8Y62: C16:0 ceramide-bound FPR2-Gi complex

Cryo-EM structure of the C16:0 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: 8,160
Mol. weight: 156.23 kDa
Ligands: 16C
Released: 5 Feb 2025

Explore 8Y62 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8Y62 contains 34 α-helices and 66 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: 8 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	9-30	22
β-strand	34-38	5	1
α-helix	46-51	6
β-strand	185-191	7	1
β-strand	194-200	7	1
α-helix	208-211	4
α-helix	212-215	4
β-strand	220-222	3	1
β-strand	223-226	4	2
α-helix	244-254	11
β-strand	263	1	1
β-strand	266-269	4	2
α-helix	271-278	8
α-helix	296-308	13
β-strand	321-323	3	2
α-helix	331-351	21

Chain B: 4 helices, 28 β-strands

Element	Residues	Length	Sheet
α-helix	7-25	19
α-helix	30-33	4
α-helix	34-36	3
β-strand	47-50	4	3
β-strand	58-63	6	4
β-strand	69-74	6	4
β-strand	78-83	6	4
β-strand	91-94	4	4
α-helix	95	1
β-strand	102-105	4	5
β-strand	111-115	5	5
β-strand	121-125	5	5
β-strand	134-139	6	5
β-strand	146-151	6	6
β-strand	157-161	5	6
β-strand	166-168	3	6
β-strand	178-180	3	6
β-strand	187-192	6	7
β-strand	199-203	5	7
β-strand	208-210	3	7
β-strand	220-222	3	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	304-308	5	9
β-strand	315-320	6	3
β-strand	327-331	5	3
β-strand	336-339	4	3

Chain C: 4 helices, 0 β-strands

Element	Residues	Length
α-helix	10-22	13
α-helix	30-44	15
α-helix	45-47	3
α-helix	54-56	3

Chain E: 6 helices, 28 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	10
β-strand	10-12	3	11
β-strand	17-24	8	10
α-helix	29-31	3
β-strand	33-38	6	12
β-strand	46-51	6	12
α-helix	53-55	3
β-strand	58-60	3	12
α-helix	62-64	3
β-strand	68-73	6	10
α-helix	74-76	3
β-strand	78-84	7	10
β-strand	92-94	3	11
β-strand	95	1	12
β-strand	97	1	13
β-strand	98-99	2	12
β-strand	111	1	13
β-strand	115-119	5	11
β-strand	140	1	14
β-strand	146	1	15
β-strand	155-160	6	16
β-strand	161	1	14
β-strand	166	1	17
β-strand	172	1	17
β-strand	174-179	6	15
β-strand	186-190	5	15
β-strand	194-195	2	15
α-helix	196	1
β-strand	205-208	4	16
β-strand	211-216	6	16
α-helix	221-223	3
β-strand	226-231	6	15
β-strand	239	1	15
β-strand	243-244	2	15

Chain R: 12 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	28-50	23
α-helix	59-87	29
α-helix	95-128	34
α-helix	130-135	6
α-helix	139-163	25
β-strand	164-166	3	18
β-strand	176-178	3	18
α-helix	187-205	19
α-helix	206-211	6
α-helix	212-230	19
α-helix	239-274	36
α-helix	279-282	4
α-helix	284-302	19
α-helix	307-316	10

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
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	59	Homo sapiens	P59768 (AlphaFold model)
scFv16	E	protein	285	synthetic construct
N-formyl peptide receptor 2	R	protein	351	Homo sapiens	P25090 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>8Y62_1 Guanine nucleotide-binding protein G(i) subunit alpha-1 (chains A)
MGCTLSAEDKAAVERSKMIDRNLREDGEKAAREVKLLLLGAGESGKSTIVKQMKIIHEAG
YSEEECKQYKAVVYSNTIQSIIAIIRAMGRLKIDFGDSARADDARQLFVLAGAAEEGFMT
AELAGVIKRLWKDSGVQACFNRSREYQLNDSAAYYLNDLDRIAQPNYIPTQQDVLRTRVK
TTGIVETHFTFKDLHFKMFDVGGQRSERKKWIHCFEGVTAIIFCVALSDYDLVLAEDEEM
NRMHESMKLFDSICNNKWFTDTSIILFLNKKDLFEEKIKKSPLTICYPEYAGSNTYEEAA
AYIQCQFEDLNKRKDTKEIYTHFTCATDTKNVQFVFDAVTDVIIKNNLKDCGLF

