8KH5: GPR174-Gs complex

Cryo-EM structure of the GPR174-Gs complex bound to endogenous lysoPS. Determined by electron microscopy at 2.83 Å resolution. Released 18 Oct 2023.

Method: Electron microscopy
Resolution: 2.83 Å
Organisms: Homo sapiens, Lama glama
Chains: 5
Atoms: 7,838
Mol. weight: 134.1 kDa
Ligands: LPS, CLR
Released: 18 Oct 2023

Explore 8KH5 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8KH5 contains 33 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: 14 helices, 0 β-strands

Element	Residues	Length
α-helix	16-50	35
α-helix	56-81	26
α-helix	88-121	34
α-helix	123-126	4
α-helix	134-148	15
α-helix	151-155	5
α-helix	172-175	4
α-helix	179-190	12
α-helix	191-195	5
α-helix	196-212	17
α-helix	224-257	34
α-helix	264-289	26
α-helix	290-294	5
α-helix	297-302	6

Chain B: 10 helices, 6 β-strands

Element	Residues	Length	Sheet
α-helix	13-38	26
β-strand	40-46	7	1
α-helix	53-59	7
β-strand	209-214	6	1
β-strand	217-223	7	1
α-helix	232-235	4
β-strand	243-249	7	1
α-helix	266-278	13
β-strand	286-292	7	1
α-helix	294-303	10
α-helix	308-311	4
α-helix	313-317	5
α-helix	326-327	2
α-helix	332-351	20
β-strand	359-363	5	1
α-helix	371-390	20

Chain C: 4 helices, 28 β-strands

Element	Residues	Length	Sheet
α-helix	4-25	22
α-helix	30-34	5
α-helix	38-39	2
β-strand	47-52	6	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	100-105	6	4
β-strand	111-116	6	4
β-strand	121-125	5	4
β-strand	134-139	6	4
β-strand	146-151	6	5
β-strand	156-161	6	5
β-strand	165-170	6	5
β-strand	176-181	6	5
β-strand	187-192	6	6
β-strand	198-203	6	6
β-strand	208-212	5	6
β-strand	218-222	5	6
β-strand	229-234	6	7
β-strand	240-245	6	7
β-strand	250-254	5	7
β-strand	259-264	6	7
α-helix	272	1
β-strand	273-278	6	8
β-strand	284-289	6	8
β-strand	294-298	5	8
β-strand	304-308	5	8
β-strand	315-320	6	2
β-strand	327-331	5	2
β-strand	335-339	5	2

Chain D: 3 helices, 0 β-strands

Element	Residues	Length
α-helix	9-24	16
α-helix	30-43	14
α-helix	56-58	3

Chain E: 2 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	9
β-strand	10-12	3	10
β-strand	17-25	9	9
α-helix	29-31	3
β-strand	34-39	6	10
β-strand	45-51	7	10
β-strand	58-60	3	10
β-strand	68-73	6	9
β-strand	78-84	7	9
α-helix	88-90	3
β-strand	92-98	7	10
β-strand	118	1	10
β-strand	122-126	5	10

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Probable G-protein coupled receptor 174	A	protein	340	Homo sapiens	Q9BXC1 (AlphaFold model)
Guanine nucleotide-binding protein G(s) subunit alpha isoforms short	B	protein	248	Homo sapiens	P63092 (AlphaFold model)
Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1	C	protein	357	Homo sapiens	P62873 (AlphaFold model)
Nanobody 35	E	protein	160	Lama glama
Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2	D	protein	71	Homo sapiens	P59768 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>8KH5_1 Probable G-protein coupled receptor 174 (chains A)
DYKDDDDKAPANYTCTRPDGDNTDFRYFIYAVTYTVILVPGLIGNILALWVFYGYMKETK
RAVIFMINLAIADLLQVLSLPLRIFYYLNHDWPFGPGLCMFCFYLKYVNMYASIYFLVCI
SVRRFWFLMYPFRFHDCKQKYDLYISIAGWLIICLACVLFPLLRTSDDTSGNRTKCFVDL
PTRNVNLAQSVVMMTIGELIGFVTPLLIVLYCTWKTVLSLQDKYPMAQDLGEKQKALKMI
LTCAGVFLICFAPYHFSFPLDFLVKSNEIKSCLARRVILIFHSVALCLASLNSCLDPVIY
YFSTNEFRRRLSRQDLHDSIQLHAKSFVSNHELEVLFQGP

