defense and cell clearance. In addition, FPRs, especially FPR2, can also recognize other ligands with a large chemical diversity generated at different stages of inflammation to either promote or resolve inflammation in order to maintain a balanced inflammatory response. The mechanism underlying promiscuous ligand recognition and activation of FPRs is not clear. Here we report a cryo-EM structure of FPR2-G _i signaling complex with a peptide agonist. The structure reveals a widely open extracellular region with an amphiphilic environment for ligand binding. Together with computational docking and simulation, the structure suggests a molecular basis for the recognition of formylpeptides and a potential mechanism of receptor activation, and reveals conserved and divergent features in G _i coupling. Our results provide a basis for understanding the molecular mechanism of the functional promiscuity of FPRs.

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Organizational Affiliation: 

Laboratory for GPCR Biology, Department of Pharmacology and Chemical Biology, University of Pittsburgh School of Medicine, University of Pittsburgh, Pittsburgh, PA, 15261, USA. [e-mail].

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
N-formyl peptide receptor 2	R	363	Homo sapiens	Mutation(s): 0  Gene Names: FPR2, FPRH1, FPRL1, LXA4R
Membrane protein Mpstruc	Group:  TRANSMEMBRANE PROTEINS: ALPHA-HELICAL		Sub Group:  G Protein-Coupled Receptors (GPCRs): Class A	Protein:  Formylpeptide receptor FPR2-Gi coomplex
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
Peptide agonist	L	6	synthetic construct	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Guanine nucleotide-binding protein G(i) subunit alpha-1	A	353	Homo sapiens	Mutation(s): 3  Gene Names: GNAI1
Membrane protein Mpstruc	Group:  TRANSMEMBRANE PROTEINS: ALPHA-HELICAL		Sub Group:  G Protein-Coupled Receptors (GPCRs): Class A	Protein:  Formylpeptide receptor FPR2-Gi coomplex
Find proteins for P63096 (Homo sapiens) Explore P63096  Go to UniProtKB:  P63096
NIH Common Fund Data Resources
PHAROS  P63096

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1	B	353	Homo sapiens	Mutation(s): 3  Gene Names: GNB1
Find proteins for P62873 (Homo sapiens) Explore P62873  Go to UniProtKB:  P62873
NIH Common Fund Data Resources
PHAROS  P62873 GTEx  ENSG00000078369

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2	C	67	Homo sapiens	Mutation(s): 2  Gene Names: GNG2
Membrane protein Mpstruc	Group:  TRANSMEMBRANE PROTEINS: ALPHA-HELICAL		Sub Group:  G Protein-Coupled Receptors (GPCRs): Class A	Protein:  Formylpeptide receptor FPR2-Gi coomplex
Find proteins for P59768 (Homo sapiens) Explore P59768  Go to UniProtKB:  P59768
NIH Common Fund Data Resources
PHAROS  P59768 GTEx  ENSG00000186469

Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
scFv16	E	247	synthetic construct	Mutation(s): 0

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CLR	R	CHOLESTEROL C27 H46 O HVYWMOMLDIMFJA-DPAQBDIFSA-N
PLM	R	PALMITIC ACID C16 H32 O2 IPCSVZSSVZVIGE-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.17 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Structure Validation

Entry History & Funding Information

Deposition Data

• Deposited Date: 2019-04-19 
• Released Date: 2020-02-26 
Deposition Author(s): Zhuang, Y., Liu, H., de Waal, P.W., Zhou, X.E., Wang, L., Meng, X., Zhao, G., Kang, Y., Melcher, K., Xu, H.E., Zhang, C.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)	United States	1R35GM128641
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)	United States	1R01GM127710

Revision History 

• Version 1.0: 2020-02-26
  Type: Initial release