8JV6: Zebrafish P2X4 receptor

Cryo-EM structure of the zebrafish P2X4 receptor in complex with BAY-1797. Determined by electron microscopy at 3.43 Å resolution. Released 18 Oct 2023.

Method: Electron microscopy
Resolution: 3.43 Å
Organism: Danio rerio
Chains: 3
Atoms: 7,458
Mol. weight: 122 kDa
Ligands: P6E, NAG
Released: 18 Oct 2023

Explore 8JV6 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8JV6 contains 31 α-helices and 66 β-strands across 3 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: 11 helices, 22 β-strands

Element	Residues	Length	Sheet
α-helix	44-54	11
β-strand	58-61	4	1
β-strand	64-72	9	2
β-strand	75-79	5	3
β-strand	83-87	5	3
β-strand	98	1	4
β-strand	101-114	14	4
β-strand	115-119	5	5
α-helix	125-127	3
β-strand	128	1	5
α-helix	136	1
β-strand	140	1	5
β-strand	147-153	7	5
β-strand	161-168	8	5
α-helix	170-172	3
α-helix	175-177	3
α-helix	183-187	5
β-strand	189-198	10	2
β-strand	203-206	4	2
α-helix	214-218	5
β-strand	223	1	6
β-strand	227	1	6
β-strand	232-234	3	2
α-helix	235-240	6
α-helix	246-249	4
β-strand	254-262	9	4
β-strand	265	1	1
α-helix	270-272	3
β-strand	276-281	6	4
β-strand	296-304	9	4
β-strand	310-328	19	4
β-strand	330-333	4	1
α-helix	335-357	23

Chain B: 10 helices, 22 β-strands

Element	Residues	Length	Sheet
α-helix	44-54	11
β-strand	58-62	5	7
β-strand	64-72	9	8
β-strand	75-79	5	9
β-strand	83-87	5	9
β-strand	98	1	10
β-strand	101-114	14	10
β-strand	115-119	5	11
β-strand	128	1	11
α-helix	136	1
β-strand	140	1	11
β-strand	147-153	7	11
β-strand	161-168	8	11
α-helix	170-172	3
α-helix	175-177	3
α-helix	183-187	5
β-strand	189-198	10	8
β-strand	203-206	4	8
α-helix	214-218	5
β-strand	223	1	12
β-strand	227	1	12
β-strand	232-234	3	8
α-helix	235-240	6
α-helix	246-249	4
β-strand	254-262	9	10
β-strand	265	1	7
α-helix	270-272	3
β-strand	276-281	6	10
β-strand	296-304	9	10
β-strand	310-328	19	10
β-strand	329-333	5	7
α-helix	335-357	23

Chain C: 10 helices, 22 β-strands

Element	Residues	Length	Sheet
α-helix	44-54	11
β-strand	58-61	4	13
β-strand	64-72	9	14
β-strand	75-79	5	15
β-strand	83-87	5	15
β-strand	98	1	16
β-strand	101-114	14	16
β-strand	115-119	5	17
β-strand	128	1	17
α-helix	136	1
β-strand	140	1	17
β-strand	147-153	7	17
β-strand	161-168	8	17
α-helix	170-172	3
α-helix	175-177	3
α-helix	183-187	5
β-strand	189-198	10	14
β-strand	203-206	4	14
α-helix	214-218	5
β-strand	223	1	18
β-strand	227	1	18
β-strand	232-234	3	14
α-helix	235-240	6
α-helix	246-252	7
β-strand	254-262	9	16
β-strand	265	1	13
α-helix	270-272	3
β-strand	276-281	6	16
β-strand	296-304	9	16
β-strand	310-328	19	16
β-strand	330-333	4	13
α-helix	335-357	23

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
P2X purinoceptor	A, B, C	protein	350	Danio rerio	F8W463 (AlphaFold model)

Sequence of entity 1 (A, B, C), FASTA

>8JV6_1 P2X purinoceptor (chains A, B, C)
DSVSQCFFDYYTSKILIIRSKKVGTLNRFTQALVIAYVIGYVCVYNKGYQDTDTVLSSVT
TKVKGIALTNTSELGERIWDVADYIIPPQEDGSFFVLTNMIITTNQTQSKCAENPTPAST
CTSHRDCKRGFNDARGDGVRTGRCVSYSASVKTCEVLSWCPLEKIVDPPNPPLLADAENF
TVLIKNNIRYPKFNFNKRNILPNINSSYLTHCVFSRKTDPDCPIFRLGDIVGEAEEDFQI
MAVRGGVMGVQIRWDCDLDMPQSWCVPRYTFRRLDNKDPDNNVAPGYNFRFAKYYKNSDG
TETRTLIKGYGIRFDVMVFGQAGKFNIIPTLLNIGAGLALLGLVNVICDW

Ligands and cofactors

ID	Name	Formula	Copies
P6E	N-[4-(3-chloranylphenoxy)-3-sulfamoyl-phenyl]-2-phenyl-ethanamide	C20 H17 Cl N2 O4 S	3
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	12

Primary citation

Structural insights into the allosteric inhibition of P2X4 receptors. Shen, C., Zhang, Y., Cui, W. et al. Nat Commun (2023) 14:6437-6437. DOI 10.1038/s41467-023-42164-y · PubMed

Other PDB entries of the same protein (UniProt F8W463 (AlphaFold model), which also has an AlphaFold model), best resolution first:

5WZY 2.8 Å, Crystal structure of the P2X4 receptor from zebrafish in the presence of CTP at 2.8…
4DW1 2.8 Å, Crystal structure of the ATP-gated P2X4 ion channel in the ATP-bound, open state at 2.8…
4DW0 2.9 Å, Crystal structure of the ATP-gated P2X4 ion channel in the closed, apo state at 2.9…
3H9V 3.1 Å, Crystal structure of the ATP-gated P2X4 ion channel in the closed, apo state at 3.1…
8JV5 3.23 Å, Cryo-EM structure of the zebrafish P2X4 receptor in complex with BX430
3I5D 3.46 Å, Crystal structure of the ATP-gated P2X4 ion channel in the closed, apo state at 3.5…

Browse structure collections

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