8KGG: LPS-bound P2Y10

LPS-bound P2Y10 in complex with G13. Determined by electron microscopy at 3.06 Å resolution. Released 31 Jul 2024.

Method: Electron microscopy
Resolution: 3.06 Å
Organism: Homo sapiens
Chains: 5
Atoms: 8,972
Mol. weight: 137.94 kDa
Ligands: WJS
Released: 31 Jul 2024

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

Secondary structure: helices and β-sheets

8KGG contains 36 α-helices and 58 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	11-29	19
β-strand	34-40	7	1
α-helix	46-51	6
β-strand	70-76	7	1
β-strand	79-85	7	1
α-helix	89-91	3
β-strand	105-111	7	1
α-helix	115-117	3
α-helix	118-129	12
β-strand	138-144	7	1
α-helix	148-155	8
α-helix	158-160	3
α-helix	172-184	13
α-helix	190-192	3
β-strand	195-200	6	1
α-helix	207-226	20

Chain B: 4 helices, 28 β-strands

Element	Residues	Length	Sheet
α-helix	4-24	21
α-helix	30-33	4
α-helix	34-36	3
α-helix	38-39	2
β-strand	47-51	5	2
β-strand	58-63	6	3
β-strand	69-74	6	3
β-strand	78-83	6	3
β-strand	89-94	6	3
β-strand	100-105	6	4
β-strand	111-116	6	4
β-strand	120-125	6	4
β-strand	134-140	7	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	189-192	4	6
β-strand	198-202	5	6
β-strand	207-212	6	6
β-strand	218-223	6	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
β-strand	273-278	6	8
β-strand	284-289	6	8
β-strand	294-298	5	8
β-strand	303-308	6	8
β-strand	315-320	6	2
β-strand	327-331	5	2
β-strand	336-339	4	2

Chain E: 4 helices, 24 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	33-39	7	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	92-99	8	10
β-strand	111	1	10
β-strand	115-119	5	10
β-strand	141-143	3	11
β-strand	147-149	3	12
β-strand	155-162	8	11
β-strand	167	1	13
β-strand	173	1	13
β-strand	175-180	6	12
β-strand	187-191	5	12
β-strand	195-196	2	12
α-helix	197	1
β-strand	204-209	6	11
β-strand	212-218	7	11
β-strand	226-232	7	12
α-helix	238	1
β-strand	240	1	12
β-strand	244-247	4	12

Chain G: 4 helices, 0 β-strands

Element	Residues	Length
α-helix	7-23	17
α-helix	30-43	14
α-helix	53-55	3
α-helix	56-58	3

Chain R: 14 helices, 0 β-strands

Element	Residues	Length
α-helix	33-59	27
α-helix	70-84	15
α-helix	88-96	9
α-helix	103-136	34
α-helix	140-142	3
α-helix	146-163	18
α-helix	166-170	5
α-helix	182-184	3
α-helix	192-203	12
α-helix	204-208	5
α-helix	209-223	15
α-helix	235-270	36
α-helix	277-294	18
α-helix	297-306	10

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Guanine nucleotide-binding protein G(i) subunit alpha-2,Guanine nucleotide-binding protein subunit…	A	protein	230	Homo sapiens	P04899 (AlphaFold model), Q14344 (AlphaFold model)
Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1	B	protein	345	Homo sapiens	P62873 (AlphaFold model)
scFv16	E	protein	247	Homo sapiens
Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2	G	protein	71	Homo sapiens	P59768 (AlphaFold model)
Putative P2Y purinoceptor 10	R	protein	339	Homo sapiens	O00398

Sequence of entity 1 (A), FASTA

>8KGG_1 Guanine nucleotide-binding protein G(i) subunit alpha-2,Guanine nucleotide-binding protein subunit alpha-13 (chains A)
MGSTVSAEDKAAAERSKEIDKCLSREKTYVKRLVKILLLGADNSGKSTFLKQMRIIHGGS
GGSGGTKGIHEYDFEIKNVPFKMVDVGGQRSERKRWFECFDSVTSILFLVDSSDFNRLTE
SLNDFETIVNNRVFSNVSIILFLNKTDLLEEKVQIVSIKDYFLEFEGDPHCLRDVQKFLV
ECFRNKRRDQQQKPLYHHFTTAINTENARLIFRDVKDTILHDNLKQLMLQ

