SMTL ID : 6wlw.1

The Vo region of human V-ATPase in state 1 (focused refinement)

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-9-1-1-1-1-1-1-mer

Ligands

1 x BGC- GAL- NGA- GAL- SIA: beta-D-galactopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-galactopyranose-(1-4)-[N-acetyl-alpha-neuraminic acid-(2-3)]beta-D-galactopyranose-(1-4)-beta-D-glucopyranose

BGC-GAL-NGA-GAL-SIA.1: 8 residues within 4Å: Chain L: F.616, L.617, F.618, S.619, C.637 Ligands: GAL-NGA-GAL-SIA.2, GAL-NGA-GAL-SIA.2, GAL-NGA-GAL-SIA.2 No protein-ligand interaction detected (PLIP)

1 x GAL- NGA- GAL- SIA: beta-D-galactopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-galactopyranose-(1-4)-[N-acetyl-alpha-neuraminic acid-(2-3)]beta-D-galactopyranose

GAL-NGA-GAL-SIA.2: 12 residues within 4Å: Chain D: N.78, S.79, N.81, K.88, S.153, T.154, K.155 Chain L: L.617, S.619 Ligands: BGC-GAL-NGA-GAL-SIA.1, BGC-GAL-NGA-GAL-SIA.1, BGC-GAL-NGA-GAL-SIA.1 3 PLIP interactions: 1 interactions with chain L, 2 interactions with chain D Hydrogen bonds: L:S.619, D:S.79, D:S.79, D:K.88, D:K.88, D:T.154, D:K.155 Hydrophobic interactions: L:L.617

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

NAG-NAG.3: 4 residues within 4Å: Chain L: L.494, R.495, N.497 Chain M: N.70 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 5 residues within 4Å: Chain O: Y.278, F.317, G.318, T.319, N.350 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 6 residues within 4Å: Chain O: S.259, N.261, P.265, Q.293, E.410 Chain P: Y.293 2 PLIP interactions: 2 interactions with chain O Hydrogen bonds: O:E.410, O:E.410 NAG-NAG.7: 3 residues within 4Å: Chain O: F.301, N.303, F.306 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 2 residues within 4Å: Chain O: N.273, D.284 No protein-ligand interaction detected (PLIP)

1 x NAG- NAG- BMA- MAN- MAN- MAN- GLC- GLC- GLC- MAN- MAN: alpha-D-glucopyranose-(1-2)-alpha-D-glucopyranose-(1-3)-alpha-D-glucopyranose-(1-3)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)-alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA-MAN-MAN-MAN-GLC-GLC-GLC-MAN-MAN.4: 20 residues within 4Å: Chain L: M.484, E.492, T.493, G.496, N.497, Q.501, L.502, N.503, A.505, S.534, K.593, A.599, S.602, E.603, N.604, A.605, P.606 Chain M: L.63, F.64 Ligands: WJP.29 1 PLIP interactions: 1 interactions with chain L Hydrogen bonds: L:E.603, L:E.492, L:T.493, L:N.604

10 x WSS: tri(methyl)-[2-[[(2~{R})-2-[(~{Z})-octadec-9-enoyl]oxy-3-[(~{E})-1-oxidanylideneoctadec-9-enoxy]propoxy]-oxidanyl-phosphoryl]oxyethyl]azanium(Non-covalent)(Covalent)

