SMTL ID : 6omm.1

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

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-1-1-1-1-mer

Ligands

1 x TRP- LYS- TYR- MET- VAL- QXV: Peptide agonist(Non-covalent)

TRP-LYS-TYR-MET-VAL-QXV.1: 17 residues within 4Å: Chain A: E.110, H.123, D.127, L.130, F.131, L.185, T.198, F.199, L.219, R.222, R.226, F.278, A.282, M.292, D.302, V.305, N.306 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:L.130, A:F.131, A:F.199, A:F.199, A:L.219, A:V.305 Hydrogen bonds: A:E.110, A:D.127, A:D.127, A:R.222, A:R.226, A:D.302

5 x CLR: CHOLESTEROL(Non-covalent)

CLR.2: 7 residues within 4Å: Chain A: I.48, L.51, V.52, G.55, V.56, V.59 Ligands: CLR.5 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:I.48, A:L.51, A:V.56, A:V.59, A:V.59 CLR.3: 6 residues within 4Å: Chain A: F.139, L.142, I.146, H.150, W.153, V.166 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:F.139, A:L.142, A:I.146, A:W.153, A:W.153, A:W.153 CLR.4: 3 residues within 4Å: Chain A: L.280, L.283, V.287 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:L.280, A:L.283, A:V.287 CLR.5: 3 residues within 4Å: Chain A: F.58, V.104 Ligands: CLR.2 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:F.58, A:V.104 CLR.6: 5 residues within 4Å: Chain A: A.239, G.243, A.246, H.250, L.261 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:A.239, A:A.246, A:L.261

3 x PLM: PALMITIC ACID(Non-covalent)

PLM.7: 3 residues within 4Å: Chain A: M.321, R.331 Ligands: PLM.9 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:M.321 PLM.8: 5 residues within 4Å: Chain A: C.145, H.150, L.233, S.236, I.240 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:L.233, A:I.240 PLM.9: 8 residues within 4Å: Chain A: R.259, R.262, V.263, T.265, A.266, A.269, R.331 Ligands: PLM.7 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:R.262, A:V.263, A:T.265, A:A.266, A:A.269 Salt bridges: A:R.259, A:R.331

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zhuang, Y. et al., Structure of formylpeptide receptor 2-Gicomplex reveals insights into ligand recognition and signaling. Nat Commun (2020)

Release Date

2020-02-26

Peptides

N-formyl peptide receptor 2: A
Guanine nucleotide-binding protein G(i) subunit alpha-1: B
Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1: C
Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2: D
scFv16: E

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
R

B
A

C
B

D
C

E
E

Membrane

We predict this structure to be a membrane protein.
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N-formyl peptide receptor 2

Guanine nucleotide-binding protein G(i) subunit alpha-1

Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1

Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2

scFv16

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