9K25: Apo-P2Y purinoceptor 2-miniGq-Nb35 complex

Cryo-EM structure of apo-P2Y purinoceptor 2-miniGq-Nb35 complex. Determined by electron microscopy at 3.31 Å resolution. Released 11 Jun 2025.

Method: Electron microscopy
Resolution: 3.31 Å
Organisms: Homo sapiens, Vicugna pacos
Chains: 5
Atoms: 7,117
Mol. weight: 137.03 kDa
Released: 11 Jun 2025

Explore 9K25 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9K25 contains 25 α-helices and 55 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: 6 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	15-37	23
β-strand	41-47	7	1
β-strand	210-214	5	1
β-strand	217-222	6	1
β-strand	243-249	7	1
α-helix	253-277	15
β-strand	286-292	7	1
α-helix	294-302	9
α-helix	313-315	3
α-helix	333-351	19
β-strand	354	1	2
β-strand	357	1	2
β-strand	359-362	4	1
α-helix	371-390	20

Chain B: 5 helices, 32 β-strands

Element	Residues	Length	Sheet
α-helix	15-24	10
α-helix	30-33	4
α-helix	39-41	3
β-strand	49-51	3	3
β-strand	58-63	6	4
β-strand	70-74	5	4
β-strand	78-81	4	4
β-strand	91-94	4	4
α-helix	95	1
β-strand	104-105	2	5
β-strand	111-113	3	5
β-strand	123-125	3	5
β-strand	137	1	5
β-strand	149-151	3	6
β-strand	157-159	3	6
β-strand	166-168	3	6
β-strand	178-180	3	6
β-strand	187-192	6	7
β-strand	198-203	6	7
β-strand	208-212	5	7
β-strand	220-221	2	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
α-helix	272-273	2
β-strand	275-277	3	9
β-strand	284-288	5	9
β-strand	294	1	10
β-strand	295-298	4	9
β-strand	304	1	9
β-strand	308	1	10
β-strand	315	1	11
β-strand	319-320	2	3
β-strand	327-328	2	3
β-strand	331	1	11
β-strand	336-339	4	3

Chain G: 2 helices, 0 β-strands

Element	Residues	Length	Sheet
α-helix	15-23	9
α-helix	30-43	14

Chain I: 11 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	16-24	9
α-helix	30-60	31
α-helix	67-94	28
α-helix	103-136	34
α-helix	138-143	6
α-helix	150-164	15
α-helix	166-171	6
β-strand	174	1	12
β-strand	183	1	12
α-helix	192-206	15
α-helix	208-226	19
α-helix	240-269	30
α-helix	278-307	30

Chain N: 1 helix, 13 β-strands

Element	Residues	Length	Sheet
β-strand	5-7	3	13
β-strand	11	1	14
β-strand	18-23	6	13
β-strand	34-39	6	15
β-strand	49	1	16
β-strand	51	1	15
β-strand	60	1	16
β-strand	68-73	6	13
β-strand	78-83	6	13
α-helix	88-90	3
β-strand	93-98	6	15
β-strand	118	1	15
β-strand	122-123	2	15
β-strand	125	1	14

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Guanine nucleotide-binding protein G(s) subunit alpha isoforms short	A	protein	243	Homo sapiens	A0A804HIH4 (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

>9K25_1 Guanine nucleotide-binding protein G(s) subunit alpha isoforms short (chains A)
TLSAEDKAAVERSKMIEKQLQKDKQVYRATHRLLLLGADNSGKSTIVKQMRILHGGSGGS
GGTSGIFETKFQVDKVNFHMFDVGGQRDERRKWIQCFNDVTAIIFVVDSSDYNRLQEALN
DFKSIWNNRWLRTISVILFLNKQDLLAEKVLAGKSKIEDYFPEFARYTTPEDATPEPGED
PRVTRAKYFIRDEFLRISTASGDGRHYCYPHFTCAVDTENARRIFNDCKDIILQMNLREY
NLV

Sequence of entity 2 (B), FASTA

>9K25_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

>9K25_3 Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 (chains G)
MASNNTASIAQARKLVEQLKMEANIDRIKVSKAAADLMAYCEAHAKEDPLLTPVPASENP
FREKKFFCAIL

Sequence of entity 4 (I), FASTA

>9K25_4 P2Y purinoceptor 2 (chains I)
MKTIIALSYIFCLVFADYKDDDDAMAADLGPWNDTINGTWDGDELGYRCRFNEDFKYVLL
PVSYGVVCVLGLCLNAVALYIFLCRLKTWNASTTYMFHLAVSDALYAASLPLLVYYYARG
DHWPFSTVLCKLVRFLFYTNLYCSILFLTCISVHRCLGVLRPLRSLRWGRARYARRVAGA
VWVLVLACQAPVLYFVTTSARGGRVTCHDTSAPELFSRFVAYSSVMLGLLFAVPFAVILV
CYVLMARRLLKPAYGTSGGLPRAKRKSVRTIAVVLAVFALCFLPFHVTRTLYYSFRSLDL
SCHTLNAINMAYKVTRPLASANSCLNPVLYFLAGQSLVRFARDAKPPTGPSPATPARRRL
GLRRSDRTDMQRIEDVLGSSEDSRRTESTPAGSENTKDIRLHHHHHHGGSGGLEVLFQGP

Sequence of entity 5 (N), FASTA

>9K25_5 Nanobody 35 (chains N)
QVQLQESGGGLVQPGGSLRLSCAASGFTFSNYKMNWVRQAPGKGLEWVSDISQSGASISY
TGSVKGRFTISRDNAKNTLYLQMNSLKPEDTAVYYCARCPAPFTPFCFDVTSTTYAYRGQ
GTQVTVSSHHHHHH

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 A0A804HIH4 (AlphaFold model), which also has an AlphaFold model), best resolution first:

9BIP 2.8 Å, Human proton sensing receptor GPR4 in complex with miniGs
9GGG 3.25 Å, Cryo-EM structure of Thromboxane A2 receptor-miniGq Protein Complex bound to I-BOP
9JFT 3.27 Å, Cryo-EM structure of GPR65 complexed with miniGs in pH6.5

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