7WVY: Human formyl peptide receptor 2

Cryo-EM structure of the human formyl peptide receptor 2 in complex with Abeta42 and Gi2. Determined by electron microscopy at 3.0 Å resolution. Released 13 Apr 2022.

Method: Electron microscopy
Resolution: 3.0 Å
Organism: Homo sapiens
Chains: 5
Atoms: 7,094
Mol. weight: 148.34 kDa
Released: 13 Apr 2022

Explore 7WVY in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7WVY contains 36 α-helices and 40 β-strands across 4 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: 11 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	7-32	26
β-strand	33-39	7	3
α-helix	46-53	8
β-strand	186-192	7	3
β-strand	195-201	7	3
α-helix	209-212	4
α-helix	213-216	4
β-strand	221-227	7	3
α-helix	228-232	5
β-strand	234	1	4
β-strand	242	1	4
α-helix	243-256	14
α-helix	258-260	3
β-strand	264-270	7	3
α-helix	272-281	10
α-helix	284-286	3
α-helix	297-311	15
β-strand	320-324	5	3
α-helix	332-352	21

Chain B: 5 helices, 28 β-strands

Element	Residues	Length	Sheet
α-helix	8-25	18
α-helix	30-33	4
α-helix	34-36	3
α-helix	38-39	2
β-strand	47-51	5	5
β-strand	58-63	6	6
β-strand	69-74	6	6
β-strand	78-83	6	6
β-strand	88-94	7	6
β-strand	100-105	6	7
β-strand	111-116	6	7
β-strand	120-125	6	7
β-strand	134-140	7	7
β-strand	146-151	6	8
β-strand	156-161	6	8
β-strand	165-170	6	8
β-strand	176-181	6	8
β-strand	189-192	4	9
β-strand	198-202	5	9
β-strand	208-212	5	9
β-strand	218-222	5	9
β-strand	229-234	6	10
β-strand	240-245	6	10
β-strand	249-254	6	10
β-strand	259-265	7	10
α-helix	272-273	2
β-strand	276-278	3	11
β-strand	284-288	5	11
β-strand	294-298	5	11
β-strand	304-307	4	11
β-strand	315-320	6	5
β-strand	327-331	5	5
β-strand	336-339	4	5

Chain C: 3 helices, 0 β-strands

Element	Residues	Length
α-helix	13-23	11
α-helix	30-43	14
α-helix	45-47	3

Chain R: 17 helices, 4 β-strands

Element	Residues	Length	Sheet
α-helix	20-47	28
α-helix	48-53	6
α-helix	54	1
α-helix	59-76	18
α-helix	78-86	9
α-helix	95-128	34
α-helix	130-136	7
α-helix	139-162	24
β-strand	164	1	1
β-strand	167-168	2	2
β-strand	174-175	2	2
β-strand	178	1	1
α-helix	181-184	4
α-helix	187-204	18
α-helix	205-211	7
α-helix	212-231	20
α-helix	238-266	29
α-helix	268-269	2
α-helix	270-274	5
α-helix	279-302	24
α-helix	307-315	9

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Amyloid-beta A4 protein	L	protein	42	Homo sapiens	P05067 (AlphaFold model)
Soluble cytochrome b562,N-formyl peptide receptor 2	R	protein	513	Homo sapiens	P0ABE7 (AlphaFold model), P25090 (AlphaFold model)
Guanine nucleotide-binding protein G(i) subunit alpha-2	A	protein	355	Homo sapiens	P04899 (AlphaFold model)
Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1	B	protein	351	Homo sapiens	P62873
Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2	C	protein	71	Homo sapiens	P59768

Sequence of entity 1 (L), FASTA

>7WVY_1 Amyloid-beta A4 protein (chains L)
DAEFRHDSGYEVHHQKLVFFAEDVGSNKGAIIGLMVGGVVIA

Sequence of entity 2 (R), FASTA

>7WVY_2 Soluble cytochrome b562,N-formyl peptide receptor 2 (chains R)
GAPADLEDNWETLNDNLKVIEKADNAAQVKDALTKMRAAALDAQKATPPKLEDKSPDSPE
MKDFRHGFDILVGQIDDALKLANEGKVKEAQAAAEQLKTTRNAYIQKYLGSGSENLYFQS
ETNFSTPLNEYEEVSYESAGYTVLRILPLVVLGVTFVLGVLGNGLVIWVAGFRMTRTVTT
ICYLNLALADFSFTATLPFLIVSMAMGEKWPFGWFLCKLIHIVVDINLFGSVFLIGFIAL
DRCICVLHPVWAQNHRTVSLAMKVIVGPWILALVLTLPVFLFLTTVTIPNGDTYCTFNFA
SWGGTPEERLKVAITMLTARGIIRFVIGFLLPMSIVAICYGLIAAKIHKKGMIKSSRPLR
VLTAVVASFFICWFPFQLVALLGTVWLKEMLFYGKYKIIDILVNPTSSLAFFNSCLNPML
YVFVGQDFRERLIHSLPTSLERALSEDSAPTNDTAANSASPPAETEFLEVLFQGPGSWSH
PQFEKGSGAGASAGSWSHPQFEKGSDYKDDDDK

