SMTL ID : 6tt7.1

Ovine ATP synthase 1a state

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-3-1-1-1-1-1-1-1-8-1-1-1-1-1-1-1-mer

Ligands

3 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 4 residues within 4Å: Chain A: T.219, Q.251, D.312 Ligands: ADP.2 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:T.219 MG.3: 4 residues within 4Å: Chain B: T.219, Q.251, D.312 Ligands: ADP.4 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:T.219 MG.5: 2 residues within 4Å: Chain C: T.219 Ligands: ADP.6 No protein-ligand interaction detected (PLIP)

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

ADP.2: 12 residues within 4Å: Chain A: Q.215, T.216, G.217, K.218, T.219, S.220, F.400, R.405, Q.473, G.474, Q.475 Ligands: MG.1 14 PLIP interactions: 1 interactions with chain D, 13 interactions with chain A Salt bridges: D:R.406, A:K.218, A:K.218 Hydrogen bonds: A:Q.215, A:G.217, A:K.218, A:T.219, A:S.220, A:S.220, A:Q.251, A:Q.473, A:Q.475, A:Q.475 pi-Cation interactions: A:R.405 ADP.4: 15 residues within 4Å: Chain B: Q.215, T.216, G.217, K.218, T.219, S.220, F.400, R.405, P.406, Q.473, G.474, Q.475 Chain F: Y.418, R.422 Ligands: MG.3 11 PLIP interactions: 9 interactions with chain B, 2 interactions with chain F Hydrogen bonds: B:Q.215, B:Q.215, B:T.216, B:G.217, B:K.218, B:T.219, B:S.220, B:S.220, B:Q.473, F:M.408, F:R.422 ADP.6: 12 residues within 4Å: Chain C: R.214, Q.215, T.216, G.217, K.218, T.219, S.220, E.371, P.406, Q.475 Chain E: S.405 Ligands: MG.5 10 PLIP interactions: 9 interactions with chain C, 1 interactions with chain E Hydrogen bonds: C:Q.215, C:Q.215, C:T.216, C:G.217, C:T.219, C:S.220, C:E.371, E:S.405 Salt bridges: C:K.218, C:K.218 ADP.7: 15 residues within 4Å: Chain B: V.414, R.416 Chain E: G.207, A.208, G.209, V.210, G.211, K.212, T.213, V.214, Y.395, Q.466, F.468, A.471, F.474 15 PLIP interactions: 12 interactions with chain E, 3 interactions with chain B Hydrogen bonds: E:G.207, E:G.209, E:V.210, E:G.211, E:K.212, E:T.213, E:T.213, E:T.213, E:V.214, E:Q.466, E:F.468, B:S.415 Salt bridges: E:K.212, B:R.416, B:R.416 ADP.8: 15 residues within 4Å: Chain A: R.416 Chain F: G.207, G.209, G.211, K.212, T.213, V.214, E.238, R.239, E.242, Y.395, F.468, A.471, F.474, T.475 14 PLIP interactions: 11 interactions with chain F, 3 interactions with chain A Hydrogen bonds: F:G.209, F:G.211, F:K.212, F:T.213, F:T.213, F:V.214, F:E.238, F:E.242, A:R.416 Salt bridges: F:K.212, F:R.239, A:R.416, A:R.416 pi-Stacking: F:Y.395

6 x LHG: 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE(Non-covalent)

