SMTL ID : 9byk.1

Cryo-EM structure of ATP synthase E state

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

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

Ligands

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

ATP.1: 17 residues within 4Å: Chain B: D.210, R.211, Q.212, T.213, G.214, K.215, T.216, S.217, F.397, R.402, P.403, Q.470, Q.472 Chain C: S.447, R.448, Y.460 Ligands: MG.2 16 PLIP interactions: 12 interactions with chain B, 4 interactions with chain C Hydrogen bonds: B:Q.212, B:T.213, B:G.214, B:K.215, B:T.216, B:T.216, B:S.217, B:S.217, B:Q.470, B:Q.472, C:S.447, C:Y.460 Salt bridges: B:K.215, B:K.215, C:R.448, C:R.448 ATP.7: 18 residues within 4Å: Chain 0: D.210, R.211, Q.212, T.213, G.214, K.215, T.216, S.217, F.397, R.402, P.403, Q.470, Q.472 Chain E: S.447, M.450, D.451, Y.460 Ligands: MG.8 14 PLIP interactions: 4 interactions with chain E, 10 interactions with chain 0 Hydrogen bonds: E:S.447, E:D.451, E:D.451, E:Y.460, 0:Q.212, 0:T.213, 0:G.214, 0:K.215, 0:T.216, 0:S.217, 0:S.217, 0:Q.470 Salt bridges: 0:K.215, 0:K.215 ATP.9: 15 residues within 4Å: Chain 2: D.210, 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 D: R.448, D.451 19 PLIP interactions: 15 interactions with chain 2, 4 interactions with chain D Hydrogen bonds: 2:Q.212, 2:T.213, 2:T.213, 2:G.214, 2:K.215, 2:T.216, 2:T.216, 2:S.217, 2:S.217, 2:R.402, 2:Q.470, 2:Q.472, D:R.448, D:D.451, D:D.451 Salt bridges: 2:K.215, 2:K.215, D:R.448 pi-Stacking: 2:F.397

4 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 2 residues within 4Å: Chain B: T.216 Ligands: ATP.1 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:T.216 MG.4: 5 residues within 4Å: Chain C: T.255, E.280, R.281, E.284 Ligands: ADP.3 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:T.255 MG.6: 4 residues within 4Å: Chain E: T.255, R.281, E.284 Ligands: ADP.5 1 PLIP interactions: 1 interactions with chain E Metal complexes: E:T.255 MG.8: 2 residues within 4Å: Chain 0: T.216 Ligands: ATP.7 1 PLIP interactions: 1 interactions with chain 0 Metal complexes: 0:T.216

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

ADP.3: 14 residues within 4Å: Chain 0: R.413 Chain C: G.249, G.251, V.252, G.253, K.254, T.255, V.256, Y.437, F.510, A.513, F.516, T.517 Ligands: MG.4 15 PLIP interactions: 13 interactions with chain C, 2 interactions with chain 0 Hydrogen bonds: C:G.249, C:G.251, C:V.252, C:G.253, C:K.254, C:T.255, C:T.255, C:V.256, C:R.281, C:E.284 Salt bridges: C:K.254, 0:R.413, 0:R.413 pi-Stacking: C:Y.437, C:Y.437 ADP.5: 14 residues within 4Å: Chain 2: V.411, R.413 Chain E: G.249, G.251, V.252, G.253, K.254, T.255, V.256, R.281, Y.437, F.510, A.513 Ligands: MG.6 15 PLIP interactions: 13 interactions with chain E, 2 interactions with chain 2 Hydrogen bonds: E:G.249, E:G.251, E:V.252, E:G.253, E:K.254, E:T.255, E:T.255, E:V.256, E:R.281, E:R.281, 2:R.413 Salt bridges: E:K.254, 2:R.413 pi-Stacking: E:Y.437, E:Y.437

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

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

Release Date

2025-08-06

Peptides

ATP synthase protein 8: A
ATP synthase subunit alpha: B02
ATP synthase subunit beta: CDE
ATP synthase subunit gamma: F
ATP synthase F1 subunit delta: G
ATP synthase F1 subunit epsilon: H
ATPase inhibitor, mitochondrial: I
ATP synthase lipid-binding protein: JKLMNOPQ
ATP synthase subunit O, mitochondrial: R
ATP synthase subunit: S
ATP synthase subunit a: T
ATP synthase subunit b: U
ATP synthase-coupling factor 6, mitochondrial: V
ATP synthase subunit d, mitochondrial: W
ATP synthase subunit e, mitochondrial: X
ATP synthase membrane subunit K, mitochondrial: Y
unkown protein: Z
ATP synthase subunit f, mitochondrial: 1

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
8

B
A

0
C

2
B

C
D

D
E

E
F

F
G

G
H

H
I

I
J

J
K

K
L

L
M

M
N

N
O

O
P

P
Q

Q
R

R
S

S
T

T
a

U
b

V
c

W
d

X
e

Y
i

Z
k

1
f

ATP synthase protein 8

ATP synthase subunit alpha

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 a

ATP synthase subunit b

ATP synthase-coupling factor 6, mitochondrial

ATP synthase subunit d, mitochondrial

ATP synthase subunit e, mitochondrial

ATP synthase membrane subunit K, mitochondrial

unkown protein

ATP synthase subunit f, mitochondrial

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