WSS.9: 13 residues within 4Å: Chain A: C.25, F.29, D.30, L.31 Chain F: Y.10, F.14 Chain G: Y.10, F.14, F.90 Chain O: Y.414 Ligands: WSS.31, WSS.36, CLR.37 6 PLIP interactions: 3 interactions with chain G, 2 interactions with chain F, 1 interactions with chain O Hydrophobic interactions: G:F.14, G:F.90, F:Y.10, F:F.14 Hydrogen bonds: G:Y.10 pi-Cation interactions: O:Y.414 WSS.10: 13 residues within 4Å: Chain A: A.19, G.23, T.27, G.32 Chain H: Y.10, F.13 Chain I: P.8, Y.10, L.86, F.90 Chain O: S.335, R.337 Ligands: WSS.32 6 PLIP interactions: 1 interactions with chain O, 2 interactions with chain H, 1 interactions with chain A, 2 interactions with chain I Salt bridges: O:R.337, H:E.9 Hydrophobic interactions: H:F.13, A:T.27, I:F.90 Hydrogen bonds: I:Y.10 WSS.11: 10 residues within 4Å: Chain A: V.22, Y.26, R.34, F.35, D.36, W.39 Chain O: S.420, F.421, F.422, W.427 6 PLIP interactions: 4 interactions with chain A, 2 interactions with chain O Hydrogen bonds: A:D.36, O:F.421, O:F.422 Salt bridges: A:R.34 pi-Cation interactions: A:W.39, A:W.39 WSS.12: 8 residues within 4Å: Chain A: G.3, L.4, L.6 Chain O: L.448 Chain P: I.323, Y.326, N.327 Ligands: CLR.38 6 PLIP interactions: 4 interactions with chain P, 2 interactions with chain A Hydrophobic interactions: P:I.323, P:I.323, P:Y.326, A:L.6 Hydrogen bonds: P:N.327, A:G.3 WSS.15: 16 residues within 4Å: Chain B: Y.10, F.13 Chain C: Y.10, F.13, F.14 Chain O: S.423, G.425, I.426, G.429, S.433 Chain P: F.301, S.304, V.305, N.308, W.312, I.313 7 PLIP interactions: 2 interactions with chain O, 2 interactions with chain C, 2 interactions with chain P, 1 interactions with chain B Hydrogen bonds: O:S.423, O:G.425 Hydrophobic interactions: C:F.13, C:F.14, P:W.312, P:I.313, B:F.13 WSS.17: 15 residues within 4Å: Chain D: E.9, Y.10, F.13 Chain E: Y.10, L.86, F.90 Chain P: K.298, N.300, Y.303, V.306, F.307, V.310, M.314 Ligands: WSS.36, CLR.37 7 PLIP interactions: 1 interactions with chain E, 4 interactions with chain P, 2 interactions with chain D Hydrophobic interactions: E:F.90, P:Y.303, P:F.307, P:V.310, D:F.13, D:F.13 Hydrogen bonds: P:N.300 WSS.28: 15 residues within 4Å: Chain L: L.415, L.418, F.468, S.471, L.472, N.473, I.474 Chain M: H.79, W.80 Chain N: W.60, I.63, L.68, F.71, S.76, V.78 11 PLIP interactions: 7 interactions with chain N, 3 interactions with chain L, 1 interactions with chain M Hydrophobic interactions: N:I.63, N:L.68, N:F.71, N:F.71, N:F.71, L:L.415, L:L.418, L:F.468 Hydrogen bonds: N:S.76, N:A.77 Salt bridges: M:H.79 WSS.31: 16 residues within 4Å: Chain A: F.15, A.21, V.22, C.25, Y.26, F.29, L.31, R.34 Chain O: A.419, F.421, F.422 Chain P: Y.299, Y.303, F.307 Ligands: WSS.9, CLR.37 8 PLIP interactions: 1 interactions with chain O, 4 interactions with chain A, 3 interactions with chain P Hydrophobic interactions: O:F.422, A:F.15, A:V.22, A:V.22, A:Y.26, P:F.307 pi-Cation interactions: P:Y.299, P:Y.303 WSS.32: 17 residues within 4Å: Chain A: G.32, F.35, D.36, V.37, A.38 Chain I: Y.10, F.13, F.14 Chain J: Y.10, F.14, F.90 Chain O: Y.332, V.334, S.335, W.339, T.362 Ligands: WSS.10 10 PLIP interactions: 2 interactions with chain A, 2 interactions with chain J, 5 interactions with chain I, 1 interactions with chain O Hydrogen bonds: A:V.37, A:A.38 Hydrophobic interactions: J:F.14, J:F.90, I:Y.10, I:Y.10, I:Y.10, I:F.13, I:F.14 pi-Cation interactions: O:Y.332 WSS.36: 11 residues within 4Å: Chain E: Y.10, F.13, F.14 Chain F: Y.10, L.93 Chain P: Y.297, Y.299, Y.303 Ligands: WSS.9, WSS.17, CLR.37 5 PLIP interactions: 3 interactions with chain E, 1 interactions with chain P, 1 interactions with chain F Hydrophobic interactions: E:F.13, F:L.93 Hydrogen bonds: E:Y.10 Salt bridges: E:E.9 pi-Cation interactions: P:Y.297

13 x PTY: PHOSPHATIDYLETHANOLAMINE(Non-covalent)

