8Y63: C20:0 ceramide-bound FPR2-Gi complex

Cryo-EM structure of the C20:0 ceramide-bound FPR2-Gi complex. Determined by electron microscopy at 3.2 Å resolution. Released 5 Feb 2025.

Method: Electron microscopy
Resolution: 3.2 Å
Organisms: Homo sapiens, synthetic construct
Chains: 5
Atoms: 7,804
Mol. weight: 156.16 kDa
Ligands: A1LXR
Released: 5 Feb 2025

Explore 8Y63 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8Y63 contains 36 α-helices and 56 β-strands across 5 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain A: 10 helices, 7 β-strands

Element	Residues	Length	Sheet
α-helix	9-30	22
β-strand	34-40	7	2
α-helix	46-51	6
β-strand	185-190	6	2
β-strand	195-200	6	2
α-helix	208-211	4
α-helix	213-215	3
β-strand	220-226	7	2
α-helix	244-254	11
α-helix	257-259	3
β-strand	263-269	7	2
α-helix	271-278	8
α-helix	283-285	3
α-helix	296-309	14
β-strand	319	1	2
β-strand	323	1	2
α-helix	331-350	20

Chain B: 2 helices, 30 β-strands

Element	Residues	Length	Sheet
α-helix	6-24	19
α-helix	30-34	5
β-strand	47-51	5	3
β-strand	58-63	6	4
β-strand	70-74	5	4
β-strand	78-81	4	4
β-strand	91-94	4	4
β-strand	100-105	6	5
β-strand	111-116	6	5
β-strand	121-125	5	5
β-strand	134-139	6	5
β-strand	146-153	8	6
β-strand	156-161	6	6
β-strand	166-168	3	6
β-strand	178-180	3	6
β-strand	187	1	7
β-strand	191-192	2	8
β-strand	198-202	5	8
β-strand	203	1	7
β-strand	207-212	6	8
β-strand	217-223	7	8
β-strand	229-234	6	9
β-strand	240-245	6	9
β-strand	250-254	5	9
β-strand	260-264	5	9
β-strand	273-278	6	10
β-strand	284-289	6	10
β-strand	294-298	5	10
β-strand	303-308	6	10
β-strand	315-320	6	3
β-strand	327-331	5	3
β-strand	336-339	4	3

Chain C: 2 helices, 0 β-strands

Element	Residues	Length	Sheet
α-helix	10-23	14
α-helix	30-42	13

Chain E: 5 helices, 17 β-strands

Element	Residues	Length	Sheet
β-strand	3	1	11
β-strand	25	1	11
α-helix	29-31	3
β-strand	33-37	5	12
β-strand	47-51	5	12
α-helix	53-55	3
α-helix	62-64	3
α-helix	88-90	3
β-strand	95-99	5	12
β-strand	110-111	2	12
β-strand	140-141	2	13
β-strand	147-148	2	14
β-strand	155-161	7	13
β-strand	176-178	3	15
β-strand	186-190	5	15
β-strand	194-195	2	15
β-strand	203-206	4	13
β-strand	211-216	6	13
α-helix	221-223	3
β-strand	227-228	2	15
β-strand	243	1	15
β-strand	245-246	2	14

Chain R: 17 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	28-46	19
α-helix	47-51	5
α-helix	59-86	28
α-helix	95-127	33
α-helix	130-135	6
α-helix	139-161	23
β-strand	164	1	1
β-strand	178	1	1
α-helix	187-199	13
α-helix	204-206	3
α-helix	207-211	5
α-helix	212-230	19
α-helix	239-251	13
α-helix	255-266	12
α-helix	268-272	5
α-helix	278-282	5
α-helix	284-297	14
α-helix	299-302	4
α-helix	307-316	10

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
N-formyl peptide receptor 2	R	protein	351	Homo sapiens	P25090 (AlphaFold model)
Guanine nucleotide-binding protein G(i) subunit alpha-1	A	protein	354	Homo sapiens	P63096 (AlphaFold model)
Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1	B	protein	358	Homo sapiens	P62873 (AlphaFold model)
Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2	C	protein	58	Homo sapiens	P59768 (AlphaFold model)
scFv16	E	protein	285	synthetic construct

Sequence of entity 1 (R), FASTA

>8Y63_1 N-formyl peptide receptor 2 (chains R)
METNFSTPLNEYEEVSYESAGYTVLRILPLVVLGVTFVLGVLGNGLVIWVAGFRMTRTVT
TICYLNLALADFSFTATLPFLIVSMAMGEKWPFGWFLCKLIHIVVDINLFGSVFLIGFIA
LDRCICVLHPVWAQNHRTVSLAMKVIVGPWILALVLTLPVFLFLTTVTIPNGDTYCTFNF
ASWGGTPEERLKVAITMLTARGIIRFVIGFSLPMSIVAICYGLIAAKIHKKGMIKSSRPL
RVLTAVVASFFICWFPFQLVALLGTVWLKEMLFYGKYKIIDILVNPTSSLAFFNSCLNPM
LYVFVGQDFRERLIHSLPTSLERALSEDSAPTNDTAANSASPPAETELQAM