LHG.9: 13 residues within 4Å: Chain 0: R.26, F.30, L.38, W.86 Chain 1: V.2 Chain K: R.55, F.56, E.61, Q.65, V.73, T.74, Y.77, T.81 19 PLIP interactions: 9 interactions with chain K, 9 interactions with chain 0, 1 interactions with chain 1 Hydrophobic interactions: K:F.56, K:T.74, K:Y.77, K:Y.77, K:T.81, 0:F.30, 0:F.30, 0:F.30, 0:L.38, 0:L.38, 0:W.86 Hydrogen bonds: K:E.61, K:Q.65, 0:T.29, 1:V.2 Salt bridges: K:R.55, K:R.55, 0:R.26, 0:R.26 LHG.10: 12 residues within 4Å: Chain K: Y.86, L.87, K.90, I.92 Chain Z: F.69, Y.72, C.73, Y.76, K.77, H.88 Ligands: CDL.13, CDL.15 10 PLIP interactions: 6 interactions with chain Z, 4 interactions with chain K Hydrophobic interactions: Z:F.69, Z:Y.76, Z:K.77, K:L.87, K:I.92 Hydrogen bonds: Z:Y.76, K:Y.86, K:K.90 Salt bridges: Z:R.83, Z:H.88 LHG.12: 8 residues within 4Å: Chain O: F.134 Chain V: I.106, F.150, V.154 Chain X: I.34, I.38, S.45 Chain Y: L.4 6 PLIP interactions: 4 interactions with chain X, 1 interactions with chain V, 1 interactions with chain Y Hydrophobic interactions: X:I.34, X:I.34, X:I.38, V:V.154, Y:L.4 Hydrogen bonds: X:S.45 LHG.16: 14 residues within 4Å: Chain Z: K.11, L.12, L.13, A.37, F.38, R.40, G.41, R.44, A.66, F.69, L.70, C.73 Ligands: CDL.14, CDL.15 12 PLIP interactions: 12 interactions with chain Z Hydrophobic interactions: Z:F.38, Z:F.38, Z:A.66, Z:F.69, Z:L.70 Hydrogen bonds: Z:L.12, Z:L.13, Z:R.40, Z:G.41, Z:R.44 Salt bridges: Z:R.44, Z:R.44 LHG.17: 10 residues within 4Å: Chain 0: G.97, I.98, I.99, D.102 Chain K: I.84, L.85, L.88, F.100, I.103 Chain V: M.182 12 PLIP interactions: 5 interactions with chain K, 5 interactions with chain 0, 2 interactions with chain Z Hydrophobic interactions: K:I.84, K:L.88, K:F.100, K:F.100, K:I.103, 0:I.98, 0:I.98, 0:I.99 Hydrogen bonds: 0:I.98, 0:I.99, Z:R.85 Salt bridges: Z:R.85 LHG.18: 12 residues within 4Å: Chain 0: L.53, K.55, I.56, S.59, L.68, A.73, L.74, N.76 Chain 1: G.14 Chain Z: L.17, L.20, I.24 8 PLIP interactions: 2 interactions with chain Z, 6 interactions with chain 0 Hydrophobic interactions: Z:L.20, Z:I.24, 0:L.53, 0:L.74, 0:N.76 Hydrogen bonds: 0:K.55, 0:K.55, 0:N.76

1 x P5S: O-[(R)-{[(2R)-2,3-bis(octadecanoyloxy)propyl]oxy}(hydroxy)phosphoryl]-L-serine(Non-covalent)

P5S.11: 18 residues within 4Å: Chain N: I.95, R.99 Chain O: I.95, R.99 Chain P: T.88, I.95, R.99 Chain Q: A.84, I.95, R.99 Chain R: A.84, R.99 Chain S: T.88, R.99 Chain T: T.88, I.95, R.99 Chain U: R.99 14 PLIP interactions: 3 interactions with chain T, 2 interactions with chain R, 2 interactions with chain P, 2 interactions with chain Q, 1 interactions with chain N, 1 interactions with chain S, 1 interactions with chain O, 2 interactions with chain U Hydrophobic interactions: T:T.88, R:A.84, P:T.88, Q:A.84 Hydrogen bonds: T:R.99, P:R.99, N:R.99, S:R.99, U:R.99 Salt bridges: T:R.99, R:R.99, Q:R.99, O:R.99, U:R.99

3 x CDL: CARDIOLIPIN(Non-covalent)

