SMTL ID : 6wm2.1

Human V-ATPase in state 1 with SidK and ADP

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-3-1-1-1-3-3-3-1-1-1-9-1-1-1-1-1-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: 7 residues within 4Å: Chain I: F.616, L.617, F.618, S.619 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: 8 residues within 4Å: Chain I: L.617, S.619 Chain X: N.78, N.81, T.154, K.155 Ligands: BGC-GAL-NGA-GAL-SIA.1, BGC-GAL-NGA-GAL-SIA.1 3 PLIP interactions: 1 interactions with chain I, 2 interactions with chain X Hydrogen bonds: I:N.614, I:S.619, X:N.81, X:T.154, X:K.155 Hydrophobic interactions: I: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 7: Y.278, F.317, T.319, N.350 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 4 residues within 4Å: Chain 7: S.259, N.261, E.410 Chain 8: Y.293 2 PLIP interactions: 2 interactions with chain 7 Hydrogen bonds: 7:E.410, 7:E.410 NAG-NAG.5: 3 residues within 4Å: Chain 7: F.301, N.303, F.306 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 3 residues within 4Å: Chain 7: N.273, D.284, T.286 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 5 residues within 4Å: Chain 5: N.70 Chain 6: E.87 Chain I: L.494, R.495, N.497 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.8: 20 residues within 4Å: Chain 5: L.63, F.64 Chain I: M.484, E.492, T.493, G.496, N.497, Q.501, L.502, N.503, A.505, S.534, K.593, S.602, E.603, N.604, A.605, P.606 Ligands: NAG.14, WJP.15 1 PLIP interactions: 1 interactions with chain I Hydrogen bonds: I:S.602, I:E.603, I:E.492, I:T.493, I:N.604

4 x CLR: CHOLESTEROL(Non-covalent)

CLR.9: 7 residues within 4Å: Chain I: F.370, Y.448, L.451, L.452, F.456, Y.459 Ligands: PTY.12 7 PLIP interactions: 7 interactions with chain I Hydrophobic interactions: I:F.370, I:F.370, I:Y.448, I:L.451, I:L.452, I:F.456, I:Y.459 CLR.20: 7 residues within 4Å: Chain 7: F.421 Chain 8: Y.303 Chain U: C.18 Ligands: WSS.17, WSS.18, WSS.26, WSS.39 1 PLIP interactions: 1 interactions with chain 7 Hydrophobic interactions: 7:F.421 CLR.28: 5 residues within 4Å: Chain Z: L.104, F.108 Ligands: PTY.29, CLR.40, PTY.41 2 PLIP interactions: 2 interactions with chain Z Hydrophobic interactions: Z:L.104, Z:F.108 CLR.40: 6 residues within 4Å: Chain 8: I.322 Ligands: WSS.21, PTY.22, CLR.28, PTY.29, PTY.41 2 PLIP interactions: 2 interactions with chain 8 Hydrophobic interactions: 8:I.322, 8:I.322

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

PSF.10: 5 residues within 4Å: Chain I: G.373, I.377, T.442, F.799 Chain Y: K.54 2 PLIP interactions: 1 interactions with chain Y, 1 interactions with chain I Hydrophobic interactions: Y:K.54, I:F.799

13 x PTY: PHOSPHATIDYLETHANOLAMINE(Non-covalent)

