9K20: P2Y purinoceptor 2

Cryo-EM structure of ATP-bound P2Y purinoceptor 2-miniGo-scFv16 complex. Determined by electron microscopy at 2.65 Å resolution. Released 11 Jun 2025.

Method: Electron microscopy
Resolution: 2.65 Å
Organisms: Homo sapiens, Mus musculus
Chains: 5
Atoms: 8,292
Mol. weight: 150.87 kDa
Ligands: ATP
Released: 11 Jun 2025

Explore 9K20 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9K20 contains 33 α-helices and 63 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: 13 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	32-56	25
α-helix	57-61	5
α-helix	69-84	16
α-helix	86-94	9
α-helix	103-136	34
α-helix	138-142	5
α-helix	148-165	18
α-helix	167-171	5
β-strand	174-176	3	1
β-strand	181-183	3	1
α-helix	192-203	12
α-helix	204-208	5
α-helix	209-225	17
α-helix	238-273	36
α-helix	278-307	30

Chain B: 11 helices, 7 β-strands

Element	Residues	Length	Sheet
α-helix	4-12	9
α-helix	13-17	5
α-helix	18-28	11
β-strand	31-37	7	2
α-helix	44-51	8
β-strand	68-73	6	2
β-strand	78-83	6	2
α-helix	91-93	3
β-strand	103-109	7	2
α-helix	114-127	14
α-helix	130-132	3
β-strand	137-142	6	2
α-helix	144-151	8
α-helix	156-158	3
α-helix	169-181	13
β-strand	191	1	2
β-strand	194-195	2	2
α-helix	203-222	20

Chain C: 3 helices, 28 β-strands

Element	Residues	Length	Sheet
α-helix	11-25	15
α-helix	30-33	4
α-helix	34-36	3
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	89-94	6	4
β-strand	100-105	6	5
β-strand	111-116	6	5
β-strand	120-125	6	5
β-strand	134-140	7	5
β-strand	146-151	6	6
β-strand	156-161	6	6
β-strand	165-170	6	6
β-strand	175-181	7	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	249-254	6	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	304-307	4	9
β-strand	317-320	4	3
β-strand	327-330	4	3
β-strand	336-339	4	3

Chain D: 3 helices, 0 β-strands

Element	Residues	Length
α-helix	13-21	9
α-helix	30-43	14
α-helix	53-55	3

Chain E: 3 helices, 26 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	10
β-strand	11-12	2	11
β-strand	17-25	9	10
α-helix	29-31	3
β-strand	33-40	8	12
β-strand	44-51	8	12
β-strand	58-60	3	12
β-strand	68-73	6	10
β-strand	78-84	7	10
α-helix	88-90	3
β-strand	93-99	7	12
β-strand	110-111	2	12
β-strand	113	1	10
β-strand	115-116	2	12
β-strand	118-119	2	11
β-strand	128-129	2	13
β-strand	134-136	3	14
β-strand	143-149	7	13
β-strand	154	1	15
β-strand	160	1	15
β-strand	162-167	6	14
β-strand	173-177	5	14
β-strand	183	1	14
β-strand	191-194	4	13
β-strand	199-204	6	13
β-strand	213-219	7	14
β-strand	227	1	14
α-helix	228-229	2
β-strand	231-234	4	14

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
P2Y purinoceptor 2	A	protein	420	Homo sapiens	P41231 (AlphaFold model)
Guanine nucleotide-binding protein G(o) subunit alpha	B	protein	226	Homo sapiens	P09471 (AlphaFold model)
Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1	C	protein	358	Homo sapiens	P62873 (AlphaFold model)
Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2	D	protein	71	Homo sapiens	P59768 (AlphaFold model)
Single Fab chain (svFv16)	E	protein	289	Mus musculus