PTY.13: 3 residues within 4Å: Chain A: L.6, V.13 Ligands: CLR.38 No protein-ligand interaction detected (PLIP) PTY.14: 13 residues within 4Å: Chain A: W.67, L.142, L.146, L.149, F.150 Chain J: M.17, S.20, A.21, L.28 Chain K: L.7 Chain O: F.435 Ligands: PTY.33, PTY.34 4 PLIP interactions: 2 interactions with chain J, 1 interactions with chain O, 1 interactions with chain A Hydrophobic interactions: J:M.17, J:A.21, O:F.435, A:F.150 PTY.16: 12 residues within 4Å: Chain C: F.25, L.28, Y.32, A.35, K.36, L.101 Chain D: F.108, A.109 Chain O: M.436, L.437, F.440 Ligands: WJS.18 4 PLIP interactions: 3 interactions with chain C, 1 interactions with chain O Hydrophobic interactions: C:F.25, C:F.25, C:L.101, O:F.440 PTY.20: 6 residues within 4Å: Chain F: F.25, Y.32, A.35 Ligands: CLR.19, PTY.21, CLR.38 2 PLIP interactions: 2 interactions with chain F Hydrophobic interactions: F:F.25, F:F.25 PTY.21: 6 residues within 4Å: Chain F: L.28 Chain G: Y.32, L.101, F.108 Ligands: PTY.20, PTY.22 3 PLIP interactions: 1 interactions with chain F, 2 interactions with chain G Hydrophobic interactions: F:L.28, G:L.101 Hydrogen bonds: G:Y.32 PTY.22: 8 residues within 4Å: Chain G: F.25, L.28, Y.32, F.108 Chain H: L.104, F.108 Ligands: PTY.21, PTY.23 5 PLIP interactions: 1 interactions with chain H, 4 interactions with chain G Hydrophobic interactions: H:L.104, G:F.25, G:L.28 Hydrogen bonds: G:Y.32, G:Y.32 PTY.23: 14 residues within 4Å: Chain H: M.17, V.24, F.25, L.28, Y.32, A.35, K.36, F.108 Chain I: L.101, F.108, A.109, I.112 Ligands: PTY.22, PTY.24 4 PLIP interactions: 3 interactions with chain H, 1 interactions with chain I Hydrophobic interactions: H:F.25, H:L.28, H:F.108, I:L.101 PTY.24: 7 residues within 4Å: Chain I: Y.32, A.35, K.36, F.108 Chain J: F.108 Chain K: F.3 Ligands: PTY.23 6 PLIP interactions: 3 interactions with chain I, 3 interactions with chain J Hydrophobic interactions: I:Y.32, I:A.35, I:F.108, J:F.108, J:F.108, J:F.108 PTY.27: 8 residues within 4Å: Chain L: N.368, K.369, F.370 Chain M: N.33, M.40, L.41, C.44 Ligands: CLR.25 4 PLIP interactions: 3 interactions with chain L, 1 interactions with chain M Hydrophobic interactions: L:F.370 Hydrogen bonds: L:K.369, M:N.33 Salt bridges: L:K.369 PTY.30: 8 residues within 4Å: Chain L: I.546, H.547 Chain M: P.25, G.35, I.38, T.39, V.42, T.43 4 PLIP interactions: 1 interactions with chain L, 3 interactions with chain M Hydrophobic interactions: L:I.546, M:P.25, M:I.38, M:V.42 PTY.33: 6 residues within 4Å: Chain A: T.2 Chain K: Y.8 Chain O: F.438, H.445 Ligands: PTY.14, PTY.34 3 PLIP interactions: 3 interactions with chain O Hydrophobic interactions: O:F.438 Salt bridges: O:H.445, O:H.445 PTY.34: 10 residues within 4Å: Chain A: W.67 Chain K: L.7 Chain O: F.435, F.438, I.439, T.441, Y.442, H.445 Ligands: PTY.14, PTY.33 10 PLIP interactions: 9 interactions with chain O, 1 interactions with chain K Hydrophobic interactions: O:F.435, O:F.438, O:F.438, O:F.438, O:I.439, O:T.441, O:Y.442, O:Y.442 Salt bridges: O:H.445 Hydrogen bonds: K:L.7 PTY.39: 10 residues within 4Å: Chain E: F.25, L.101 Chain P: V.321, I.322, S.325, Y.326, W.329, N.330 Ligands: CLR.19, CLR.38 5 PLIP interactions: 3 interactions with chain P, 2 interactions with chain E Hydrophobic interactions: P:V.321, P:I.322, E:F.25, E:L.101 Hydrogen bonds: P:N.330

1 x WJS: (2~{S})-2-$l^{4}-azanyl-3-[[(2~{R})-3-octadecanoyloxy-2-oxidanyl-propoxy]-oxidanyl-oxidanylidene-$l^{6}-phosphanyl]oxy-propanoic acid(Non-covalent)