PTY.11: 7 residues within 4Å: Chain 5: G.35, T.39, T.43 Chain I: E.3, I.546, H.547, F.550 2 PLIP interactions: 2 interactions with chain I Hydrophobic interactions: I:I.546, I:F.550 PTY.12: 8 residues within 4Å: Chain 5: N.33, M.40, L.41, C.44 Chain I: N.368, K.369, F.370 Ligands: CLR.9 6 PLIP interactions: 3 interactions with chain 5, 3 interactions with chain I Hydrophobic interactions: 5:M.40, 5:L.41, I:F.370 Hydrogen bonds: 5:N.33, I:N.368, I:K.369 PTY.22: 3 residues within 4Å: Chain U: L.6, V.13 Ligands: CLR.40 No protein-ligand interaction detected (PLIP) PTY.23: 12 residues within 4Å: Chain 3: M.17, S.20, A.21, L.28 Chain 4: L.7 Chain 7: F.435 Chain U: W.67, L.146, L.149, F.150 Ligands: PTY.34, PTY.37 4 PLIP interactions: 1 interactions with chain U, 1 interactions with chain 7, 2 interactions with chain 3 Hydrophobic interactions: U:F.150, 7:F.435, 3:M.17, 3:A.21 PTY.25: 12 residues within 4Å: Chain 7: M.436, L.437, F.440 Chain W: F.25, L.28, Y.32, A.35, K.36, L.101 Chain X: F.108, A.109 Ligands: WJS.27 4 PLIP interactions: 3 interactions with chain W, 1 interactions with chain X Hydrophobic interactions: W:F.25, W:F.25, W:L.101 Hydrogen bonds: X:F.108 PTY.29: 6 residues within 4Å: Chain Z: F.25, Y.32, A.35 Ligands: CLR.28, PTY.30, CLR.40 2 PLIP interactions: 2 interactions with chain Z Hydrophobic interactions: Z:F.25, Z:F.25 PTY.30: 5 residues within 4Å: Chain 0: Y.32, F.108, I.112 Ligands: PTY.29, PTY.31 1 PLIP interactions: 1 interactions with chain 0 Hydrogen bonds: 0:Y.32 PTY.31: 8 residues within 4Å: Chain 0: M.17, L.28, Y.32, F.108 Chain 1: L.104, F.108 Ligands: PTY.30, PTY.32 3 PLIP interactions: 1 interactions with chain 1, 2 interactions with chain 0 Hydrophobic interactions: 1:L.104 Hydrogen bonds: 0:Y.32, 0:Y.32 PTY.32: 13 residues within 4Å: Chain 1: M.17, V.24, L.28, Y.32, A.35, K.36, F.108 Chain 2: L.101, L.104, F.108, A.109 Ligands: PTY.31, PTY.33 5 PLIP interactions: 3 interactions with chain 2, 2 interactions with chain 1 Hydrophobic interactions: 2:L.101, 2:L.104, 1:L.28, 1:F.108 Hydrogen bonds: 2:F.108 PTY.33: 8 residues within 4Å: Chain 2: A.31, Y.32, A.35, K.36, F.108 Chain 3: F.108 Chain 4: F.3 Ligands: PTY.32 5 PLIP interactions: 2 interactions with chain 2, 3 interactions with chain 3 Hydrophobic interactions: 2:A.35, 2:F.108, 3:F.108, 3:F.108, 3:F.108 PTY.34: 5 residues within 4Å: Chain 4: Y.8 Chain 7: H.445 Chain U: T.2 Ligands: PTY.23, PTY.37 3 PLIP interactions: 2 interactions with chain 7, 1 interactions with chain U Salt bridges: 7:H.445, 7:H.445 Hydrogen bonds: U:T.2 PTY.37: 10 residues within 4Å: Chain 4: L.7 Chain 7: F.435, F.438, I.439, T.441, Y.442, H.445 Chain U: W.67 Ligands: PTY.23, PTY.34 9 PLIP interactions: 8 interactions with chain 7, 1 interactions with chain 4 Hydrophobic interactions: 7:F.435, 7:F.438, 7:F.438, 7:F.438, 7:I.439, 7:T.441, 7:Y.442 Salt bridges: 7:H.445 Hydrogen bonds: 4:L.7 PTY.41: 9 residues within 4Å: Chain 8: V.321, S.325, Y.326, W.329, N.330 Chain Y: F.25, L.97 Ligands: CLR.28, CLR.40 4 PLIP interactions: 2 interactions with chain Y, 2 interactions with chain 8 Hydrophobic interactions: Y:F.25, Y:L.97, 8:V.321 Hydrogen bonds: 8:N.330

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(Covalent)(Non-covalent)