Sequence of entity 1 (A), FASTA

>9K20_1 P2Y purinoceptor 2 (chains A)
MKTIIALSYIFCLVFADYKDDDDAMAADLGPWNDTINGTWDGDELGYRCRFNEDFKYVLL
PVSYGVVCVLGLCLNAVALYIFLCRLKTWNASTTYMFHLAVSDALYAASLPLLVYYYARG
DHWPFSTVLCKLVRFLFYTNLYCSILFLTCISVHRCLGVLRPLRSLRWGRARYARRVAGA
VWVLVLACQAPVLYFVTTSARGGRVTCHDTSAPELFSRFVAYSSVMLGLLFAVPFAVILV
CYVLMARRLLKPAYGTSGGLPRAKRKSVRTIAVVLAVFALCFLPFHVTRTLYYSFRSLDL
SCHTLNAINMAYKVTRPLASANSCLNPVLYFLAGQSLVRFARDAKPPTGPSPATPARRRL
GLRRSDRTDMQRIEDVLGSSEDSRRTESTPAGSENTKDIRLHHHHHHGGSGGLEVLFQGP

Sequence of entity 2 (B), FASTA

>9K20_2 Guanine nucleotide-binding protein G(o) subunit alpha (chains B)
TLSAEDKAAVERSKMGIEKNLKEDGISAAKDVKLLLLGADNSGKSTIVKQMKIIHGGSGG
SGGTTGIVETHFTFKNLHFRLFDVGGQRSERKKWIHCFEDVTAIIFCVDLSDYNRMHESL
MDFDSICNNKFFIDTSIILFLNKKDLFGEKIKKSPLTICFPEYTGPNTYEDAAAYIQAQF
ESKNRSPNKEIYCHMTCATDTNNAQVIFDAVTDIIIANNLRGCGLY

Sequence of entity 3 (C), FASTA

>9K20_3 Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 (chains C)
MHHHHHHLEVLFQGPGSSGSELDQLRQEAEQLKNQIRDARKACADATLSQITNNIDPVGR
IQMRTRRTLRGHLAKIYAMHWGTDSRLLVSASQDGKLIIWDSYTTNKVHAIPLRSSWVMT
CAYAPSGNYVACGGLDNICSIYNLKTREGNVRVSRELAGHTGYLSCCRFLDDNQIVTSSG
DTTCALWDIETGQQTTTFTGHTGDVMSLSLAPDTRLFVSGACDASAKLWDVREGMCRQTF
TGHESDINAICFFPNGNAFATGSDDATCRLFDLRADQELMTYSHDNIICGITSVSFSKSG
RLLLAGYDDFNCNVWDALKADRAGVLAGHDNRVSCLGVTDDGMAVATGSWDSFLKIWN

Sequence of entity 4 (D), FASTA

>9K20_4 Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 (chains D)
MASNNTASIAQARKLVEQLKMEANIDRIKVSKAAADLMAYCEAHAKEDPLLTPVPASENP
FREKKFFCAIL

Sequence of entity 5 (E), FASTA

>9K20_5 Single Fab chain (svFv16) (chains E)
MVSAIVLYVLLAAAAHSAFADVQLVESGGGLVQPGGSRKLSCSASGFAFSSFGMHWVRQA
PEKGLEWVAYISSGSGTIYYADTVKGRFTISRDDPKNTLFLQMTSLRSEDTAMYYCVRSI
YYYGSSPFDFWGQGTTLTVSSGGGGSGGGGSGGGGSDIVMTQATSSVPVTPGESVSISCR
SSKSLLHSNGNTYLYWFLQRPGQSPQLLIYRMSNLASGVPDRFSGSGSGTAFTLTISRLE
AEDVGVYYCMQHLEYPLTFGAGTKLELKGSLEVLFQGPAAAHHHHHHHH

Ligands and cofactors

ID	Name	Formula	Copies
ATP	Adenosine-5'-triphosphate	C10 H16 N5 O13 P3	1

Primary citation

Structural insight into the self-activation and G-protein coupling of P2Y2 receptor. Lan, B., Zhang, S., Chen, K. et al. Cell Discov (2025) 11:47-47. DOI 10.1038/s41421-025-00797-x · PubMed

Other PDB entries of the same protein (UniProt P41231 (AlphaFold model), which also has an AlphaFold model), best resolution first:

9K0X 2.83 Å, Cryo-EM structure of ATP-bound P2Y purinoceptor 2-miniGq-Nb35 complex
9K25 3.31 Å, Cryo-EM structure of apo-P2Y purinoceptor 2-miniGq-Nb35 complex

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