SMTL ID : 9bxu.1

Cryo-EM structure of ATP synthase DP state

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

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

Ligands

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

ADP.1: 11 residues within 4Å: Chain 1: R.413 Chain B: A.250, G.251, V.252, G.253, K.254, T.255, V.256, Y.437, A.513 Ligands: MG.2 12 PLIP interactions: 10 interactions with chain B, 2 interactions with chain 1 Hydrogen bonds: B:G.249, B:G.251, B:V.252, B:G.253, B:K.254, B:T.255, B:V.256 Salt bridges: B:K.254, 1:R.413, 1:R.413 pi-Stacking: B:Y.437, B:Y.437 ADP.3: 13 residues within 4Å: Chain 2: V.411, R.413 Chain D: G.249, G.251, V.252, G.253, K.254, T.255, V.256, Y.437, F.510, F.516 Ligands: MG.4 12 PLIP interactions: 10 interactions with chain D, 2 interactions with chain 2 Hydrogen bonds: D:G.249, D:G.251, D:V.252, D:G.253, D:K.254, D:T.255, D:V.256, 2:R.413 Salt bridges: D:K.254, 2:R.413 pi-Stacking: D:Y.437, D:Y.437

5 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 2 residues within 4Å: Chain B: T.255 Ligands: ADP.1 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:T.255 MG.4: 2 residues within 4Å: Chain D: T.255 Ligands: ADP.3 No protein-ligand interaction detected (PLIP) MG.6: 2 residues within 4Å: Chain 0: T.216 Ligands: ATP.5 1 PLIP interactions: 1 interactions with chain 0 Metal complexes: 0:T.216 MG.8: 2 residues within 4Å: Chain 1: T.216 Ligands: ATP.7 1 PLIP interactions: 1 interactions with chain 1 Metal complexes: 1:T.216 MG.10: 3 residues within 4Å: Chain 2: K.215, T.216 Ligands: ATP.9 1 PLIP interactions: 1 interactions with chain 2 Metal complexes: 2:T.216

3 x ATP: ADENOSINE-5'-TRIPHOSPHATE(Non-covalent)

ATP.5: 11 residues within 4Å: Chain 0: R.211, Q.212, T.213, G.214, K.215, T.216, S.217, F.397, G.471, Q.472 Ligands: MG.6 11 PLIP interactions: 11 interactions with chain 0 Hydrogen bonds: 0:Q.212, 0:T.213, 0:G.214, 0:K.215, 0:T.216, 0:T.216, 0:S.217, 0:S.217, 0:Q.470, 0:Q.472 Salt bridges: 0:K.215 ATP.7: 12 residues within 4Å: Chain 1: R.211, Q.212, T.213, G.214, K.215, T.216, S.217, F.397, Q.470, G.471, Q.472 Ligands: MG.8 11 PLIP interactions: 11 interactions with chain 1 Hydrogen bonds: 1:Q.212, 1:T.213, 1:G.214, 1:K.215, 1:T.216, 1:S.217, 1:S.217, 1:Q.470, 1:Q.472 Salt bridges: 1:K.215, 1:K.215 ATP.9: 15 residues within 4Å: Chain 2: R.211, Q.212, T.213, G.214, K.215, T.216, S.217, F.397, R.402, Q.470, G.471, Q.472 Chain C: R.448, D.451 Ligands: MG.10 13 PLIP interactions: 12 interactions with chain 2, 1 interactions with chain C Hydrogen bonds: 2:Q.212, 2:T.213, 2:G.214, 2:K.215, 2:T.216, 2:S.217, 2:S.217, 2:R.402, 2:Q.470, 2:Q.472 Salt bridges: 2:K.215, 2:K.215, C:R.448

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zhang, Z. et al., Cryo-EM structure of ATP synthase DP state. To Be Published

Release Date

2025-08-06

Peptides

ATP synthase protein 8: A
ATP synthase subunit beta: BCD
ATP synthase subunit gamma: E
ATP synthase F1 subunit delta: F
ATP synthase F1 subunit epsilon: G
ATPase inhibitor, mitochondrial: H
ATP synthase lipid-binding protein: IJKLMNOP
ATP synthase subunit O, mitochondrial: Q
ATP synthase subunit: R
ATP synthase subunit e, mitochondrial: S
ATP synthase subunit b: T
ATP synthase subunit f, mitochondrial: U
ATP synthase subunit a: V
ATP synthase-coupling factor 6, mitochondrial: W
ATP synthase subunit d, mitochondrial: X
ATP synthase membrane subunit K, mitochondrial: Y
unknow peptide: Z
ATP synthase subunit alpha: 012

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
8

B
D

C
E

D
F

E
G

F
H

G
I

H
J

I
K

J
L

K
M

L
N

M
O

N
P

O
Q

P
R

Q
S

R
T

S
U

T
V

U
W

V
a

W
c

X
d

Y
i

Z
k

0
A

1
C

2
B

ATP synthase protein 8

ATP synthase subunit beta

ATP synthase subunit gamma

ATP synthase F1 subunit delta

ATP synthase F1 subunit epsilon

ATPase inhibitor, mitochondrial

ATP synthase lipid-binding protein

ATP synthase subunit O, mitochondrial

ATP synthase subunit

ATP synthase subunit e, mitochondrial

ATP synthase subunit b

ATP synthase subunit f, mitochondrial

ATP synthase subunit a

ATP synthase-coupling factor 6, mitochondrial

ATP synthase subunit d, mitochondrial

ATP synthase membrane subunit K, mitochondrial

unknow peptide

ATP synthase subunit alpha

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