SMTL ID : 7vh6.1

Cryo-EM structure of the hexameric plasma membrane H+-ATPase in the active state (pH 6.0, BeF3-, conformation 1, C1 symmetry)

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

homo-hexamer

Ligands

6 x BEF: BERYLLIUM TRIFLUORIDE ION(Non-covalent)

BEF.1: 10 residues within 4Å: Chain A: S.228, A.229, G.232, D.378, T.380, G.381, D.634, G.635, N.637, D.638 No protein-ligand interaction detected (PLIP) BEF.13: 10 residues within 4Å: Chain B: S.228, A.229, G.232, D.378, T.380, G.381, D.634, G.635, N.637, D.638 No protein-ligand interaction detected (PLIP) BEF.23: 10 residues within 4Å: Chain C: S.228, A.229, G.232, D.378, T.380, G.381, D.634, G.635, N.637, D.638 No protein-ligand interaction detected (PLIP) BEF.33: 10 residues within 4Å: Chain D: S.228, A.229, G.232, D.378, T.380, G.381, D.634, G.635, N.637, D.638 No protein-ligand interaction detected (PLIP) BEF.44: 9 residues within 4Å: Chain E: S.228, A.229, D.378, T.380, G.381, D.634, G.635, N.637, D.638 No protein-ligand interaction detected (PLIP) BEF.54: 10 residues within 4Å: Chain F: S.228, A.229, G.232, D.378, T.380, G.381, D.634, G.635, N.637, D.638 No protein-ligand interaction detected (PLIP)