Sequence of entity 3 (A), FASTA

>7WVY_3 Guanine nucleotide-binding protein G(i) subunit alpha-2 (chains A)
MGCTVSAEDKAAAERSKMIDKNLREDGEKAAREVKLLLLGAGESGKNTIVKQMKIIHEDG
YSEEECRQYRAVVYSNTIQSIMAIVKAMGNLQIDFADPSRADDARQLFALSCTAEEQGVL
PDDLSGVIRRLWADHGVQACFGRSREYQLNDSAAYYLNDLERIAQSDYIPTQQDVLRTRV
KTTGIVETHFTFKDLHFKMFDVGAQRSERKKWIHCFEGVTAIIFCVALSAYDLVLAEDEE
MNRMHASMKLFDSICNNKWFTDTSIILFLNKKDLFEEKITHSPLTICFPEYTGANKYDEA
ASYIQSKFEDLNKRKDTKEIYTHFTCSTDTKNVQFVFDAVTDVIIKNNLKDCGLF

Sequence of entity 4 (B), FASTA

>7WVY_4 Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 (chains B)
MHHHHHHGSLLQSELDQLRQEAEQLKNQIRDARKACADATLSQITNNIDPVGRIQMRTRR
TLRGHLAKIYAMHWGTDSRLLVSASQDGKLIIWDSYTTNKVHAIPLRSSWVMTCAYAPSG
NYVACGGLDNICSIYNLKTREGNVRVSRELAGHTGYLSCCRFLDDNQIVTSSGDTTCALW
DIETGQQTTTFTGHTGDVMSLSLAPDTRLFVSGACDASAKLWDVREGMCRQTFTGHESDI
NAICFFPNGNAFATGSDDATCRLFDLRADQELMTYSHDNIICGITSVSFSKSGRLLLAGY
DDFNCNVWDALKADRAGVLAGHDNRVSCLGVTDDGMAVATGSWDSFLKIWN

Sequence of entity 5 (C), FASTA

>7WVY_5 Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 (chains C)
MASNNTASIAQARKLVEQLKMEANIDRIKVSKAAADLMAYCEAHAKEDPLLTPVPASENP
FREKKFFCAIL

Primary citation

Structural basis of FPR2 in recognition of A beta 42 and neuroprotection by humanin. Zhu, Y., Lin, X., Zong, X. et al. Nat Commun (2022) 13:1775-1775. DOI 10.1038/s41467-022-29361-x · PubMed

Other PDB entries of the same protein (UniProt P05067 (AlphaFold model), which also has an AlphaFold model), best resolution first:

2FMA 0.85 Å, Structure of the Alzheimer's Amyloid Precursor Protein (APP) Copper Binding Domain in…
6NB9 1.05 Å, Amyloid-Beta (20-34) with L-isoaspartate 23
6OIZ 1.1 Å, Amyloid-Beta (20-34) wild type
8T82 1.1 Å, Racemic mixture of amyloid beta segment 35-MVGGVV-40 forms heterochiral rippled…
5ONQ 1.17 Å, Alzheimer's Amyloid-Beta Peptide Fragment 29-40 in Complex with Cd-substituted Thermolysin
3JQL 1.2 Å, Crystal Structure of the Complex Formed Between Phospholipase A2 and a Hexapeptide…
3PZZ 1.29 Å, Structure of an amyloid forming peptide GAIIGL (29-34) from amyloid beta
4PQD 1.33 Å, The longer crystal structure of the grow factor like domain from Beta amypoid precusor…
5ONP 1.34 Å, Alzheimer's Amyloid-Beta Peptide Fragment 1-40 in Complex with Cd-substituted Thermolysin
5ONR 1.39 Å, Alzheimer's Amyloid-Beta Peptide Fragment 1-40 in Complex with Thermolysin
4PWQ 1.4 Å, High-resolution crystal structure of the E1-domain of the amyloid precursor protein
7OW1 1.4 Å, Crystal Structure of TAP01 in complex with amyloid beta peptide

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