SMTL ID : 7vh5.1

Cryo-EM structure of the hexameric plasma membrane H+-ATPase in the autoinhibited state (pH 7.4, C1 symmetry)

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

homo-hexamer

Ligands

51 x POV: (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate(Covalent)(Non-covalent)(Non-functional Binders)

POV.1: 12 residues within 4Å: Chain A: T.304, L.307, R.315, L.708, A.711, I.712, L.713, D.714 Ligands: POV.2, POV.3, POV.4, POV.5 Ligand excluded by PLIP POV.2: 11 residues within 4Å: Chain A: I.704, L.708, I.712, I.768, W.771, T.775, F.778, L.779 Ligands: POV.1, POV.3, POV.5 Ligand excluded by PLIP POV.3: 7 residues within 4Å: Chain A: P.780 Ligands: POV.1, POV.2, POV.4, POV.5, POV.8, POV.47 Ligand excluded by PLIP POV.4: 6 residues within 4Å: Ligands: POV.1, POV.3, POV.5, POV.6, POV.8, POV.16 Ligand excluded by PLIP POV.5: 6 residues within 4Å: Ligands: POV.1, POV.2, POV.3, POV.4, POV.11, POV.16 Ligand excluded by PLIP POV.6: 5 residues within 4Å: Ligands: POV.4, POV.7, POV.8, POV.16, POV.49 Ligand excluded by PLIP POV.7: 6 residues within 4Å: Ligands: POV.6, POV.14, POV.15, POV.16, POV.49, POV.51 Ligand excluded by PLIP POV.8: 7 residues within 4Å: Ligands: POV.3, POV.4, POV.6, POV.46, POV.47, POV.48, POV.49 Ligand excluded by PLIP POV.9: 12 residues within 4Å: Chain B: T.304, L.307, R.315, L.708, A.711, I.712, L.713, D.714 Ligands: POV.10, POV.11, POV.12, POV.13 Ligand excluded by PLIP POV.10: 11 residues within 4Å: Chain B: I.704, L.708, I.712, I.768, W.771, T.775, F.778, L.779 Ligands: POV.9, POV.11, POV.13 Ligand excluded by PLIP POV.11: 7 residues within 4Å: Chain B: P.780 Ligands: POV.5, POV.9, POV.10, POV.12, POV.13, POV.16 Ligand excluded by PLIP POV.12: 6 residues within 4Å: Ligands: POV.9, POV.11, POV.13, POV.14, POV.16, POV.24 Ligand excluded by PLIP POV.13: 6 residues within 4Å: Ligands: POV.9, POV.10, POV.11, POV.12, POV.19, POV.24 Ligand excluded by PLIP POV.14: 5 residues within 4Å: Ligands: POV.7, POV.12, POV.15, POV.16, POV.24 Ligand excluded by PLIP POV.15: 7 residues within 4Å: Ligands: POV.7, POV.14, POV.22, POV.23, POV.24, POV.25, POV.51 Ligand excluded by PLIP POV.16: 7 residues within 4Å: Ligands: POV.4, POV.5, POV.6, POV.7, POV.11, POV.12, POV.14 Ligand excluded by PLIP POV.17: 12 residues within 4Å: Chain C: T.304, L.307, R.315, L.708, A.711, I.712, L.713, D.714 Ligands: POV.18, POV.19, POV.20, POV.21 Ligand excluded by PLIP POV.18: 11 residues within 4Å: Chain C: I.704, L.708, I.712, I.768, W.771, T.775, F.778, L.779 Ligands: POV.17, POV.19, POV.21 Ligand excluded by PLIP POV.19: 7 residues within 4Å: Chain C: P.780 Ligands: POV.13, POV.17, POV.18, POV.20, POV.21, POV.24 Ligand excluded by PLIP POV.20: 6 residues within 4Å: Ligands: POV.17, POV.19, POV.21, POV.22, POV.24, POV.33 Ligand excluded by PLIP POV.21: 6 residues within 4Å: Ligands: POV.17, POV.18, POV.19, POV.20, POV.28, POV.33 Ligand excluded by PLIP POV.22: 5 residues within 4Å: Ligands: POV.15, POV.20, POV.23, POV.24, POV.33 Ligand excluded by PLIP POV.23: 6 residues within 4Å: Ligands: POV.15, POV.22, POV.25, POV.31, POV.32, POV.33 Ligand excluded by PLIP POV.24: 7 residues within 4Å: Ligands: POV.12, POV.13, POV.14, POV.15, POV.19, POV.20, POV.22 Ligand excluded by PLIP POV.25: 6 residues within 4Å: Ligands: POV.15, POV.23, POV.32, POV.42, POV.51, SPH.52 Ligand excluded by PLIP POV.26: 12 residues within 4Å: Chain D: T.304, L.307, R.315, L.708, A.711, I.712, L.713, D.714 Ligands: POV.27, POV.28, POV.29, POV.30 Ligand excluded by PLIP POV.27: 12 residues within 4Å: Chain C: Y.314 Chain D: