7XV3: LPS-bound GPR174

Cryo-EM structure of LPS-bound GPR174 in complex with Gs protein. Determined by electron microscopy at 2.76 Å resolution. Released 15 Feb 2023.

Method: Electron microscopy
Resolution: 2.76 Å
Organisms: Homo sapiens, Lama glama
Chains: 5
Atoms: 8,347
Mol. weight: 144.07 kDa
Ligands: WJS
Released: 15 Feb 2023

Explore 7XV3 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7XV3 contains 29 α-helices and 45 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: 9 helices, 6 β-strands

Element	Residues	Length	Sheet
α-helix	14-38	25
β-strand	41-47	7	1
α-helix	53-59	7
β-strand	207-214	8	1
β-strand	217-224	8	1
α-helix	234-238	5
β-strand	243-249	7	1
α-helix	266-278	13
β-strand	286-292	7	1
α-helix	294-303	10
α-helix	308-310	3
α-helix	313-317	5
α-helix	332-351	20
β-strand	359-363	5	1
α-helix	371-390	20

Chain B: 2 helices, 28 β-strands

Element	Residues	Length	Sheet
α-helix	4-23	20
α-helix	30-34	5
β-strand	47-51	5	4
β-strand	58-63	6	5
β-strand	69-74	6	5
β-strand	78-83	6	5
β-strand	88-94	7	5
β-strand	100-105	6	6
β-strand	111-116	6	6
β-strand	121-125	5	6
β-strand	134-139	6	6
β-strand	146-151	6	7
β-strand	156-161	6	7
β-strand	166-170	5	7
β-strand	176-180	5	7
β-strand	187-192	6	8
β-strand	198-203	6	8
β-strand	205-212	8	8
β-strand	217-222	6	8
β-strand	229-234	6	9
β-strand	240-245	6	9
β-strand	250-254	5	9
β-strand	259-264	6	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	4
β-strand	327-331	5	4
β-strand	336-339	4	4

Chain G: 3 helices, 0 β-strands

Element	Residues	Length
α-helix	9-22	14
α-helix	30-43	14
α-helix	53-55	3

Chain N: 3 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	2
β-strand	10-12	3	3
β-strand	18-25	8	2
α-helix	29-31	3
β-strand	34-39	6	3
β-strand	45-51	7	3
β-strand	58-60	3	3
α-helix	62-64	3
β-strand	68-73	6	2
β-strand	78-83	6	2
α-helix	88-90	3
β-strand	92-98	7	3
β-strand	118	1	3
β-strand	122-126	5	3

Chain R: 12 helices, 0 β-strands

Element	Residues	Length
α-helix	19-48	30
α-helix	57-70	14
α-helix	73-81	9
α-helix	88-121	34
α-helix	134-148	15
α-helix	151-154	4
α-helix	179-190	12
α-helix	191-195	5
α-helix	196-211	16
α-helix	224-257	34
α-helix	264-281	18
α-helix	284-291	8

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Probable G-protein coupled receptor 174	R	protein	333	Homo sapiens	Q9BXC1 (AlphaFold model)
Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2	G	protein	71	Homo sapiens	P59768 (AlphaFold model)
Engineered G protein subunit S (mini-Gs)	A	protein	361	Homo sapiens
Nb35	N	protein	161	Lama glama
Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1	B	protein	345	Homo sapiens	P62873 (AlphaFold model)

Sequence of entity 1 (R), FASTA

>7XV3_1 Probable G-protein coupled receptor 174 (chains R)
MPANYTCTRPDGDNTDFRYFIYAVTYTVILVPGLIGNILALWVFYGYMKETKRAVIFMIN
LAIADLLQVLSLPLRIFYYLNHDWPFGPGLCMFCFYLKYVNMYASIYFLVCISVRRFWFL
MYPFRFHDCKQKYDLYISIAGWLIICLACVLFPLLRTSDDTSGNRTKCFVDLPTRNVNLA
QSVVMMTIGELIGFVTPLLIVLYCTWKTVLSLQDKYPMAQDLGEKQKALKMILTCAGVFL
ICFAPYHFSFPLDFLVKSNEIKSCLARRVILIFHSVALCLASLNSCLDPVIYYFSTNEFR
RRLSRQDLHDSIQLHAKSFVSNHTASTMTPELC