Sequence of entity 2 (A), FASTA

>8Y63_2 Guanine nucleotide-binding protein G(i) subunit alpha-1 (chains A)
MGCTLSAEDKAAVERSKMIDRNLREDGEKAAREVKLLLLGAGESGKSTIVKQMKIIHEAG
YSEEECKQYKAVVYSNTIQSIIAIIRAMGRLKIDFGDSARADDARQLFVLAGAAEEGFMT
AELAGVIKRLWKDSGVQACFNRSREYQLNDSAAYYLNDLDRIAQPNYIPTQQDVLRTRVK
TTGIVETHFTFKDLHFKMFDVGGQRSERKKWIHCFEGVTAIIFCVALSDYDLVLAEDEEM
NRMHESMKLFDSICNNKWFTDTSIILFLNKKDLFEEKIKKSPLTICYPEYAGSNTYEEAA
AYIQCQFEDLNKRKDTKEIYTHFTCATDTKNVQFVFDAVTDVIIKNNLKDCGLF

Sequence of entity 3 (B), FASTA

>8Y63_3 Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 (chains B)
MHHHHHHLEVLFQGPGSSGSELDQLRQEAEQLKNQIRDARKACADATLSQITNNIDPVGR
IQMRTRRTLRGHLAKIYAMHWGTDSRLLVSASQDGKLIIWDSYTTNKVHAIPLRSSWVMT
CAYAPSGNYVACGGLDNICSIYNLKTREGNVRVSRELAGHTGYLSCCRFLDDNQIVTSSG
DTTCALWDIETGQQTTTFTGHTGDVMSLSLAPDTRLFVSGACDASAKLWDVREGMCRQTF
TGHESDINAICFFPNGNAFATGSDDATCRLFDLRADQELMTYSHDNIICGITSVSFSKSG
RLLLAGYDDFNCNVWDALKADRAGVLAGHDNRVSCLGVTDDGMAVATGSWDSFLKIWN

Sequence of entity 4 (C), FASTA

>8Y63_4 Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 (chains C)
NTASIAQARKLVEQLKMEANIDRIKVSKAAADLMAYCEAHAKEDPLLTPVPASENPFR

Sequence of entity 5 (E), FASTA

>8Y63_5 scFv16 (chains E)
MLLVNQSHQGFNKEHTSKMVSAIVLYVLLAAAAHSAFAVQLVESGGGLVQPGGSRKLSCS
ASGFAFSSFGMHWVRQAPEKGLEWVAYISSGSGTIYYADTVKGRFTISRDDPKNTLFLQM
TSLRSEDTAMYYCVRSIYYYGSSPFDFWGQGTTLTVSAGGGGSGGGGSGGGGSADIVMTQ
ATSSVPVTPGESVSISCRSSKSLLHSNGNTYLYWFLQRPGQSPQLLIYRMSNLASGVPDR
FSGSGSGTAFTLTISRLEAEDVGVYYCMQHLEYPLTFGAGTKLEL

Ligands and cofactors

ID	Name	Formula	Copies
A1LXR	Cer(d18:0/20:0)	C38 H77 N O3	1

Primary citation

Metabolic signaling of ceramides through the FPR2 receptor inhibits adipocyte thermogenesis. Lin, H., Ma, C., Cai, K. et al. Science (2025) 388:eado4188-eado4188. DOI 10.1126/science.ado4188 · PubMed

Other PDB entries of the same protein (UniProt P25090 (AlphaFold model), which also has an AlphaFold model), best resolution first:

8ZBW 2.58 Å, Cryo-EM structure of formyl peptide receptor 2/C1R receptor in complex with Gi
6LW5 2.8 Å, Crystal structure of the human formyl peptide receptor 2 in complex with WKYMVm
7WVX 2.8 Å, Cryo-EM structure of the human formyl peptide receptor 2 in complex with fhumanin and Gi2
7T6U 2.9 Å, Structure of the human FPR2-Gi complex with CGEN-855A
7WVV 2.9 Å, Cryo-EM structure of the human formyl peptide receptor 2 in complex with fMLFII and Gi2
7T6S 3.0 Å, Structure of the human FPR2-Gi complex with compound C43
7WVY 3.0 Å, Cryo-EM structure of the human formyl peptide receptor 2 in complex with Abeta42 and Gi2
7T6V 3.1 Å, Structure of the human FPR2-Gi complex with fMLFII
7WVW 3.1 Å, Cryo-EM structure of the human formyl peptide receptor 2 in complex with fMYFINILTL and…
6OMM 3.17 Å, Cryo-EM structure of formyl peptide receptor 2/lipoxin A4 receptor in complex with Gi
8Y62 3.2 Å, Cryo-EM structure of the C16:0 ceramide-bound FPR2-Gi complex
9JHJ 3.2 Å, Cryo-EM structure of the C18:0 ceramide-bound FPR2-Gi complex

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