I.704, L.708, I.712, I.768, W.771, T.775, F.778, L.779 Ligands: POV.26, POV.28, POV.30 Ligand excluded by PLIP POV.28: 7 residues within 4Å: Chain D: P.780 Ligands: POV.21, POV.26, POV.27, POV.29, POV.30, POV.33 Ligand excluded by PLIP POV.29: 6 residues within 4Å: Ligands: POV.26, POV.28, POV.30, POV.31, POV.33, POV.41 Ligand excluded by PLIP POV.30: 6 residues within 4Å: Ligands: POV.26, POV.27, POV.28, POV.29, POV.36, POV.41 Ligand excluded by PLIP POV.31: 5 residues within 4Å: Ligands: POV.23, POV.29, POV.32, POV.33, POV.41 Ligand excluded by PLIP POV.32: 7 residues within 4Å: Ligands: POV.23, POV.25, POV.31, POV.39, POV.40, POV.41, POV.42 Ligand excluded by PLIP POV.33: 7 residues within 4Å: Ligands: POV.20, POV.21, POV.22, POV.23, POV.28, POV.29, POV.31 Ligand excluded by PLIP POV.34: 12 residues within 4Å: Chain E: T.304, L.307, R.315, L.708, A.711, I.712, L.713, D.714 Ligands: POV.35, POV.36, POV.37, POV.38 Ligand excluded by PLIP POV.35: 11 residues within 4Å: Chain E: I.704, L.708, I.712, I.768, W.771, T.775, F.778, L.779 Ligands: POV.34, POV.36, POV.38 Ligand excluded by PLIP POV.36: 7 residues within 4Å: Chain E: P.780 Ligands: POV.30, POV.34, POV.35, POV.37, POV.38, POV.41 Ligand excluded by PLIP POV.37: 6 residues within 4Å: Ligands: POV.34, POV.36, POV.38, POV.39, POV.41, POV.50 Ligand excluded by PLIP POV.38: 6 residues within 4Å: Ligands: POV.34, POV.35, POV.36, POV.37, POV.45, POV.50 Ligand excluded by PLIP POV.39: 5 residues within 4Å: Ligands: POV.32, POV.37, POV.40, POV.41, POV.50 Ligand excluded by PLIP POV.40: 6 residues within 4Å: Ligands: POV.32, POV.39, POV.42, POV.48, POV.49, POV.50 Ligand excluded by PLIP POV.41: 7 residues within 4Å: Ligands: POV.29, POV.30, POV.31, POV.32, POV.36, POV.37, POV.39 Ligand excluded by PLIP POV.42: 6 residues within 4Å: Ligands: POV.25, POV.32, POV.40, POV.49, POV.51, SPH.52 Ligand excluded by PLIP POV.43: 12 residues within 4Å: Chain F: T.304, L.307, R.315, L.708, A.711, I.712, L.713, D.714 Ligands: POV.44, POV.45, POV.46, POV.47 Ligand excluded by PLIP POV.44: 11 residues within 4Å: Chain F: I.704, L.708, I.712, I.768, W.771, T.775, F.778, L.779 Ligands: POV.43, POV.45, POV.47 Ligand excluded by PLIP POV.45: 7 residues within 4Å: Chain F: P.780 Ligands: POV.38, POV.43, POV.44, POV.46, POV.47, POV.50 Ligand excluded by PLIP POV.46: 6 residues within 4Å: Ligands: POV.8, POV.43, POV.45, POV.47, POV.48, POV.50 Ligand excluded by PLIP POV.47: 6 residues within 4Å: Ligands: POV.3, POV.8, POV.43, POV.44, POV.45, POV.46 Ligand excluded by PLIP POV.48: 5 residues within 4Å: Ligands: POV.8, POV.40, POV.46, POV.49, POV.50 Ligand excluded by PLIP POV.49: 7 residues within 4Å: Ligands: POV.6, POV.7, POV.8, POV.40, POV.42, POV.48, POV.51 Ligand excluded by PLIP POV.50: 7 residues within 4Å: Ligands: POV.37, POV.38, POV.39, POV.40, POV.45, POV.46, POV.48 Ligand excluded by PLIP POV.51: 6 residues within 4Å: Ligands: POV.7, POV.15, POV.25, POV.42, POV.49, SPH.52 Ligand excluded by PLIP

1 x SPH: SPHINGOSINE(Non-functional Binders)

SPH.52: 3 residues within 4Å: Ligands: POV.25, POV.42, POV.51 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zhao, P. et al., Structure and activation mechanism of the hexameric plasma membrane H + -ATPase. Nat Commun (2021)

Release Date

2021-11-24

Peptides

Plasma membrane ATPase 1: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

Membrane

We predict this structure to be a membrane protein.
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Plasma membrane ATPase 1

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