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

POV.2: 16 residues within 4Å: Chain A: L.306, L.307, T.310, A.311, Y.314, R.315 Chain B: I.768, G.769, I.772, L.779, K.781, I.865 Ligands: POV.3, POV.7, POV.17, POV.18 Ligand excluded by PLIP POV.3: 11 residues within 4Å: Chain A: T.304, L.307, R.315, L.708, I.712, L.713 Ligands: POV.2, POV.4, POV.5, POV.6, POV.7 Ligand excluded by PLIP POV.4: 11 residues within 4Å: Chain A: I.704, L.708, I.712, I.768, W.771, T.775, F.778 Ligands: POV.3, POV.5, POV.7, POV.10 Ligand excluded by PLIP POV.5: 7 residues within 4Å: Ligands: POV.3, POV.4, POV.6, POV.7, POV.10, POV.11, POV.59 Ligand excluded by PLIP POV.6: 6 residues within 4Å: Ligands: POV.3, POV.5, POV.7, POV.8, POV.11, POV.14 Ligand excluded by PLIP POV.7: 7 residues within 4Å: Ligands: POV.2, POV.3, POV.4, POV.5, POV.6, POV.14, POV.18 Ligand excluded by PLIP POV.8: 5 residues within 4Å: Ligands: POV.6, POV.9, POV.11, POV.14, POV.62 Ligand excluded by PLIP POV.9: 7 residues within 4Å: Ligands: POV.8, POV.12, POV.14, POV.21, POV.22, POV.61, POV.62 Ligand excluded by PLIP POV.10: 14 residues within 4Å: Chain A: I.768, G.769, I.772, L.779, K.781, I.865 Chain F: L.307, T.310, Y.314, R.315 Ligands: POV.4, POV.5, POV.55, POV.59 Ligand excluded by PLIP POV.11: 7 residues within 4Å: Ligands: POV.5, POV.6, POV.8, POV.58, POV.59, POV.60, POV.62 Ligand excluded by PLIP POV.12: 5 residues within 4Å: Ligands: POV.9, POV.22, POV.31, POV.41, POV.61 Ligand excluded by PLIP POV.14: 7 residues within 4Å: Ligands: POV.6, POV.7, POV.8, POV.9, POV.18, POV.19, POV.21 Ligand excluded by PLIP POV.15: 17 residues within 4Å: Chain B: L.306, L.307, T.310, A.311, Y.314, R.315 Chain C: I.768, G.769, I.772, L.779, K.781, W.861, I.865 Ligands: POV.16, POV.20, POV.26, POV.27 Ligand excluded by PLIP POV.16: 11 residues within 4Å: Chain B: T.304, L.307, R.315, L.708, I.712, L.713 Ligands: POV.15, POV.17, POV.18, POV.19, POV.20 Ligand excluded by PLIP POV.17: 12 residues within 4Å: Chain B: I.704, L.708, I.712, I.768, W.771, T.775, F.778, P.780 Ligands: POV.2, POV.16, POV.18, POV.20 Ligand excluded by PLIP POV.18: 7 residues within 4Å: Ligands: POV.2, POV.7, POV.14, POV.16, POV.17, POV.19, POV.20 Ligand excluded by PLIP POV.19: 6 residues within 4Å: Ligands: POV.14, POV.16, POV.18, POV.20, POV.21, POV.32 Ligand excluded by PLIP POV.20: 7 residues within 4Å: Ligands: POV.15, POV.16, POV.17, POV.18, POV.19, POV.27, POV.32 Ligand excluded by PLIP POV.21: 5 residues within 4Å: Ligands: POV.9, POV.14, POV.19, POV.22, POV.32 Ligand excluded by PLIP POV.22: 6 residues within 4Å: Ligands: POV.9, POV.12, POV.21, POV.30, POV.31, POV.32 Ligand excluded by PLIP POV.24: 15 residues within 4Å: Chain C: L.307, T.310, A.311, Y.314, R.315 Chain D: I.768, I.772, L.779, I.865, V.868, F.872 Ligands: POV.25, POV.29, POV.36, POV.37 Ligand excluded by PLIP POV.25: 13 residues within 4Å: Chain C: T.304, L.307, R.315, I.704, L.708, I.712, L.713, D.714 Ligands: POV.24, POV.26, POV.27, POV.28, POV.29 Ligand excluded by PLIP POV.26: 14 residues within 4Å: Chain B: Y.314 Chain C: I.704, L.708, I.764, I.768, W.771, T.775, M.777, F.778, L.779 Ligands: POV.15, POV.25, POV.27, POV.29 Ligand excluded by PLIP POV.27: 7 residues within 4Å: Ligands: POV.15, POV.20, POV.25, POV.26, POV.28, POV.29, POV.32 Ligand excluded by PLIP POV.28: 6 residues within 4Å: Ligands: POV.25, POV.27, POV.29, POV.30, POV.32, POV.43 Ligand excluded by PLIP POV.29: 7 residues within 4Å: Ligands: POV.24, POV.25, POV.26, POV.27, POV.28, POV.37, POV.43 Ligand excluded by PLIP POV.30: 5 residues within 4Å: Ligands: POV.22, POV.28, POV.31, POV.32, POV.43 Ligand excluded by PLIP POV.31: 7 residues within 4Å: Ligands: POV.12, POV.22, POV.30, POV.40, POV.41, POV.42, POV.43 Ligand excluded by PLIP POV.32: 7 residues