3H9V: P2X purinoceptor

Crystal structure of the ATP-gated P2X4 ion channel in the closed, apo state at 3.1 Angstroms. Determined by X-ray diffraction at 3.1 Å resolution. Released 28 Jul 2009.

Method: X-ray diffraction
Resolution: 3.1 Å
Organism: Danio rerio
Chains: 1
Atoms: 2,501
Mol. weight: 41.46 kDa
Ligands: GD
Released: 28 Jul 2009

Explore 3H9V in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

3H9V contains 12 α-helices and 19 β-strands across 1 chain. 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: 12 helices, 19 β-strands

Element	Residues	Length	Sheet
α-helix	33-43	11
α-helix	44-51	8
β-strand	58	1	1
α-helix	62-63	2
β-strand	64-72	9	2
β-strand	74-79	6	3
β-strand	83-88	6	3
β-strand	102-114	13	4
β-strand	115-120	6	5
α-helix	121-122	2
β-strand	128	1	5
α-helix	141-143	3
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	216-218	3
β-strand	232-234	3	2
α-helix	235-241	7
α-helix	246-250	5
β-strand	254-263	10	4
β-strand	264-265	2	6
β-strand	274-281	8	4
β-strand	296-304	9	4
β-strand	310-327	18	4
β-strand	330-331	2	6
β-strand	333	1	1
α-helix	335-359	25

Molecules and chains

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

Sequence of entity 1 (A), FASTA

>3H9V_1 P2X purinoceptor (chains A)
GSSKKVGTLNRFTQALVIAYVIGYVFVYNKGYQDTDTVLSSVTTKVKGIALTKTSELGER
IWDVADYIIPPQEDGSFFVLTNMIITTNQTQSKCAENPTPASTCTSHRDCKRGFNDARGD
GVRTGRCVSYSASVKTCEVLSWCPLEKIVDPPNPPLLADAERFTVLIKNNIRYPKFNFNK
RNILPNINSSYLTHCVFSRKTDPDCPIFRLGDIVGEAEEDFQIMAVRGGVMGVQIRWDCD
LDMPQSWCVPRYTFRRLDNKDPDNNVAPGYNFRFAKYYKNSDGTETRTLIKGYGIRFDVM
VFGQAGKFNIIPTLLNIGAGLALLGLVNVICDWIVLTFMKRKQHYKEQKYTYVDDF

Ligands and cofactors

ID	Name	Formula	Copies
GD	Gadolinium atom	Gd	2

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…
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
3I5D 3.46 Å, Crystal structure of the ATP-gated P2X4 ion channel in the closed, apo state at 3.5…

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3H9V is part of these collections:

Ion channels

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