SMTL ID : 9bym.1

Cryo-EM structure of ATP synthase non-stator state

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

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

Ligands

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

ATP.1: 17 residues within 4Å: Chain A: D.210, Q.212, T.213, G.214, K.215, T.216, S.217, E.368, F.397, R.402, P.403, Q.470, Q.472 Chain C: S.447, M.450, Y.460 Ligands: MG.2 13 PLIP interactions: 11 interactions with chain A, 2 interactions with chain C Hydrogen bonds: A:Q.212, A:T.213, A:G.214, A:K.215, A:T.216, A:S.217, A:E.368, A:Q.470, A:Q.472, C:S.447, C:M.450 Salt bridges: A:K.215, A:K.215 ATP.3: 18 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, Q.470, G.471, Q.472 Chain E: S.447, R.448, Y.460, R.464 Ligands: MG.4 15 PLIP interactions: 12 interactions with chain B, 3 interactions with chain E Hydrogen bonds: B:Q.212, B:Q.212, B:T.213, B:G.214, B:K.215, B:T.216, B:S.217, B:S.217, B:Q.470, B:Q.472, E:S.447, E:R.448, E:R.464 Salt bridges: B:K.215, B:K.215 ATP.9: 16 residues within 4Å: Chain D: R.448, D.451 Chain R: D.210, R.211, Q.212, T.213, G.214, K.215, T.216, S.217, E.368, F.397, R.402, Q.470, G.471, Q.472 16 PLIP interactions: 12 interactions with chain R, 4 interactions with chain D Hydrogen bonds: R:Q.212, R:T.213, R:G.214, R:K.215, R:T.216, R:T.216, R:S.217, R:S.217, R:E.368, R:Q.470, D:D.451 Salt bridges: R:K.215, R:K.215, D:R.448, D:R.448, D:R.448

4 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 2 residues within 4Å: Chain A: T.216 Ligands: ATP.1 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:T.216 MG.4: 3 residues within 4Å: Chain B: T.216, Q.248 Ligands: ATP.3 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:T.216 MG.6: 5 residues within 4Å: Chain C: T.255, E.280, R.281, E.284 Ligands: ADP.5 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:T.255 MG.8: 5 residues within 4Å: Chain E: T.255, E.280, R.281, E.284 Ligands: ADP.7 No protein-ligand interaction detected (PLIP)

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

ADP.5: 13 residues within 4Å: Chain C: G.249, A.250, G.251, V.252, G.253, K.254, T.255, V.256, Y.437, A.513, F.516, T.517 Ligands: MG.6 10 PLIP interactions: 10 interactions with chain C Hydrogen bonds: C:G.249, C:G.251, C:V.252, C:G.253, C:K.254, C:T.255, C:V.256 Salt bridges: C:K.254 pi-Stacking: C:Y.437, C:Y.437 ADP.7: 14 residues within 4Å: Chain E: A.250, G.251, V.252, G.253, K.254, T.255, V.256, Y.437, F.510, A.513, F.516 Chain R: V.411, R.413 Ligands: MG.8 12 PLIP interactions: 10 interactions with chain E, 2 interactions with chain R Hydrogen bonds: E:G.249, E:G.251, E:V.252, E:G.253, E:K.254, E:T.255, E:V.256, R:R.413 Salt bridges: E:K.254, R: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 non-stator state. To Be Published

Release Date

2025-08-06

Peptides

ATP synthase subunit alpha: ABR
ATP synthase subunit beta: CDE
ATPase inhibitor, mitochondrial: F
ATP synthase subunit gamma: G
ATP synthase F1 subunit delta: H
ATP synthase F1 subunit epsilon: I
ATP synthase lipid-binding protein: JKLMNOPQ

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
C

R
B

C
D

D
E

E
F

F
J

G
G

H
H

I
I

J
K

K
L

L
N

M
O

N
P

O
Q

P
R

Q
M

Membrane

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

ATP synthase subunit beta

ATPase inhibitor, mitochondrial

ATP synthase subunit gamma

ATP synthase F1 subunit delta

ATP synthase F1 subunit epsilon

ATP synthase lipid-binding protein

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