9JHJ: C18:0 ceramide-bound FPR2-Gi complex

Cryo-EM structure of the C18:0 ceramide-bound FPR2-Gi complex. Determined by electron microscopy at 3.2 Å resolution. Released 19 Mar 2025.

Method: Electron microscopy
Resolution: 3.2 Å
Organism: Homo sapiens
Chains: 5
Atoms: 7,761
Mol. weight: 156.13 kDa
Ligands: 18C
Released: 19 Mar 2025

Explore 9JHJ in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9JHJ contains 28 α-helices and 63 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, 6 β-strands

Element	Residues	Length	Sheet
α-helix	9-31	23
β-strand	34-39	6	1
α-helix	46-52	7
β-strand	185-190	6	1
β-strand	195-200	6	1
α-helix	208-210	3
α-helix	212-215	4
β-strand	220-226	7	1
α-helix	244-255	12
α-helix	257-259	3
β-strand	263-269	7	1
α-helix	271-278	8
α-helix	283-285	3
α-helix	296-308	13
β-strand	319-323	5	1
α-helix	331-351	21

Chain B: 2 helices, 30 β-strands

Element	Residues	Length	Sheet
α-helix	7-25	19
α-helix	30-33	4
β-strand	47-51	5	2
β-strand	58-63	6	3
β-strand	69-74	6	3
β-strand	78-83	6	3
β-strand	88-94	7	3
β-strand	102-105	4	4
β-strand	111-115	5	4
β-strand	121-125	5	4
β-strand	134-139	6	4
β-strand	146-153	8	5
β-strand	156-161	6	5
β-strand	166-170	5	5
β-strand	175-180	6	5
β-strand	187	1	6
β-strand	191-192	2	7
β-strand	198-201	4	7
β-strand	203	1	6
β-strand	209-212	4	7
β-strand	220-221	2	7
β-strand	229-234	6	8
β-strand	240-245	6	8
β-strand	250-254	5	8
β-strand	259-264	6	8
β-strand	273-278	6	9
β-strand	284-289	6	9
β-strand	294-298	5	9
β-strand	306-308	3	9
β-strand	315-319	5	2
β-strand	327-331	5	2
β-strand	336-339	4	2

Chain C: 2 helices, 0 β-strands

Element	Residues	Length	Sheet
α-helix	10-24	15
α-helix	30-43	14

Chain E: 1 helix, 27 β-strands

Element	Residues	Length	Sheet
β-strand	17-18	2	10
β-strand	36-37	2	11
β-strand	47-49	3	11
α-helix	53-55	3
β-strand	68-73	6	10
β-strand	78-84	7	10
β-strand	95-96	2	11
β-strand	98	1	12
β-strand	110	1	12
β-strand	140-141	2	13
β-strand	155-159	5	14
β-strand	160-161	2	13
β-strand	166	1	15
β-strand	172	1	15
β-strand	174	1	16
β-strand	175-178	4	17
β-strand	179	1	18
β-strand	186-190	5	17
β-strand	194	1	17
β-strand	203	1	14
β-strand	206-208	3	14
β-strand	211-216	6	14
β-strand	225	1	19
β-strand	226	1	18
β-strand	230	1	20
β-strand	231	1	16
β-strand	239	1	20
β-strand	245	1	19

Chain R: 13 helices, 0 β-strands

Element	Residues	Length
α-helix	27-53	27
α-helix	59-87	29
α-helix	95-128	34
α-helix	130-136	7
α-helix	139-145	7
α-helix	147-163	17
α-helix	187-204	18
α-helix	205-211	7
α-helix	212-230	19
α-helix	238-266	29
α-helix	269-272	4
α-helix	279-302	24
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	Homo sapiens

Sequence of entity 1 (R), FASTA

>9JHJ_1 N-formyl peptide receptor 2 (chains R)
METNFSTPLNEYEEVSYESAGYTVLRILPLVVLGVTFVLGVLGNGLVIWVAGFRMTRTVT
TICYLNLALADFSFTATLPFLIVSMAMGEKWPFGWFLCKLIHIVVDINLFGSVFLIGFIA
LDRCICVLHPVWAQNHRTVSLAMKVIVGPWILALVLTLPVFLFLTTVTIPNGDTYCTFNF
ASWGGTPEERLKVAITMLTARGIIRFVIGFSLPMSIVAICYGLIAAKIHKKGMIKSSRPL
RVLTAVVASFFICWFPFQLVALLGTVWLKEMLFYGKYKIIDILVNPTSSLAFFNSCLNPM
LYVFVGQDFRERLIHSLPTSLERALSEDSAPTNDTAANSASPPAETELQAM

Sequence of entity 2 (A), FASTA

>9JHJ_2 Guanine nucleotide-binding protein G(i) subunit alpha-1 (chains A)
MGCTLSAEDKAAVERSKMIDRNLREDGEKAAREVKLLLLGAGESGKSTIVKQMKIIHEAG
YSEEECKQYKAVVYSNTIQSIIAIIRAMGRLKIDFGDSARADDARQLFVLAGAAEEGFMT
AELAGVIKRLWKDSGVQACFNRSREYQLNDSAAYYLNDLDRIAQPNYIPTQQDVLRTRVK
TTGIVETHFTFKDLHFKMFDVGGQRSERKKWIHCFEGVTAIIFCVALSDYDLVLAEDEEM
NRMHESMKLFDSICNNKWFTDTSIILFLNKKDLFEEKIKKSPLTICYPEYAGSNTYEEAA
AYIQCQFEDLNKRKDTKEIYTHFTCATDTKNVQFVFDAVTDVIIKNNLKDCGLF

Sequence of entity 3 (B), FASTA

>9JHJ_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

>9JHJ_4 Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 (chains C)
NTASIAQARKLVEQLKMEANIDRIKVSKAAADLMAYCEAHAKEDPLLTPVPASENPFR

Sequence of entity 5 (E), FASTA

>9JHJ_5 scFv16 (chains E)
MLLVNQSHQGFNKEHTSKMVSAIVLYVLLAAAAHSAFAVQLVESGGGLVQPGGSRKLSCS
ASGFAFSSFGMHWVRQAPEKGLEWVAYISSGSGTIYYADTVKGRFTISRDDPKNTLFLQM
TSLRSEDTAMYYCVRSIYYYGSSPFDFWGQGTTLTVSAGGGGSGGGGSGGGGSADIVMTQ
ATSSVPVTPGESVSISCRSSKSLLHSNGNTYLYWFLQRPGQSPQLLIYRMSNLASGVPDR
FSGSGSGTAFTLTISRLEAEDVGVYYCMQHLEYPLTFGAGTKLEL

Ligands and cofactors

ID	Name	Formula	Copies
18C	N-((E,2S,3R)-1,3-dihydroxyoctadec-4-en-2-yl)stearamide	C36 H71 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
8Y63 3.2 Å, Cryo-EM structure of the C20:0 ceramide-bound FPR2-Gi complex

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