SMTL ID : 9c48.1

Cryo-EM structure of the full-length human P2X4 receptor in the ATP-bound desensitized state

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-trimer

Ligands

6 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-NAG.1: 4 residues within 4Å: Chain A: K.180, A.181, E.183, N.184 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 1 residues within 4Å: Chain A: N.199 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 4 residues within 4Å: Chain B: K.180, A.181, E.183, N.184 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 1 residues within 4Å: Chain B: N.199 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 4 residues within 4Å: Chain C: K.180, A.181, E.183, N.184 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 1 residues within 4Å: Chain C: N.199 No protein-ligand interaction detected (PLIP)

3 x NAG- NAG- BMA: beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA.3: 7 residues within 4Å: Chain A: L.206, N.208, K.222, T.223, P.225, F.226, L.271 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:F.226 Hydrogen bonds: A:T.223, A:K.222 NAG-NAG-BMA.6: 7 residues within 4Å: Chain B: L.206, N.208, K.222, T.223, P.225, F.226, L.271 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:F.226 Hydrogen bonds: B:T.223, B:K.222 NAG-NAG-BMA.9: 7 residues within 4Å: Chain C: L.206, N.208, K.222, T.223, P.225, F.226, L.271 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:F.226 Hydrogen bonds: C:T.223, C:K.222

3 x ATP: ADENOSINE-5'-TRIPHOSPHATE(Non-covalent)

ATP.10: 16 residues within 4Å: Chain A: K.67, V.68, K.69, T.186, L.187, L.188, K.215, I.229 Chain B: T.139, H.140, D.170, S.289, N.293, R.295, K.313 Ligands: MG.15 15 PLIP interactions: 4 interactions with chain B, 11 interactions with chain A Hydrogen bonds: B:N.293, A:K.69, A:T.186, A:L.188, A:K.215 Salt bridges: B:R.295, B:K.313, B:K.313, A:K.67, A:K.67, A:K.67, A:K.69 Water bridges: A:K.190, A:K.215 pi-Cation interactions: A:K.69 ATP.16: 16 residues within 4Å: Chain B: K.67, V.68, K.69, T.186, L.187, L.188, K.215, I.229 Chain C: T.139, H.140, D.170, S.289, N.293, R.295, K.313 Ligands: MG.20 15 PLIP interactions: 11 interactions with chain B, 4 interactions with chain C Hydrogen bonds: B:K.69, B:T.186, B:L.188, B:K.215, C:N.293 Water bridges: B:K.190, B:K.215 Salt bridges: B:K.67, B:K.67, B:K.67, B:K.69, C:R.295, C:K.313, C:K.313 pi-Cation interactions: B:K.69 ATP.21: 16 residues within 4Å: Chain A: T.139, H.140, D.170, S.289, N.293, R.295, K.313 Chain C: K.67, V.68, K.69, T.186, L.187, L.188, K.215, I.229 Ligands: MG.14 15 PLIP interactions: 4 interactions with chain A, 11 interactions with chain C Hydrogen bonds: A:N.293, C:K.69, C:T.186, C:L.188, C:K.215 Salt bridges: A:R.295, A:K.313, A:K.313, C:K.67, C:K.67, C:K.67, C:K.69 Water bridges: C:K.190, C:K.215 pi-Cation interactions: C:K.69

9 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG.11: 2 residues within 4Å: Chain A: N.75, F.81 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:F.81 NAG.12: 4 residues within 4Å: Chain A: N.110, Q.308 Chain B: R.301, G.305 No protein-ligand interaction detected (PLIP) NAG.13: 5 residues within 4Å: Chain A: P.120, F.152, N.153, S.155, V.156 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.155 NAG.17: 2 residues within 4Å: Chain B: N.75, F.81 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:F.81 NAG.18: 4 residues within 4Å: Chain B: N.110, Q.308 Chain C: R.301, G.305 No protein-ligand interaction detected (PLIP) NAG.19: 5 residues within 4Å: Chain B: P.120, F.152, N.153, S.155, V.156 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:S.155 NAG.22: 2 residues within 4Å: Chain C: N.75, F.81 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:F.81 NAG.23: 4 residues within 4Å: Chain A: R.301, G.305 Chain C: N.110, Q.308 No protein-ligand interaction detected (PLIP) NAG.24: 5 residues within 4Å: Chain C: P.120, F.152, N.153, S.155, V.156 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:S.155

3 x MG: MAGNESIUM ION(Non-covalent)

MG.14: 3 residues within 4Å: Chain A: D.170, K.313 Ligands: ATP.21 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:D.170 MG.15: 3 residues within 4Å: Chain B: D.170, K.313 Ligands: ATP.10 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:D.170 MG.20: 3 residues within 4Å: Chain C: D.170, K.313 Ligands: ATP.16 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:D.170

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Shi, H. et al., Human P2X4 receptor gating is modulated by a stable cytoplasmic cap and a unique allosteric pocket. Sci Adv (2025)

Release Date

2025-01-29

Peptides

P2X purinoceptor 4: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

Membrane

We predict this structure to be a membrane protein.
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P2X purinoceptor 4

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