CDL.13: 25 residues within 4Å: Chain K: F.56, G.57, L.58, Y.93, A.102, I.106, L.109, V.110, V.113, K.114, G.117, V.120 Chain V: R.41, L.42, L.45, Q.46, L.84, L.88 Chain Z: S.56, I.57, L.60, S.61, L.64 Ligands: LHG.10, CDL.15 15 PLIP interactions: 10 interactions with chain K, 3 interactions with chain V, 2 interactions with chain Z Hydrophobic interactions: K:F.56, K:L.58, K:A.102, K:I.106, K:L.109, K:L.109, K:V.110, K:V.113, K:V.120, V:L.84, V:L.84, V:L.88 Hydrogen bonds: K:G.57, Z:I.57, Z:S.61 CDL.14: 20 residues within 4Å: Chain V: L.19, L.22, L.25, F.26, L.29, T.33 Chain X: K.8, V.9, W.25 Chain Y: L.18, I.22, I.23, K.27, K.30 Chain Z: Q.39, Y.42, Y.43, L.70 Ligands: CDL.15, LHG.16 23 PLIP interactions: 9 interactions with chain V, 4 interactions with chain Y, 3 interactions with chain X, 7 interactions with chain Z Hydrophobic interactions: V:L.19, V:L.22, V:L.22, V:L.25, V:L.25, V:F.26, V:L.29, Y:I.22, Y:I.23, X:V.9, X:W.25, Z:Y.42, Z:Y.42, Z:Y.42, Z:L.70, Z:L.70 Hydrogen bonds: V:T.33, V:T.33, Z:Q.39, Z:Y.43 Salt bridges: Y:K.27, Y:K.27, X:K.8 CDL.15: 25 residues within 4Å: Chain 0: L.78 Chain K: L.58, I.59, E.62, F.63, F.66, P.76, Y.77, L.79, G.80 Chain V: L.29, L.42 Chain Z: L.13, G.41, Y.42, R.44, Y.45, K.48, Y.49, M.62, V.63 Ligands: LHG.10, CDL.13, CDL.14, LHG.16 17 PLIP interactions: 7 interactions with chain K, 6 interactions with chain Z, 2 interactions with chain V, 2 interactions with chain 0 Hydrophobic interactions: K:L.58, K:F.63, K:F.63, K:F.63, K:F.63, K:F.66, K:L.79, Z:Y.42, Z:Y.45, Z:Y.49, Z:V.63, V:L.29, V:L.42, 0:L.78, 0:L.78 Salt bridges: Z:R.44, Z:R.44

1 x S12: O-[(S)-hydroxy{[(2S)-2-hydroxy-3-(octadec-9-enoyloxy)propyl]oxy}phosphoryl]-L-serine(Non-covalent)

S12.19: 8 residues within 4Å: Chain 1: E.66, L.70, K.71 Chain N: I.70 Chain S: I.70 Chain T: I.70 Chain U: I.70, A.74 8 PLIP interactions: 1 interactions with chain T, 2 interactions with chain U, 3 interactions with chain 1, 1 interactions with chain S, 1 interactions with chain N Hydrophobic interactions: T:I.70, U:I.70, U:A.74, S:I.70, N:I.70 Hydrogen bonds: 1:E.66, 1:K.71, 1:K.71

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Pinke, G. et al., Cryo-EM structure of the entire mammalian F-type ATP synthase. Nat.Struct.Mol.Biol. (2020)

Release Date

2020-09-23

Peptides

ATP synthase subunit alpha: ABC
ATP synthase subunit beta: DEF
ATP synthase subunit gamma: G
ATP synthase F1 subunit delta: H
ATP synthase F1 subunit epsilon: I
ATP synthase peripheral stalk subunit OSCP: J
ATP synthase subunit b: K
ATP synthase-coupling factor 6, mitochondrial: L
ATP synthase subunit d, mitochondrial: M
ATP synthase F(0) complex subunit C1, mitochondrial: NOPQRSTU
ATP synthase subunit a: V
Subunit DAPIT: W
ATP synthase membrane subunit 6.8PL: X
ATP synthase protein 8: Y
ATP synthase membrane subunit f: Z
ATP synthase subunit: 0
Subunit e: 1

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

B
C

C
A

D
E

E
D

F
F

G
G

H
H

I
I

J
J

K
K

L
L

M
M

N
1

O
2

P
3

Q
4

R
5

S
6

T
7

U
8

V
N

W
O

X
P

Y
Q

Z
R

0
S

1
T

Membrane

We predict this structure to be a membrane protein.
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ATP synthase subunit alpha

ATP synthase subunit beta

ATP synthase subunit gamma

ATP synthase F1 subunit delta

ATP synthase F1 subunit epsilon

ATP synthase peripheral stalk subunit OSCP

ATP synthase subunit b

ATP synthase-coupling factor 6, mitochondrial

ATP synthase subunit d, mitochondrial

ATP synthase F(0) complex subunit C1, mitochondrial

ATP synthase subunit a

Subunit DAPIT

ATP synthase membrane subunit 6.8PL

ATP synthase protein 8

ATP synthase membrane subunit f

ATP synthase subunit

Subunit e

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