9K0X: ATP-bound P2Y purinoceptor 2-miniGq-Nb35 complex

Cryo-EM structure of ATP-bound P2Y purinoceptor 2-miniGq-Nb35 complex. Determined by electron microscopy at 2.83 Å resolution. Released 11 Jun 2025.

Method: Electron microscopy
Resolution: 2.83 Å
Organisms: Homo sapiens, Vicugna pacos
Chains: 5
Atoms: 7,300
Mol. weight: 137.54 kDa
Ligands: ATP
Released: 11 Jun 2025

Explore 9K0X in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9K0X contains 27 α-helices and 46 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	14-37	24
β-strand	40-47	8	1
α-helix	49-51	3
α-helix	53-59	7
β-strand	208-214	7	1
β-strand	217-223	7	1
α-helix	234-237	4
β-strand	243-248	6	1
α-helix	266-277	12
β-strand	286-291	6	1
α-helix	295-300	6
α-helix	313-315	3
α-helix	333-352	20
β-strand	359-362	4	1
α-helix	371-390	20

Chain B: 4 helices, 29 β-strands

Element	Residues	Length	Sheet
α-helix	15-24	10
α-helix	30-33	4
α-helix	38-41	4
β-strand	43	1	2
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
α-helix	95	1
β-strand	100-105	6	5
β-strand	111-116	6	5
β-strand	121-125	5	5
β-strand	134-139	6	5
β-strand	146-151	6	6
β-strand	156-161	6	6
β-strand	166-170	5	6
β-strand	176-180	5	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	250-254	5	8
β-strand	259-264	6	8
β-strand	273-278	6	2
β-strand	284-289	6	2
β-strand	294-298	5	2
β-strand	304-308	5	2
β-strand	315-320	6	3
β-strand	327-331	5	3
β-strand	336-339	4	3

Chain G: 3 helices, 0 β-strands

Element	Residues	Length
α-helix	15-23	9
α-helix	30-43	14
α-helix	45-47	3

Chain I: 10 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	32-60	29
α-helix	67-94	28
α-helix	105-136	32
α-helix	140-142	3
α-helix	149-171	23
β-strand	174-176	3	9
β-strand	181-183	3	9
α-helix	192-203	12
α-helix	204-208	5
α-helix	209-225	17
α-helix	239-273	35
α-helix	278-307	30

Chain N: 1 helix, 9 β-strands

Element	Residues	Length	Sheet
β-strand	3-5	3	10
β-strand	18-25	8	10
α-helix	29-31	3
β-strand	34-38	5	11
β-strand	50-51	2	11
β-strand	58	1	11
β-strand	70-73	4	10
β-strand	78-83	6	10
β-strand	92-98	7	11
β-strand	122-124	3	11

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Guanine nucleotide-binding protein G(s) subunit alpha isoforms short	A	protein	243	Homo sapiens	P63092 (AlphaFold model)
Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1	B	protein	358	Homo sapiens	P62873 (AlphaFold model)
Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2	G	protein	71	Homo sapiens	P59768 (AlphaFold model)
P2Y purinoceptor 2	I	protein	420	Homo sapiens	P41231 (AlphaFold model)
Nanobody 35	N	protein	134	Vicugna pacos

Sequence of entity 1 (A), FASTA

>9K0X_1 Guanine nucleotide-binding protein G(s) subunit alpha isoforms short (chains A)
TLSAEDKAAVERSKMIEKQLQKDKQVYRATHRLLLLGADNSGKSTIVKQMRILHGGSGGS
GGTSGIFETKFQVDKVNFHMFDVGGQRDERRKWIQCFNDVTAIIFVVDSSDYNRLQEALN
DFKSIWNNRWLRTISVILFLNKQDLLAEKVLAGKSKIEDYFPEFARYTTPEDATPEPGED
PRVTRAKYFIRDEFLRISTASGDGRHYCYPHFTCAVDTENARRIFNDCKDIILQMNLREY
NLV