within 4Å: Ligands: POV.19, POV.20, POV.21, POV.22, POV.27, POV.28, POV.30 Ligand excluded by PLIP POV.34: 15 residues within 4Å: Chain D: L.307, T.310, A.311, Y.314, R.315 Chain E: I.768, I.772, L.779, K.781, I.865, V.868 Ligands: POV.35, POV.39, POV.47, POV.48 Ligand excluded by PLIP POV.35: 14 residues within 4Å: Chain D: L.300, T.304, L.307, R.315, I.704, L.708, I.712, L.713, D.714 Ligands: POV.34, POV.36, POV.37, POV.38, POV.39 Ligand excluded by PLIP POV.36: 11 residues within 4Å: Chain D: I.704, L.708, I.764, I.768, W.771, T.775, F.778 Ligands: POV.24, POV.35, POV.37, POV.39 Ligand excluded by PLIP POV.37: 7 residues within 4Å: Ligands: POV.24, POV.29, POV.35, POV.36, POV.38, POV.39, POV.43 Ligand excluded by PLIP POV.38: 6 residues within 4Å: Ligands: POV.35, POV.37, POV.39, POV.40, POV.43, POV.53 Ligand excluded by PLIP POV.39: 7 residues within 4Å: Ligands: POV.34, POV.35, POV.36, POV.37, POV.38, POV.48, POV.53 Ligand excluded by PLIP POV.40: 5 residues within 4Å: Ligands: POV.31, POV.38, POV.42, POV.43, POV.53 Ligand excluded by PLIP POV.41: 5 residues within 4Å: Ligands: POV.12, POV.31, POV.42, POV.52, POV.61 Ligand excluded by PLIP POV.42: 6 residues within 4Å: Ligands: POV.31, POV.40, POV.41, POV.51, POV.52, POV.53 Ligand excluded by PLIP POV.43: 7 residues within 4Å: Ligands: POV.28, POV.29, POV.30, POV.31, POV.37, POV.38, POV.40 Ligand excluded by PLIP POV.45: 15 residues within 4Å: Chain E: L.307, T.310, A.311, Y.314, R.315 Chain F: I.768, G.769, I.772, L.779, K.781, I.865 Ligands: POV.46, POV.50, POV.56, POV.57 Ligand excluded by PLIP POV.46: 11 residues within 4Å: Chain E: T.304, L.307, R.315, L.708, I.712, L.713 Ligands: POV.45, POV.47, POV.48, POV.49, POV.50 Ligand excluded by PLIP POV.47: 11 residues within 4Å: Chain E: I.704, L.708, I.768, W.771, T.775, F.778, P.780 Ligands: POV.34, POV.46, POV.48, POV.50 Ligand excluded by PLIP POV.48: 7 residues within 4Å: Ligands: POV.34, POV.39, POV.46, POV.47, POV.49, POV.50, POV.53 Ligand excluded by PLIP POV.49: 6 residues within 4Å: Ligands: POV.46, POV.48, POV.50, POV.51, POV.53, POV.63 Ligand excluded by PLIP POV.50: 7 residues within 4Å: Ligands: POV.45, POV.46, POV.47, POV.48, POV.49, POV.57, POV.63 Ligand excluded by PLIP POV.51: 5 residues within 4Å: Ligands: POV.42, POV.49, POV.52, POV.53, POV.63 Ligand excluded by PLIP POV.52: 7 residues within 4Å: Ligands: POV.41, POV.42, POV.51, POV.60, POV.61, POV.62, POV.63 Ligand excluded by PLIP POV.53: 7 residues within 4Å: Ligands: POV.38, POV.39, POV.40, POV.42, POV.48, POV.49, POV.51 Ligand excluded by PLIP POV.55: 11 residues within 4Å: Chain F: L.307, R.315, I.704, L.708, I.712, L.713 Ligands: POV.10, POV.56, POV.57, POV.58, POV.59 Ligand excluded by PLIP POV.56: 11 residues within 4Å: Chain F: I.704, L.708, I.712, I.768, W.771, T.775, F.778 Ligands: POV.45, POV.55, POV.57, POV.59 Ligand excluded by PLIP POV.57: 7 residues within 4Å: Ligands: POV.45, POV.50, POV.55, POV.56, POV.58, POV.59, POV.63 Ligand excluded by PLIP POV.58: 6 residues within 4Å: Ligands: POV.11, POV.55, POV.57, POV.59, POV.60, POV.63 Ligand excluded by PLIP POV.59: 7 residues within 4Å: Ligands: POV.5, POV.10, POV.11, POV.55, POV.56, POV.57, POV.58 Ligand excluded by PLIP POV.60: 5 residues within 4Å: Ligands: POV.11, POV.52, POV.58, POV.62, POV.63 Ligand excluded by PLIP POV.61: 5 residues within 4Å: Ligands: POV.9, POV.12, POV.41, POV.52, POV.62 Ligand excluded by PLIP POV.62: 6 residues within 4Å: Ligands: POV.8, POV.9, POV.11, POV.52, POV.60, POV.61 Ligand excluded by PLIP POV.63: 7 residues within 4Å: Ligands: POV.49, POV.50, POV.51, POV.52, POV.57, POV.58, POV.60 Ligand excluded by 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.
Show / Hide

Plasma membrane ATPase 1

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