SMTL ID : 6za9.1

Fo domain of Ovine ATP synthase

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

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

Ligands

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

LHG.1: 9 residues within 4Å: Chain B: F.134 Chain K: I.106, F.150, V.154 Chain M: Y.33, I.34, I.38 Chain N: L.4, W.9 9 PLIP interactions: 5 interactions with chain M, 2 interactions with chain N, 2 interactions with chain K Hydrophobic interactions: M:Y.33, M:I.34, M:I.34, M:I.38, M:I.38, N:L.4, N:W.9, K:I.106, K:V.154 LHG.2: 12 residues within 4Å: Chain I: R.55, E.61, Q.65, V.73, T.74, Y.77, V.78, T.81 Chain P: R.26, F.30, W.86 Chain Q: V.2 12 PLIP interactions: 7 interactions with chain I, 4 interactions with chain P, 1 interactions with chain Q Hydrophobic interactions: I:T.74, I:Y.77, I:Y.77, I:V.78, P:F.30, P:F.30, P:W.86 Hydrogen bonds: I:R.55, I:Q.65, Q:V.2 Salt bridges: I:R.55, P:R.26 LHG.3: 12 residues within 4Å: Chain I: Y.86, L.87, K.90, I.92 Chain O: F.69, Y.72, Y.76, K.77, R.83, H.88 Ligands: CDL.5, CDL.6 11 PLIP interactions: 7 interactions with chain O, 4 interactions with chain I Hydrophobic interactions: O:Y.72, O:Y.72, O:Y.76, O:K.77, I:L.87, I:I.92 Hydrogen bonds: O:Y.76, I:Y.86, I:K.90 Salt bridges: O:R.83, O:H.88 LHG.7: 12 residues within 4Å: Chain O: K.11, L.12, L.13, A.37, F.38, R.40, G.41, R.44, F.69, L.70 Ligands: CDL.4, CDL.6 11 PLIP interactions: 11 interactions with chain O Hydrophobic interactions: O:F.38, O:F.38, O:F.69, O:L.70, O:L.70 Hydrogen bonds: O:L.12, O:L.13, O:R.40, O:R.44 Salt bridges: O:R.44, O:R.44 LHG.8: 10 residues within 4Å: Chain I: I.84, L.85, L.88, F.100, I.103 Chain K: M.182 Chain P: G.97, I.98, I.99, D.102 9 PLIP interactions: 3 interactions with chain I, 2 interactions with chain O, 4 interactions with chain P Hydrophobic interactions: I:L.85, I:F.100, I:I.103, P:I.98, P:I.99 Hydrogen bonds: O:R.85, P:I.98, P:I.99 Salt bridges: O:R.85 LHG.9: 11 residues within 4Å: Chain O: L.12, L.17 Chain P: L.53, K.55, I.56, L.68, A.73, L.74, N.76, G.77 Chain Q: G.14 7 PLIP interactions: 6 interactions with chain P, 1 interactions with chain O Hydrophobic interactions: P:L.53, P:L.74, P:N.76, O:L.12 Hydrogen bonds: P:K.55, P:N.76 Salt bridges: P:K.55

3 x CDL: CARDIOLIPIN(Non-covalent)

CDL.4: 23 residues within 4Å: Chain K: L.19, L.22, I.23, L.25, F.26, L.29, P.32, T.33 Chain M: M.1, K.8, V.9, W.25 Chain N: L.18, I.22, I.23, K.27, K.30 Chain O: Q.39, Y.42, Y.43, L.70 Ligands: CDL.6, LHG.7 19 PLIP interactions: 8 interactions with chain K, 5 interactions with chain O, 5 interactions with chain N, 1 interactions with chain M Hydrophobic interactions: K:L.19, K:L.22, K:I.23, K:L.25, K:L.25, K:F.26, O:Y.42, O:L.70, O:L.70, N:L.18, N:I.22, N:I.23, M:V.9 Hydrogen bonds: K:T.33, K:T.33, O:Q.39, O:Y.43 Salt bridges: N:K.27, N:K.27 CDL.5: 29 residues within 4Å: Chain I: 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 K: L.30, R.41, L.42, L.45, Q.46, M.49, I.76, L.77, L.84, L.88 Chain O: S.56, I.57, L.60, S.61, L.64 Ligands: LHG.3, CDL.6 20 PLIP interactions: 9 interactions with chain I, 7 interactions with chain K, 4 interactions with chain O Hydrophobic interactions: I:F.56, I:A.102, I:L.109, I:L.109, I:L.109, I:L.109, I:V.110, I:V.113, K:L.30, K:L.42, K:I.76, K:L.77, K:L.84, K:L.84, K:L.88, O:I.57, O:I.57 Hydrogen bonds: I:G.57, O:I.57, O:S.61 CDL.6: 28 residues within 4Å: Chain I: F.56, L.58, I.59, P.60, E.62, F.63, F.66, P.76, L.79, G.80 Chain K: L.29, L.42 Chain O: L.13, G.41, Y.42, R.44, Y.45, K.48, Y.49, M.62, V.63 Chain P: K.71, L.74, L.78 Ligands: LHG.3, CDL.4, CDL.5, LHG.7 19 PLIP interactions: 8 interactions with chain I, 2 interactions with chain P, 2 interactions with chain K, 7 interactions with chain O Hydrophobic interactions: I:L.58, I:I.59, I:P.60, I:F.63, I:F.63, I:F.63, I:F.66, I:L.79, P:L.74, P:L.78, K:L.29, K:L.42, O:Y.42, O:Y.45, O:Y.45, O:Y.49, O:V.63 Salt bridges: O:R.44, O:R.44

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

S12.10: 10 residues within 4Å: Chain B: I.63 Chain C: I.70 Chain F: I.63, I.70 Chain G: I.63, I.70 Chain H: I.63, I.70 Chain Q: L.70, K.71 6 PLIP interactions: 2 interactions with chain F, 2 interactions with chain G, 1 interactions with chain C, 1 interactions with chain H Hydrophobic interactions: F:I.63, F:I.70, G:I.63, G:I.70, C:I.70, H:I.70

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 F(0) complex subunit C1, mitochondrial: ABCDEFGH
ATP synthase subunit b: I
ATP synthase subunit d, mitochondrial: J
ATP synthase subunit a: K
ATP synthase membrane subunit DAPIT: L
ATP synthase membrane subunit 6.8PL: M
ATP synthase protein 8: N
ATP synthase membrane subunit f: O
ATP synthase subunit: P
ATP synthase subunit e, mitochondrial: Q

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
1

B
2

C
3

D
4

E
5

F
6

G
7

H
8

I
K

J
M

K
N

L
O

M
P

N
Q

O
R

P
S

Q
T

Membrane

We predict this structure to be a membrane protein.
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ATP synthase F(0) complex subunit C1, mitochondrial

ATP synthase subunit b

ATP synthase subunit d, mitochondrial

ATP synthase subunit a

ATP synthase membrane subunit DAPIT

ATP synthase membrane subunit 6.8PL

ATP synthase protein 8

ATP synthase membrane subunit f

ATP synthase subunit

ATP synthase subunit e, mitochondrial

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