WJS.18: 10 residues within 4Å: Chain D: Y.32, L.97, L.101, F.108 Chain P: I.313, A.316, L.317, I.323, N.327 Ligands: PTY.16 7 PLIP interactions: 3 interactions with chain P, 4 interactions with chain D Hydrophobic interactions: P:I.313, P:A.316, P:L.317, D:L.97, D:L.101 Hydrogen bonds: D:Y.32, D:Y.32

4 x CLR: CHOLESTEROL(Non-covalent)

CLR.19: 7 residues within 4Å: Chain E: F.25 Chain F: L.104, F.108 Chain P: W.329 Ligands: PTY.20, CLR.38, PTY.39 4 PLIP interactions: 1 interactions with chain E, 2 interactions with chain F, 1 interactions with chain P Hydrophobic interactions: E:F.25, F:L.104, F:F.108, P:W.329 CLR.25: 9 residues within 4Å: Chain L: F.370, Y.448, L.451, L.452, V.455, F.456, Y.459 Chain M: W.17 Ligands: PTY.27 7 PLIP interactions: 1 interactions with chain M, 6 interactions with chain L Hydrophobic interactions: M:W.17, L:F.370, L:F.370, L:L.451, L:L.452, L:F.456, L:Y.459 CLR.37: 7 residues within 4Å: Chain A: C.18 Chain O: F.421 Chain P: Y.303 Ligands: WSS.9, WSS.17, WSS.31, WSS.36 1 PLIP interactions: 1 interactions with chain O Hydrophobic interactions: O:F.421 CLR.38: 6 residues within 4Å: Chain P: I.322 Ligands: WSS.12, PTY.13, CLR.19, PTY.20, PTY.39 1 PLIP interactions: 1 interactions with chain P Hydrophobic interactions: P:I.322

1 x PSF: 1,2-DICAPROYL-SN-PHOSPHATIDYL-L-SERINE(Non-covalent)

PSF.26: 5 residues within 4Å: Chain E: K.54 Chain L: I.377, T.442, S.445, F.799 4 PLIP interactions: 1 interactions with chain E, 3 interactions with chain L Hydrophobic interactions: E:K.54, L:F.799 Hydrogen bonds: L:S.445, L:S.445

1 x WJP: methyl (3R,6Z,10E,14E)-3,7,11,15,19-pentamethylicosa-6,10,14,18-tetraen-1-yl dihydrogen diphosphate(Non-covalent)

WJP.29: 16 residues within 4Å: Chain E: I.147 Chain L: S.534, M.537, K.538, V.541, F.583, K.593, S.607, L.608, L.609, F.612, F.616, I.732, T.735, A.736 Ligands: NAG-NAG-BMA-MAN-MAN-MAN-GLC-GLC-GLC-MAN-MAN.4 15 PLIP interactions: 13 interactions with chain L, 2 interactions with chain E Hydrophobic interactions: L:V.541, L:F.583, L:L.609, L:F.612, L:F.616, L:T.735, L:A.736, E:I.147, E:I.147 Hydrogen bonds: L:L.608, L:L.609 Salt bridges: L:K.538, L:K.538, L:K.593, L:K.593

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

NAG.35: 3 residues within 4Å: Chain O: N.357, A.386, R.387 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wang, L. et al., Structures of a Complete Human V-ATPase Reveal Mechanisms of Its Assembly. Mol.Cell (2020)

Release Date

2020-11-11

Peptides

V-type proton ATPase 21 kDa proteolipid subunit: A
V-type proton ATPase 16 kDa proteolipid subunit: BCDEFGHIJ
V-type proton ATPase subunit d 1: K
V-type proton ATPase 116 kDa subunit a isoform 1: L
V-type proton ATPase subunit e 1: M
Ribonuclease kappa: N
V-type proton ATPase subunit S1: O
Renin receptor: P

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
0

B
1

C
2

D
3

E
4

F
5

G
6

H
7

I
8

J
9

K
Q

L
R

M
S

N
T

O
U

P
V

Membrane

We predict this structure to be a membrane protein.
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V-type proton ATPase 21 kDa proteolipid subunit

V-type proton ATPase 16 kDa proteolipid subunit

V-type proton ATPase subunit d 1

V-type proton ATPase 116 kDa subunit a isoform 1

V-type proton ATPase subunit e 1

Ribonuclease kappa

V-type proton ATPase subunit S1

Renin receptor

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