Sequence of entity 2 (B), FASTA

>8KGG_2 Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 (chains B)
MGSLLQSELDQLRQEAEQLKNQIRDARKACADATLSQITNNIDPVGRIQMRTRRTLRGHL
AKIYAMHWGTDSRLLVSASQDGKLIIWDSYTTNKVHAIPLRSSWVMTCAYAPSGNYVACG
GLDNICSIYNLKTREGNVRVSRELAGHTGYLSCCRFLDDNQIVTSSGDTTCALWDIETGQ
QTTTFTGHTGDVMSLSLAPDTRLFVSGACDASAKLWDVREGMCRQTFTGHESDINAICFF
PNGNAFATGSDDATCRLFDLRADQELMTYSHDNIICGITSVSFSKSGRLLLAGYDDFNCN
VWDALKADRAGVLAGHDNRVSCLGVTDDGMAVATGSWDSFLKIWN

Sequence of entity 3 (E), FASTA

>8KGG_3 scFv16 (chains E)
VQLVESGGGLVQPGGSRKLSCSASGFAFSSFGMHWVRQAPEKGLEWVAYISSGSGTIYYA
DTVKGRFTISRDDPKNTLFLQMTSLRSEDTAMYYCVRSIYYYGSSPFDFWGQGTTLTVSA
GGGGSGGGGSGGGGSADIVMTQATSSVPVTPGESVSISCRSSKSLLHSNGNTYLYWFLQR
PGQSPQLLIYRMSNLASGVPDRFSGSGSGTAFTLTISRLEAEDVGVYYCMQHLEYPLTFG
AGTKLEL

Sequence of entity 4 (G), FASTA

>8KGG_4 Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 (chains G)
MASNNTASIAQARKLVEQLKMEANIDRIKVSKAAADLMAYCEAHAKEDPLLTPVPASENP
FREKKFFCAIL

Sequence of entity 5 (R), FASTA

>8KGG_5 Putative P2Y purinoceptor 10 (chains R)
MANLDKYTETFKMGSNSTSTAEIYCNVTNVKFQYSLYATTYILIFIPGLLANSAALWVLC
RFISKKNKAIIFMINLSVADLAHVLSLPLRIYYYISHHWPFQRALCLLCFYLKYLNMYAS
ICFLTCISLQRCFFLLKPFRARDWKRRYDVGISAAIWIVVGTACLPFPILRSTDLNNNKS
CFADLGYKQMNAVALVGMITVAELAGFVIPVIIIAWCTWKTTISLRQPPMAFQGISERQK
ALRMVFMCAAVFFICFTPYHINFIFYTMVKETIISSCPVVRIALYFHPFCLCLASLCCLL
DPILYYFMASEFRDQLSRHGSSVTRSRLMSKESGSSMIG

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

Insights into lysophosphatidylserine recognition and G alpha 12/13 -coupling specificity of P2Y10. Yin, H., Kamakura, N., Qian, Y. et al. Cell Chem Biol (2024) 31:1899-1908.e5. DOI 10.1016/j.chembiol.2024.08.005 · PubMed

Other PDB entries of the same protein (UniProt P04899 (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
8THK 2.6 Å, Cryo-EM structure of A61603-bound alpha-1A-adrenergic receptor in complex with…
7YK7 2.75 Å, Cryo-EM structure of the DC591053-bound human relaxin family peptide receptor 4…
9K6L 2.77 Å, Cryo-EM structure of GPCR16-Gi2 complex
9XDQ 2.79 Å, Cryo-EM structure of BMS986187 bound DOR-Gi complex
7WVX 2.8 Å, Cryo-EM structure of the human formyl peptide receptor 2 in complex with fhumanin and Gi2
8W8A 2.8 Å, Cryo-EM structure of the RO5256390-TAAR1 complex
8ZSJ 2.8 Å, Cryo-EM structure of the apo hTAAR1-Gs complex
7WVV 2.9 Å, Cryo-EM structure of the human formyl peptide receptor 2 in complex with fMLFII and Gi2
9DQJ 2.9 Å, CryoEM structure of Gq-coupled MRGPRD with a new agonist EP-3945
9KFI 2.91 Å, Cryo-EM structure of the human relaxin family peptide receptor 3 in complex with…
9KFK 2.95 Å, Cryo-EM structure of the relaxin-3-bound human relaxin family peptide receptor 4…

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