3I5D: P2X purinoceptor

Crystal structure of the ATP-gated P2X4 ion channel in the closed, apo state at 3.5 Angstroms (R3). Determined by X-ray diffraction at 3.46 Å resolution. Released 4 Aug 2009.

Method: X-ray diffraction
Resolution: 3.46 Å
Organism: Danio rerio
Chains: 3
Atoms: 7,297
Mol. weight: 123.65 kDa
Ligands: NAG
Released: 4 Aug 2009

Explore 3I5D in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

3I5D contains 32 α-helices and 56 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, 18 β-strands

Element	Residues	Length	Sheet
α-helix	39-45	7
α-helix	46-50	5
β-strand	58	1	1
α-helix	59-60	2
β-strand	61-62	2	2
α-helix	63	1
β-strand	64-72	9	3
β-strand	75-79	5	4
β-strand	83-87	5	4
β-strand	102-114	13	2
β-strand	115-120	6	5
β-strand	128	1	5
β-strand	147-154	8	5
β-strand	160-168	9	5
α-helix	170-172	3
α-helix	175-177	3
α-helix	183-187	5
β-strand	189-198	10	3
β-strand	203-206	4	3
β-strand	232-234	3	3
α-helix	235-241	7
α-helix	246-252	7
β-strand	254-264	11	2
α-helix	270-272	3
β-strand	275-281	7	2
β-strand	296-304	9	2
β-strand	310-330	21	2
β-strand	333	1	1
α-helix	335-358	24

Chain B: 11 helices, 20 β-strands

Element	Residues	Length	Sheet
α-helix	35-45	11
α-helix	46-50	5
β-strand	58	1	6
α-helix	59-60	2
β-strand	61-62	2	7
α-helix	63	1
β-strand	64-72	9	8
β-strand	75-76	2	9
β-strand	79	1	10
β-strand	83	1	10
β-strand	86-87	2	9
β-strand	102-114	13	7
β-strand	115-120	6	11
β-strand	128	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
β-strand	232-234	3	8
α-helix	235-241	7
α-helix	246-252	7
β-strand	254-264	11	7
α-helix	270-272	3
β-strand	275-281	7	7
β-strand	296-304	9	7
β-strand	310-330	21	7
β-strand	333	1	6
α-helix	335-360	26

Chain C: 10 helices, 18 β-strands

Element	Residues	Length	Sheet
α-helix	35-45	11
α-helix	46-50	5
β-strand	58	1	12
α-helix	59-60	2
β-strand	61-62	2	13
β-strand	64-72	9	14
β-strand	75-79	5	15
β-strand	83-87	5	15
β-strand	102-114	13	13
β-strand	115-120	6	16
β-strand	128	1	16
β-strand	147-153	7	16
β-strand	161-168	8	16
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
β-strand	232-234	3	14
α-helix	235-241	7
α-helix	246-252	7
β-strand	254-264	11	13
α-helix	270-272	3
β-strand	275-281	7	13
β-strand	296-304	9	13
β-strand	310-330	21	13
β-strand	333	1	12
α-helix	335-357	23

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
P2X purinoceptor	A, B, C	protein	356	Danio rerio	F8W463 (AlphaFold model)

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

>3I5D_1 P2X purinoceptor (chains A, B, C)
GSSKKVGTLNRFTQALVIAYVIGYVCVYNKGYQDTDTVLSSVTTKVKGIALTNTSELGER
IWDVADYIIPPQEDGSFFVLTNMIITTNQTQSKCAENPTPASTCTSHRDCKRGFNDARGD
GVRTGRCVSYSASVKTCEVLSWCPLEKIVDPPNPPLLADAENFTVLIKNNIRYPKFNFNK
RNILPNINSSYLTHCVFSRKTDPDCPIFRLGDIVGEAEEDFQIMAVRGGVMGVQIRWDCD
LDMPQSWCVPRYTFRRLDNKDPDNNVAPGYNFRFAKYYKNSDGTETRTLIKGYGIRFDVM
VFGQAGKFNIIPTLLNIGAGLALLGLVNVICDWIVLTFMKRKQHYKEQKYTYVDDF

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	10

Primary citation

Crystal structure of the ATP-gated P2X(4) ion channel in the closed state. Kawate, T., Michel, J.C., Birdsong, W.T. et al. Nature (2009) 460:592-598. DOI 10.1038/nature08198 · 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
8JV6 3.43 Å, Cryo-EM structure of the zebrafish P2X4 receptor in complex with BAY-1797

Browse structure collections

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