Sequence of entity 2 (B), FASTA

>9K0X_2 Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 (chains B)
MHHHHHHLEVLFQGPGSSGSELDQLRQEAEQLKNQIRDARKACADATLSQITNNIDPVGR
IQMRTRRTLRGHLAKIYAMHWGTDSRLLVSASQDGKLIIWDSYTTNKVHAIPLRSSWVMT
CAYAPSGNYVACGGLDNICSIYNLKTREGNVRVSRELAGHTGYLSCCRFLDDNQIVTSSG
DTTCALWDIETGQQTTTFTGHTGDVMSLSLAPDTRLFVSGACDASAKLWDVREGMCRQTF
TGHESDINAICFFPNGNAFATGSDDATCRLFDLRADQELMTYSHDNIICGITSVSFSKSG
RLLLAGYDDFNCNVWDALKADRAGVLAGHDNRVSCLGVTDDGMAVATGSWDSFLKIWN

Sequence of entity 3 (G), FASTA

>9K0X_3 Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 (chains G)
MASNNTASIAQARKLVEQLKMEANIDRIKVSKAAADLMAYCEAHAKEDPLLTPVPASENP
FREKKFFCAIL

Sequence of entity 4 (I), FASTA

>9K0X_4 P2Y purinoceptor 2 (chains I)
MKTIIALSYIFCLVFADYKDDDDAMAADLGPWNDTINGTWDGDELGYRCRFNEDFKYVLL
PVSYGVVCVLGLCLNAVALYIFLCRLKTWNASTTYMFHLAVSDALYAASLPLLVYYYARG
DHWPFSTVLCKLVRFLFYTNLYCSILFLTCISVHRCLGVLRPLRSLRWGRARYARRVAGA
VWVLVLACQAPVLYFVTTSARGGRVTCHDTSAPELFSRFVAYSSVMLGLLFAVPFAVILV
CYVLMARRLLKPAYGTSGGLPRAKRKSVRTIAVVLAVFALCFLPFHVTRTLYYSFRSLDL
SCHTLNAINMAYKVTRPLASANSCLNPVLYFLAGQSLVRFARDAKPPTGPSPATPARRRL
GLRRSDRTDMQRIEDVLGSSEDSRRTESTPAGSENTKDIRLHHHHHHGGSGGLEVLFQGP

Sequence of entity 5 (N), FASTA

>9K0X_5 Nanobody 35 (chains N)
QVQLQESGGGLVQPGGSLRLSCAASGFTFSNYKMNWVRQAPGKGLEWVSDISQSGASISY
TGSVKGRFTISRDNAKNTLYLQMNSLKPEDTAVYYCARCPAPFTPFCFDVTSTTYAYRGQ
GTQVTVSSHHHHHH

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 P63092 (AlphaFold model), which also has an AlphaFold model), best resolution first:

7BPH 1.57 Å, Crystal structure of GppNHp-bound GNAS in complex with the cyclic peptide inhibitor GN13
6AU6 1.7 Å, Crystal structure of GDP-bound human GNAS R201C mutant
8F0K 1.9 Å, Human Amylin3 Receptor in complex with Gs and Pramlintide analogue peptide San385
7E5E 1.95 Å, Crystal structure of GDP-bound GNAS in complex with the cyclic peptide inhibitor GD20
7MBX 1.95 Å, Human Cholecystokinin 1 receptor (CCK1R) Gs complex
8F0J 2.0 Å, Calcitonin Receptor in complex with Gs and Pramlintide analogue peptide San45
8F2B 2.0 Å, Amylin 3 Receptor in complex with Gs and Pramlintide analogue peptide San45
9XXT 2.0 Å, Cryo-EM structure of lysophosphatidylserine (18:0)-bound GPR174-Gs complex
6X18 2.1 Å, GLP-1 peptide hormone bound to Glucagon-Like peptide-1 (GLP-1) Receptor
6X19 2.1 Å, Non peptide agonist CHU-128, bound to Glucagon-Like peptide-1 (GLP-1) Receptor
9NTU 2.1 Å, Cryo-EM structure of BETP-GLP-1(9-36)-GLP-1R-Gs complex
7RTB 2.14 Å, Peptide-19 bound to the Glucagon-Like Peptide-1 Receptor (GLP-1R)

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