WSS.13: 15 residues within 4Å: Chain 5: H.79, W.80 Chain 6: W.60, I.63, M.67, L.68, F.71, H.75, S.76, V.78 Chain I: L.415, L.418, L.472, N.473, I.474 9 PLIP interactions: 1 interactions with chain 5, 5 interactions with chain 6, 3 interactions with chain I Salt bridges: 5:H.79 Hydrophobic interactions: 6:L.68, 6:F.71, 6:F.71, I:L.415, I:L.418, I:L.472 Hydrogen bonds: 6:S.76, 6:A.77 WSS.17: 15 residues within 4Å: Chain 7: A.419, F.421 Chain 8: Y.299, Y.303, F.307 Chain U: F.15, A.21, V.22, C.25, Y.26, F.29, L.31, R.34 Ligands: WSS.18, CLR.20 7 PLIP interactions: 4 interactions with chain U, 3 interactions with chain 8 Hydrophobic interactions: U:F.15, U:V.22, U:Y.26, U:F.29, 8:F.307 pi-Cation interactions: 8:Y.299, 8:Y.303 WSS.18: 12 residues within 4Å: Chain 0: Y.10, F.14, F.90 Chain 7: Y.414 Chain U: C.25, F.29, D.30, L.31 Chain Z: Y.10 Ligands: WSS.17, CLR.20, WSS.39 6 PLIP interactions: 1 interactions with chain Z, 3 interactions with chain 0, 1 interactions with chain U, 1 interactions with chain 7 Hydrophobic interactions: Z:Y.10, 0:F.14, 0:F.90, U:F.29 Hydrogen bonds: 0:Y.10 pi-Cation interactions: 7:Y.414 WSS.19: 10 residues within 4Å: Chain 7: S.420, F.421, F.422, W.427 Chain U: V.22, Y.26, R.34, F.35, D.36, W.39 6 PLIP interactions: 2 interactions with chain 7, 4 interactions with chain U Hydrogen bonds: 7:F.421, 7:F.422, U:D.36 Salt bridges: U:R.34 pi-Cation interactions: U:W.39, U:W.39 WSS.21: 8 residues within 4Å: Chain 8: I.323, Y.326, N.327 Chain U: T.2, G.3, L.6, G.10 Ligands: CLR.40 6 PLIP interactions: 2 interactions with chain U, 4 interactions with chain 8 Hydrophobic interactions: U:L.6, 8:I.323, 8:I.323, 8:Y.326 Hydrogen bonds: U:G.3, 8:N.327 WSS.24: 14 residues within 4Å: Chain 7: S.423, G.425, I.426, G.429, S.433 Chain 8: F.301, S.304, V.305, N.308, W.312, I.313 Chain V: Y.10 Chain W: Y.10, F.14 5 PLIP interactions: 1 interactions with chain W, 2 interactions with chain 8, 2 interactions with chain 7 Hydrogen bonds: W:Y.10, 7:S.423, 7:G.425 Hydrophobic interactions: 8:W.312, 8:I.313 WSS.26: 13 residues within 4Å: Chain 8: K.298, N.300, Y.303, F.307, V.310 Chain X: E.9, Y.10, F.13 Chain Y: Y.10, L.86, F.90 Ligands: CLR.20, WSS.39 6 PLIP interactions: 4 interactions with chain 8, 1 interactions with chain Y, 1 interactions with chain X Hydrophobic interactions: 8:Y.303, 8:F.307, 8:V.310, Y:F.90, X:F.13 Hydrogen bonds: 8:N.300 WSS.35: 15 residues within 4Å: Chain 2: Y.10 Chain 3: Y.10, F.14, F.90 Chain 7: Y.332, V.334, S.335, W.339, T.362 Chain U: G.32, F.35, D.36, V.37, A.38 Ligands: WSS.36 7 PLIP interactions: 3 interactions with chain 3, 2 interactions with chain U, 1 interactions with chain 7, 1 interactions with chain 2 Hydrophobic interactions: 3:F.14, 3:F.14, 3:F.90, 2:Y.10 Hydrogen bonds: U:V.37, U:A.38 pi-Cation interactions: 7:Y.332 WSS.36: 13 residues within 4Å: Chain 1: Y.10 Chain 2: P.8, Y.10, F.14, L.86, F.90 Chain 7: S.335, R.337 Chain U: A.19, G.23, G.32, F.35 Ligands: WSS.35 6 PLIP interactions: 1 interactions with chain 7, 1 interactions with chain 1, 3 interactions with chain 2, 1 interactions with chain U Salt bridges: 7:R.337, 1:E.9 Hydrophobic interactions: 2:F.14, 2:F.90, U:F.35 Hydrogen bonds: 2:Y.10 WSS.39: 9 residues within 4Å: Chain 8: Y.297, Y.299, Y.303 Chain Y: Y.10, F.14 Chain Z: L.93 Ligands: WSS.18, CLR.20, WSS.26 4 PLIP interactions: 1 interactions with chain Y, 1 interactions with chain Z, 2 interactions with chain 8 Hydrogen bonds: Y:Y.10, 8:Y.297 Hydrophobic interactions: Z:L.93 pi-Cation interactions: 8:Y.297