Sequence of entity 2 (G), FASTA

>7XV3_2 Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 (chains G)
MASNNTASIAQARKLVEQLKMEANIDRIKVSKAAADLMAYCEAHAKEDPLLTPVPASENP
FREKKFFCAIL

Sequence of entity 3 (A), FASTA

>7XV3_3 Engineered G protein subunit S (mini-Gs) (chains A)
MGCTLSAEDKAAVERSKMIEKQLQKDKQVYRATHRLLLLGADNSGKSTIVKQMRIYHVNG
YSEEECKQYKAVVYSNTIQSIIAIIRAMGRLKIDFGDSARADDARQLFVLAGAAEEGFMT
AELAGVIKRLWKDSGVQACFNRSREYQLNDSAAYYLNDLDRIAQPNYIPTQQDVLRTRVK
TSGIFETKFQVDKVNFHMFDVGAQRDERRKWIQCFNDVTAIIFVVDSSDYNRLQEALNDF
KSIWNNRWLRTISVILFLNKQDLLAEKVLAGKSKIEDYFPEFARYTTPEDATPEPGEDPR
VTRAKYFIRDEFLRISTASGDGRHYCYPHFTCSVDTENARRIFNDCRDIIQRMHLRQYEL
L

Sequence of entity 4 (N), FASTA

>7XV3_4 Nb35 (chains N)
MKYLLPTAAAGLLLLAAQPAMAQVQLQESGGGLVQPGGSLRLSCAASGFTFSNYKMNWVR
QAPGKGLEWVSDISQSGASISYTGSVKGRFTISRDNAKNTLYLQMNSLKPEDTAVYYCAR
CPAPFTRDCFDVTSTTYAYRGQGTQVTVSSAAALEHHHHHH

Sequence of entity 5 (B), FASTA

>7XV3_5 Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 (chains B)
MGSLLQSELDQLRQEAEQLKNQIRDARKACADATLSQITNNIDPVGRIQMRTRRTLRGHL
AKIYAMHWGTDSRLLVSASQDGKLIIWDSYTTNKVHAIPLRSSWVMTCAYAPSGNYVACG
GLDNICSIYNLKTREGNVRVSRELAGHTGYLSCCRFLDDNQIVTSSGDTTCALWDIETGQ
QTTTFTGHTGDVMSLSLAPDTRLFVSGACDASAKLWDVREGMCRQTFTGHESDINAICFF
PNGNAFATGSDDATCRLFDLRADQELMTYSHDNIICGITSVSFSKSGRLLLAGYDDFNCN
VWDALKADRAGVLAGHDNRVSCLGVTDDGMAVATGSWDSFLKIWN

Ligands and cofactors

ID	Name	Formula	Copies
WJS	(2~{S})-2-$l^{4}-azanyl-3-[[(2~{R})-3-octadecanoyloxy-2-oxidanyl-propoxy]-oxida…	C24 H20 N O9 P	1

Primary citation

Structural basis of lysophosphatidylserine receptor GPR174 ligand recognition and activation. Liang, J., Inoue, A., Ikuta, T. et al. Nat Commun (2023) 14:1012-1012. DOI 10.1038/s41467-023-36575-0 · PubMed

Other PDB entries of the same protein (UniProt Q9BXC1 (AlphaFold model), which also has an AlphaFold model), best resolution first:

9XXT 2.0 Å, Cryo-EM structure of lysophosphatidylserine (18:0)-bound GPR174-Gs complex
8KH5 2.83 Å, Cryo-EM structure of the GPR174-Gs complex bound to endogenous lysoPS
8IZB 3.06 Å, Lysophosphatidylserine receptor GPR174-Gs complex
20YC 3.4 Å, Cryo-EM structure of GPR174-Gi complex

Browse structure collections

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