SMTL ID : 6yo0.1

Cryo-EM structure of Tetrahymena thermophila mitochondrial ATP synthase - F1/peripheral stalk

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

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

Ligands

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

ATP.1: 17 residues within 4Å: Chain C: R.202, Q.203, T.204, G.205, K.206, T.207, A.208, F.388, R.393, P.394, Q.461, N.462, Q.463 Chain D: T.373, Y.387, R.391 Ligands: MG.2 13 PLIP interactions: 12 interactions with chain C, 1 interactions with chain D Hydrogen bonds: C:Q.203, C:T.204, C:T.204, C:G.205, C:K.206, C:T.207, C:A.208, C:N.462, C:Q.463, C:Q.463, D:Y.387 Salt bridges: C:K.206, C:K.206 ATP.5: 16 residues within 4Å: Chain E: R.202, Q.203, T.204, G.205, K.206, T.207, A.208, F.388, R.393, P.394, Q.461, N.462, Q.463 Chain F: R.375, D.378 Ligands: MG.6 9 PLIP interactions: 7 interactions with chain E, 2 interactions with chain F Hydrogen bonds: E:Q.203, E:G.205, E:T.207, E:A.208, E:Q.461, F:D.378 Salt bridges: E:K.206, E:K.206, F:R.375 ATP.7: 20 residues within 4Å: Chain G: D.201, R.202, Q.203, T.204, G.205, K.206, T.207, A.208, F.388, R.393, P.394, Q.461, N.462, Q.463 Chain H: S.374, R.375, L.377, Y.387, R.391 Ligands: MG.8 14 PLIP interactions: 3 interactions with chain H, 11 interactions with chain G Hydrogen bonds: H:S.374, H:L.377, H:Y.387, G:Q.203, G:Q.203, G:T.204, G:T.204, G:G.205, G:K.206, G:T.207, G:A.208, G:Q.461 Salt bridges: G:K.206, G:K.206

5 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 2 residues within 4Å: Chain C: T.207 Ligands: ATP.1 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:T.207 MG.4: 4 residues within 4Å: Chain D: T.182, E.207, E.211 Ligands: ADP.3 2 PLIP interactions: 2 interactions with chain D Metal complexes: D:T.182, D:E.207 MG.6: 3 residues within 4Å: Chain E: T.207 Chain F: R.375 Ligands: ATP.5 1 PLIP interactions: 1 interactions with chain E Metal complexes: E:T.207 MG.8: 3 residues within 4Å: Chain G: T.207, Q.239 Ligands: ATP.7 1 PLIP interactions: 1 interactions with chain G Metal complexes: G:T.207 MG.10: 2 residues within 4Å: Chain H: T.182 Ligands: ADP.9 1 PLIP interactions: 1 interactions with chain H Metal complexes: H:T.182

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

ADP.3: 22 residues within 4Å: Chain D: G.176, A.177, G.178, V.179, G.180, K.181, T.182, V.183, E.207, R.208, N.276, Y.364, P.365, F.437, S.440, F.443, S.444, M.478 Chain G: V.402, S.403, R.404 Ligands: MG.4 14 PLIP interactions: 3 interactions with chain G, 11 interactions with chain D Hydrogen bonds: G:S.403, D:G.178, D:V.179, D:G.180, D:K.181, D:T.182, D:T.182, D:V.183, D:R.208 Salt bridges: G:R.404, G:R.404, D:K.181, D:K.181 pi-Stacking: D:Y.364 ADP.9: 19 residues within 4Å: Chain E: S.375, V.402, R.404 Chain H: A.177, G.178, V.179, G.180, K.181, T.182, V.183, Y.364, Q.435, P.436, F.437, S.440, F.443, S.444, M.478 Ligands: MG.10 11 PLIP interactions: 9 interactions with chain H, 2 interactions with chain E Hydrogen bonds: H:G.178, H:V.179, H:G.180, H:K.181, H:T.182, H:V.183 Salt bridges: H:K.181, E:R.404, E:R.404 pi-Stacking: H:Y.364, H:Y.364

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Flygaard, R.K. et al., Type III ATP synthase is a symmetry-deviated dimer that induces membrane curvature through tetramerization. Nat Commun (2020)

Release Date

2020-09-30

Peptides

Oligomycin sensitivity-conferring protein (OSCP): A
ATP synthase subunit gamma: B
ATP synthase subunit alpha: CEG
ATP synthase subunit beta: DFH
Inhibitor of F1 (IF1): I
ATPTT13: J
subunit b: K
subunit d: L

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
G1

B
g1

C
C1

E
B1

G
A1

D
D1

F
F1

H
E1

I
i1

J
s

K
b

L
d

Oligomycin sensitivity-conferring protein (OSCP)

ATP synthase subunit gamma

ATP synthase subunit alpha

ATP synthase subunit beta

Inhibitor of F1 (IF1)

ATPTT13

subunit b

subunit d

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