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

NAG.14: 3 residues within 4Å: Chain I: Y.487, N.488 Ligands: NAG-NAG-BMA-MAN-MAN-MAN-GLC-GLC-GLC-MAN-MAN.8 No protein-ligand interaction detected (PLIP) NAG.38: 3 residues within 4Å: Chain 7: N.357, A.386, R.387 No protein-ligand interaction detected (PLIP)

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.15: 17 residues within 4Å: Chain I: 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 Chain X: V.71 Chain Y: I.147 Ligands: NAG-NAG-BMA-MAN-MAN-MAN-GLC-GLC-GLC-MAN-MAN.8 16 PLIP interactions: 14 interactions with chain I, 1 interactions with chain X, 1 interactions with chain Y Hydrophobic interactions: I:V.541, I:F.583, I:L.609, I:F.612, I:F.616, I:F.616, I:T.735, I:A.736, X:V.71, Y:I.147 Hydrogen bonds: I:L.608, I:L.609 Salt bridges: I:K.538, I:K.538, I:K.593, I:K.593

1 x ADP: ADENOSINE-5'-DIPHOSPHATE(Non-covalent)

ADP.16: 15 residues within 4Å: Chain L: A.251, G.253, C.254, G.255, K.256, T.257, V.258, E.283, F.445, Q.522, N.523, G.524, Y.525 Chain O: R.400, K.403 13 PLIP interactions: 11 interactions with chain L, 2 interactions with chain O Hydrogen bonds: L:A.251, L:G.253, L:C.254, L:G.255, L:K.256, L:T.257, L:V.258, L:Q.522, L:G.524 Salt bridges: L:K.256, O:R.400, O:R.400 pi-Stacking: L:F.445

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.27: 11 residues within 4Å: Chain 8: I.313, A.316, L.317, T.324, N.327 Chain X: Y.32, L.97, L.101, L.104, F.108 Ligands: PTY.25 5 PLIP interactions: 2 interactions with chain X, 3 interactions with chain 8 Hydrophobic interactions: X:L.97, X:L.101, 8:I.313, 8:A.316, 8:L.317

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 subunit E 1: ABC
V-type proton ATPase subunit G 1: DEF
V-type proton ATPase subunit C 1: G
V-type proton ATPase subunit H: H
V-type proton ATPase 116 kDa subunit a isoform 1: I
V-type proton ATPase catalytic subunit A: JKL
V-type proton ATPase subunit B, brain isoform: MNO
SidK: PQR
V-type proton ATPase subunit D: S
V-type proton ATPase subunit F: T
V-type proton ATPase 21 kDa proteolipid subunit: U
V-type proton ATPase 16 kDa proteolipid subunit: VWXYZ0123
V-type proton ATPase subunit d 1: 4
V-type proton ATPase subunit e 1: 5
Ribonuclease kappa: 6
V-type proton ATPase subunit S1: 7
Renin receptor: 8

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
H

B
I

C
J

D
K

E
L

F
M

G
O

H
P

I
R

J
A

K
B

L
C

M
D

N
E

O
F

P
X

Q
Y

R
Z

S
G

T
N

U
0

V
1

W
2

X
3

Y
4

Z
5

0
6

1
7

2
8

3
9

4
Q

5
S

6
T

7
U

8
V

Membrane

We predict this structure to be a membrane protein.
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V-type proton ATPase subunit E 1

V-type proton ATPase subunit G 1

V-type proton ATPase subunit C 1

V-type proton ATPase subunit H

V-type proton ATPase 116 kDa subunit a isoform 1

V-type proton ATPase catalytic subunit A

V-type proton ATPase subunit B, brain isoform

SidK

V-type proton ATPase subunit D

V-type proton ATPase subunit F

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 subunit e 1

Ribonuclease kappa

V-type proton ATPase subunit S1

Renin receptor

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