Sequence of entity 2 (B), FASTA

>8Y62_2 Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 (chains B)
MHHHHHHLEVLFQGPGSSGSELDQLRQEAEQLKNQIRDARKACADATLSQITNNIDPVGR
IQMRTRRTLRGHLAKIYAMHWGTDSRLLVSASQDGKLIIWDSYTTNKVHAIPLRSSWVMT
CAYAPSGNYVACGGLDNICSIYNLKTREGNVRVSRELAGHTGYLSCCRFLDDNQIVTSSG
DTTCALWDIETGQQTTTFTGHTGDVMSLSLAPDTRLFVSGACDASAKLWDVREGMCRQTF
TGHESDINAICFFPNGNAFATGSDDATCRLFDLRADQELMTYSHDNIICGITSVSFSKSG
RLLLAGYDDFNCNVWDALKADRAGVLAGHDNRVSCLGVTDDGMAVATGSWDSFLKIWN

Sequence of entity 3 (C), FASTA

>8Y62_3 Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 (chains C)
NTASIAQARKLVEQLKMEANIDRIKVSKAAADLMAYCEAHAKEDPLLTPVPASENPFRE

Sequence of entity 4 (E), FASTA

>8Y62_4 scFv16 (chains E)
MLLVNQSHQGFNKEHTSKMVSAIVLYVLLAAAAHSAFAVQLVESGGGLVQPGGSRKLSCS
ASGFAFSSFGMHWVRQAPEKGLEWVAYISSGSGTIYYADTVKGRFTISRDDPKNTLFLQM
TSLRSEDTAMYYCVRSIYYYGSSPFDFWGQGTTLTVSAGGGGSGGGGSGGGGSADIVMTQ
ATSSVPVTPGESVSISCRSSKSLLHSNGNTYLYWFLQRPGQSPQLLIYRMSNLASGVPDR
FSGSGSGTAFTLTISRLEAEDVGVYYCMQHLEYPLTFGAGTKLEL

Sequence of entity 5 (R), FASTA

>8Y62_5 N-formyl peptide receptor 2 (chains R)
METNFSTPLNEYEEVSYESAGYTVLRILPLVVLGVTFVLGVLGNGLVIWVAGFRMTRTVT
TICYLNLALADFSFTATLPFLIVSMAMGEKWPFGWFLCKLIHIVVDINLFGSVFLIGFIA
LDRCICVLHPVWAQNHRTVSLAMKVIVGPWILALVLTLPVFLFLTTVTIPNGDTYCTFNF
ASWGGTPEERLKVAITMLTARGIIRFVIGFSLPMSIVAICYGLIAAKIHKKGMIKSSRPL
RVLTAVVASFFICWFPFQLVALLGTVWLKEMLFYGKYKIIDILVNPTSSLAFFNSCLNPM
LYVFVGQDFRERLIHSLPTSLERALSEDSAPTNDTAANSASPPAETELQAM

Ligands and cofactors

ID	Name	Formula	Copies
16C	N-((E,2S,3R)-1,3-dihydroxyoctadec-4-en-2-yl)palmitamide	C34 H67 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 P63096 (AlphaFold model), which also has an AlphaFold model), best resolution first:

6CRK 2.0 Å, Heterotrimeric G-protein in complex with an antibody fragment
3UMR 2.04 Å, Crystal structure of the G202D mutant of human G-alpha-i1
9P7Z 2.1 Å, NTSR1-Gi-NTS(8-13) Complex in the Canonical, AHD Open State (C-Open-Apo)
2OM2 2.2 Å, Crystal Structure Of Human G[alpha]i1 Bound To The Goloco Motif Of Rgs14
8YN9 2.3 Å, Cryo-EM structure of histamine H4 receptor in complex with histamine and Gi
9HYI 2.3 Å, DP81-bound serotonin 5-HT1A receptor - Gi Protein Complex
9O36 2.3 Å, CryoEM structure of mu-opioid receptor - Gi protein complex bound to fluornitrazene (FNZ)
9P80 2.3 Å, NTSR1-Gi-NTS(8-13) Complex in the Non-Canonical, AHD Open State (NC-Open-Apo)
8XXV 2.33 Å, Cryo-EM Structure of the Prostaglandin D2 Receptor 2-indomethacin Coupled to G Protein
3UMS 2.34 Å, Crystal structure of the G202A mutant of human G-alpha-i1
3ONW 2.38 Å, Structure of a G-alpha-i1 mutant with enhanced affinity for the RGS14 GoLoco motif.
20ZG 2.4 Å, Cryo-EM structure of the human neurotensin receptor 1 (hNTSR1)-Gi1 complex in the…

Browse structure collections

About this viewer

MolViewer shows 8Y62 directly in your browser with nothing to install. Switch between cartoon, ball-and-stick, spacefill and surface views, color by chain, secondary structure or B-factor, measure distances, angles and dihedrals, and share or embed the view.