6OMM: Formyl peptide receptor 2/lipoxin A4 receptor

Cryo-EM structure of formyl peptide receptor 2/lipoxin A4 receptor in complex with Gi. Determined by electron microscopy at 3.17 Å resolution. Released 26 Feb 2020.

Method: Electron microscopy
Resolution: 3.17 Å
Organisms: Homo sapiens, synthetic construct
Chains: 6
Atoms: 9,134
Mol. weight: 156.99 kDa
Ligands: PLM, CLR
Released: 26 Feb 2020

Explore 6OMM in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6OMM contains 40 α-helices and 60 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	9-32	24
β-strand	34-40	7	2
α-helix	43-50	8
β-strand	185-191	7	2
β-strand	194-200	7	2
α-helix	208-212	5
α-helix	213-215	3
β-strand	220-226	7	2
α-helix	242-254	13
α-helix	263-264	2
β-strand	265-269	5	2
α-helix	271-280	10
α-helix	283-285	3
α-helix	296-308	13
β-strand	320-323	4	2
α-helix	328-351	24

Chain B: 4 helices, 28 β-strands

Element	Residues	Length	Sheet
α-helix	6-24	19
α-helix	30-33	4
β-strand	47-51	5	3
β-strand	58-63	6	4
β-strand	69-74	6	4
β-strand	78-83	6	4
β-strand	88-94	7	4
β-strand	100-105	6	5
β-strand	111-116	6	5
β-strand	121-125	5	5
α-helix	133	1
β-strand	134-139	6	5
α-helix	145	1
β-strand	146-151	6	6
β-strand	156-161	6	6
β-strand	166-170	5	6
β-strand	176-180	5	6
β-strand	187-192	6	7
β-strand	198-203	6	7
β-strand	208-212	5	7
β-strand	218-222	5	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	303-308	6	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	10-23	14
α-helix	27-29	3
α-helix	30-43	14
α-helix	54-55	2

Chain E: 2 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	10
β-strand	10-12	3	11
β-strand	18-25	8	10
α-helix	29-31	3
β-strand	33-39	7	11
β-strand	45-51	7	11
β-strand	58-60	3	11
β-strand	68-73	6	10
β-strand	78-83	6	10
β-strand	92-99	8	11
β-strand	111	1	11
β-strand	115-119	5	11
β-strand	140-141	2	12
β-strand	146-148	3	13
β-strand	155-161	7	12
β-strand	166	1	14
β-strand	172	1	14
β-strand	174-179	6	13
β-strand	186-190	5	13
β-strand	194-195	2	13
β-strand	203-208	6	12
β-strand	211-216	6	12
β-strand	226-231	6	13
α-helix	237	1
β-strand	238	1	13
β-strand	243-246	4	13

Chain R: 20 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	22-49	28
α-helix	50-54	5
α-helix	59-76	18
α-helix	78-87	10
α-helix	95-128	34
α-helix	132-135	4
α-helix	139-145	7
α-helix	147-156	10
α-helix	158-163	6
α-helix	166	1
β-strand	167-168	2	1
β-strand	174-175	2	1
α-helix	181-184	4
α-helix	187-206	20
α-helix	207-211	5
α-helix	212-231	20
α-helix	238-266	29
α-helix	268-269	2
α-helix	270-274	5
α-helix	279-299	21
α-helix	300-304	5
α-helix	307-316	10

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
N-formyl peptide receptor 2	R	protein	363	Homo sapiens	P25090 (AlphaFold model)
Peptide agonist	L	protein	6	synthetic construct
Guanine nucleotide-binding protein G(i) subunit alpha-1	A	protein	353	Homo sapiens	P63096 (AlphaFold model)
Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1	B	protein	353	Homo sapiens	P62873 (AlphaFold model)
Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2	C	protein	67	Homo sapiens	P59768 (AlphaFold model)
scFv16	E	protein	247	synthetic construct

