SMTL ID : 9bqh.1

Cryo-EM structure of the full-length human P2X4 receptor in the apo closed 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: 3 residues within 4Å: Chain A: N.75, F.81 Chain B: L.115 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 4 residues within 4Å: Chain A: K.180, A.181, E.183, N.184 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 3 residues within 4Å: Chain B: N.75, F.81 Chain C: L.115 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 4 residues within 4Å: Chain B: K.180, A.181, E.183, N.184 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 3 residues within 4Å: Chain A: L.115 Chain C: N.75, F.81 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 4 residues within 4Å: Chain C: K.180, A.181, E.183, N.184 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: 9 residues within 4Å: Chain A: L.206, N.208, I.209, K.222, T.223, P.225, F.226, L.271, R.273 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:L.271 Hydrogen bonds: A:T.223 NAG-NAG-BMA.6: 9 residues within 4Å: Chain B: L.206, N.208, I.209, K.222, T.223, P.225, F.226, L.271, R.273 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:L.271 Hydrogen bonds: B:T.223 NAG-NAG-BMA.9: 9 residues within 4Å: Chain C: L.206, N.208, I.209, K.222, T.223, P.225, F.226, L.271, R.273 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:L.271 Hydrogen bonds: C:T.223

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

NAG.10: 5 residues within 4Å: Chain A: N.110, T.112, Q.308 Chain B: R.301, G.305 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.110 NAG.11: 5 residues within 4Å: Chain A: P.120, F.152, N.153, S.155, V.156 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.153, A:S.155 NAG.12: 1 residues within 4Å: Chain A: N.199 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.199 NAG.17: 5 residues within 4Å: Chain B: N.110, T.112, Q.308 Chain C: R.301, G.305 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.110 NAG.18: 5 residues within 4Å: Chain B: P.120, F.152, N.153, S.155, V.156 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.153, B:S.155 NAG.19: 1 residues within 4Å: Chain B: N.199 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.199 NAG.22: 5 residues within 4Å: Chain A: R.301, G.305 Chain C: N.110, T.112, Q.308 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:N.110 NAG.23: 5 residues within 4Å: Chain C: P.120, F.152, N.153, S.155, V.156 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:N.153, C:S.155 NAG.24: 1 residues within 4Å: Chain C: N.199 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:N.199

6 x LMT: DODECYL-BETA-D-MALTOSIDE(Non-covalent)

LMT.13: 17 residues within 4Å: Chain A: G.347, T.350, V.351, D.354 Chain B: F.11, L.12, D.16 Chain C: P.18, I.20, R.33, A.34, Q.36, L.37, L.40, L.343, L.346 Ligands: LMT.16 9 PLIP interactions: 3 interactions with chain B, 3 interactions with chain C, 3 interactions with chain A Hydrophobic interactions: B:F.11, B:L.12, C:Q.36, C:L.37 Hydrogen bonds: B:D.16, C:Q.36, A:T.350, A:T.350, A:T.350 LMT.14: 17 residues within 4Å: Chain A: P.18, I.20, R.33, A.34, Q.36, L.37, L.40, L.343, L.346 Chain B: G.347, T.350, V.351, D.354 Chain C: F.11, L.12, D.16 Ligands: LMT.21 9 PLIP interactions: 3 interactions with chain C, 3 interactions with chain A, 3 interactions with chain B Hydrophobic interactions: C:F.11, C:L.12, A:Q.36, A:L.37 Hydrogen bonds: C:D.16, A:Q.36, B:T.350, B:T.350, B:T.350 LMT.15: 22 residues within 4Å: Chain A: A.10, F.11, E.14, Y.15, D.16 Chain B: L.22, R.33, L.40, V.43, F.48, N.338, I.339, G.342, L.343, L.346 Chain C: V.351, L.358, Y.359, R.368, Y.372, Y.374 Ligands: LMT.20 16 PLIP interactions: 6 interactions with chain B, 3 interactions with chain A, 7 interactions with chain C Hydrophobic interactions: B:V.43, B:I.339, B:L.343, B:L.343 Hydrogen bonds: B:R.33, B:R.33, A:E.14, A:E.14, A:D.16, C:Y.359, C:Y.359, C:R.368, C:Y.372, C:Y.372, C:Y.374, C:Y.374 LMT.16: 22 residues within 4Å: Chain A: V.351, L.358, Y.359, R.368, Y.372, Y.374 Chain B: A.10, F.11, E.14, Y.15, D.16 Chain C: L.22, R.33, L.40, V.43, F.48, N.338, I.339, G.342, L.343, L.346 Ligands: LMT.13 16 PLIP interactions: 7 interactions with chain A, 3 interactions with chain B, 6 interactions with chain C Hydrogen bonds: A:Y.359, A:Y.359, A:R.368, A:Y.372, A:Y.372, A:Y.374, A:Y.374, B:E.14, B:E.14, B:D.16, C:R.33, C:R.33 Hydrophobic interactions: C:V.43, C:I.339, C:L.343, C:L.343 LMT.20: 17 residues within 4Å: Chain A: F.11, L.12, D.16 Chain B: P.18, I.20, R.33, A.34, Q.36, L.37, L.40, L.343, L.346 Chain C: G.347, T.350, V.351, D.354 Ligands: LMT.15 9 PLIP interactions: 3 interactions with chain A, 3 interactions with chain C, 3 interactions with chain B Hydrophobic interactions: A:F.11, A:L.12, B:Q.36, B:L.37 Hydrogen bonds: A:D.16, C:T.350, C:T.350, C:T.350, B:Q.36 LMT.21: 22 residues within 4Å: Chain A: L.22, R.33, L.40, V.43, F.48, N.338, I.339, G.342, L.343, L.346 Chain B: V.351, L.358, Y.359, R.368, Y.372, Y.374 Chain C: A.10, F.11, E.14, Y.15, D.16 Ligands: LMT.14 16 PLIP interactions: 7 interactions with chain B, 6 interactions with chain A, 3 interactions with chain C Hydrogen bonds: B:Y.359, B:Y.359, B:R.368, B:Y.372, B:Y.372, B:Y.374, B:Y.374, A:R.33, A:R.33, C:E.14, C:E.14, C:D.16 Hydrophobic interactions: A:V.43, A:I.339, A:L.343, A:L.343

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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