Sequence of entity 2 (B), FASTA

>8KH5_2 Guanine nucleotide-binding protein G(s) subunit alpha isoforms short (chains B)
NSKTEDQRNEEKAQREANKKIEKQLQKDKQVYRATHRLLLLGADNSGKSTIVKQMRILHG
GSGGSGGTSGIFETKFQVDKVNFHMFDVGGQRDERRKWIQCFNDVTAIIFVVDSSDYNRL
QEALNLFKSIWNNRWLRTISVILFLNKQDLLAEKVLAGKSKIEDYFPEFARYTTPEDATP
EPGEDPRVTRAKYFIRDEFLRISTASGDGRHYCYPHFTCAVDTENARRIFNDCRDIIQRM
HLRQYELL

Sequence of entity 3 (C), FASTA

>8KH5_3 Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 (chains C)
HHHHHHLEVLFQGPGSSGSELDQLRQEAEQLKNQIRDARKACADATLSQITNNIDPVGRI
QMRTRRTLRGHLAKIYAMHWGTDSRLLVSASQDGKLIIWDSYTTNKVHAIPLRSSWVMTC
AYAPSGNYVACGGLDNICSIYNLKTREGNVRVSRELAGHTGRLSCCRFLDDNQIVTSSGD
TTCALWDIETGQQTTTFTGHTGDVMSLSLAPDTRLFVSGACDASAKLWDVREGMCRQTFT
GHESDINAICFFPNGNAFATGSDDATCRLFDLRADQELMTYSHDNIICGITSVSFSKSGR
LLLAGYDDFNCNVWDALKADRAGVLAGHDNRVSCLGVTDDGMAVATGSWDSFLKIWN

Sequence of entity 4 (E), FASTA

>8KH5_4 Nanobody 35 (chains E)
MKYLLPTAAAGLLLLAAQPAMAQVQLQESGGGLVQPGGSLRLSCAASGFTFSNYKMNWVR
QAPGKGLEWVSDISQSGASISYTGSVKGRFTISRDNAKNTLYLQMNSLKPEDTAVYYCAR
CPAPFTRDCFDVTSTTYAYRGQGTQVTVSSHHHHHHEPEA

Sequence of entity 5 (D), FASTA

>8KH5_5 Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 (chains D)
MASNNTASIAQARKLVEQLKMEANIDRIKVSKAAADLMAYCEAHAKEDPLLTPVPASENP
FREKKFFSAIL

Ligands and cofactors

ID	Name	Formula	Copies
LPS	O-{HYDROXY[((2R)-2-hydroxy-3-{[(1S)-1-hydroxypentadecyl]oxy}propyl)oxy]phosphor…	C21 H44 N O9 P	1
CLR	Cholesterol	C27 H46 O	2

Primary citation

Specific binding of GPR174 by endogenous lysophosphatidylserine leads to high constitutive G s signaling. Nie, Y., Qiu, Z., Chen, S. et al. Nat Commun (2023) 14:5901-5901. DOI 10.1038/s41467-023-41654-3 · 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
7XV3 2.76 Å, Cryo-EM structure of LPS-bound GPR174 in complex with Gs protein
8IZB 3.06 Å, Lysophosphatidylserine receptor GPR174-Gs complex
20YC 3.4 Å, Cryo-EM structure of GPR174-Gi complex

Browse structure collections

About this viewer

MolViewer shows 8KH5 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.