Sequence of entity 1 (R), FASTA

>6OMM_1 N-formyl peptide receptor 2 (chains R)
DYKDDDDVDGSAENLYFQGASMETNFSTPLNEYEEVSYESAGYTVLRILPLVVLGVTFVL
GVLGNGLVIWVAGFRMTRTVTTICYLNLALADFSFTATLPFLIVSMAMGEKWPFGWFLCK
LIHIVVDINLFGSVFLIGFIALDRCICVLHPVWAQNHRTVSLAMKVIVGPWILALVLTLP
VFLFLTTVTIPNGDTYCTFNFASWGGTPEERLKVAITMLTARGIIRFVIGFSLPMSIVAI
CYGLIAAKIHKKGMIKSSRPLRVLTAVVASFFICWFPFQLVALLGTVWLKEMLFYGKYKI
IDILVNPTSSLAFFNSCLNPMLYVFVGQDFRERLIHSLPTSLERALSEDSAPTNDTAANS
ASP

Sequence of entity 2 (L), FASTA

>6OMM_2 Peptide agonist (chains L)
WKYMVX

Sequence of entity 3 (A), FASTA

>6OMM_3 Guanine nucleotide-binding protein G(i) subunit alpha-1 (chains A)
GCTLSAEDKAAVERSKMIDRNLREDGEKAAREVKLLLLGAGESGKSTIVKQMKIIHEAGY
SEEECKQYKAVVYSNTIQSIIAIIRAMGRLKIDFGDSARADDARQLFVLAGAAEEGFMTA
ELAGVIKRLWKDSGVQACFNRSREYQLNDSAAYYLNDLDRIAQPNYIPTQQDVLRTRVKT
TGIVETHFTFKDLHFKMFDVGAQRSERKKWIHCFEGVTAIIFCVALSDYDLVLAEDEEMN
RMHESMKLFDSICNNKWFTDTSIILFLNKKDLFEEKIKKSPLTICYPEYAGSNTYEEAAA
YIQCQFEDLNKRKDTKEIYTHFTCSTETKNVQFVFDAVTDVIIKNNLKDCGLF

Sequence of entity 4 (B), FASTA

>6OMM_4 Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 (chains B)
HHHHHHHHMGSLLQSELDELRQEAEQLKNQIRDARKACADATLSQITNNIDPVGRIQMRT
RRTLRGHLAKIYAMHWGTDSRLLVSASQDGKLIIWDSYTTNKVHAIPLRSSWVMTCAYAP
SGNYVACGGLDNICSIYNLKTRQGNVRVSRELAGHTGYLSCCRFLDDNQIVTSSGDTTCA
LWDIETGQQTTTFTGHTGDVMSLSLAPDTRLFVSGACDASAKLWDVREGMCRQTFTGHES
DINAICFFPDGNAFATGSDDATCRLFDLRADQELMTYSHDNIICGITSVSFSKSGRLLLA
GYDDFNCNVWDALKADRAGVLAGHDNRVSCLGVTDDGMAVATGSWDSFLKIWN

Sequence of entity 5 (C), FASTA

>6OMM_5 Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 (chains C)
ASNNTASIAQARKLVQQLKMEANIDRIKVSKAAADLMAYCEAHAKEDPLLTPVPASQNPF
REKKFFC

Sequence of entity 6 (E), FASTA

>6OMM_6 scFv16 (chains E)
VQLVESGGGLVQPGGSRKLSCSASGFAFSSFGMHWVRQAPEKGLEWVAYISSGSGTIYYA
DTVKGRFTISRDDPKNTLFLQMTSLRSEDTAMYYCVRSIYYYGSSPFDFWGQGTTLTVSS
GGGGSGGGGSGGGGSSDIVMTQATSSVPVTPGESVSISCRSSKSLLHSNGNTYLYWFLQR
PGQSPQLLIYRMSNLASGVPERFSGSGSGTAFTLTISRLEAEDVGVYYCMQHLEYPLTFG
AGTKLEL

Ligands and cofactors

ID	Name	Formula	Copies
PLM	Palmitic acid	C16 H32 O2	3
CLR	Cholesterol	C27 H46 O	5

Primary citation

Structure of formylpeptide receptor 2-Gicomplex reveals insights into ligand recognition and signaling. Zhuang, Y., Liu, H., Edward Zhou, X. et al. Nat Commun (2020) 11:885-885. DOI 10.1038/s41467-020-14728-9 · 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…
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
9JHJ 3.2 Å, Cryo-EM structure of the C18:0 ceramide-bound FPR2-Gi complex

Browse structure collections

About this viewer

MolViewer shows 6OMM 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.