SMTL ID : 6tmh.1

Cryo-EM structure of Toxoplasma gondii mitochondrial ATP synthase dimer, OSCP/F1/c-ring model

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-3-3-1-1-1-1-10-mer

Ligands

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

ATP.1: 17 residues within 4Å: Chain B: R.222, Q.223, T.224, G.225, K.226, T.227, A.228, E.380, F.409, R.414, P.415, Q.482, R.483, Q.484 Chain E: Y.447, R.451 Ligands: MG.2 14 PLIP interactions: 14 interactions with chain B Hydrogen bonds: B:Q.223, B:Q.223, B:T.224, B:G.225, B:K.226, B:T.227, B:A.228, B:E.380, B:R.414, B:Q.482, B:Q.484, B:Q.484 Salt bridges: B:K.226, B:K.226 ATP.3: 17 residues within 4Å: Chain C: R.222, Q.223, T.224, G.225, K.226, T.227, A.228, Q.260, F.409, R.414, P.415, Q.482, R.483, Q.484 Chain F: R.435, A.438 Ligands: MG.4 15 PLIP interactions: 14 interactions with chain C, 1 interactions with chain F Hydrogen bonds: C:Q.223, C:T.224, C:G.225, C:K.226, C:T.227, C:T.227, C:A.228, C:Q.260, C:R.414, C:Q.482, C:Q.484, C:Q.484 Salt bridges: C:K.226, C:K.226, F:R.435 ATP.5: 20 residues within 4Å: Chain D: R.222, Q.223, T.224, G.225, K.226, T.227, A.228, E.380, F.409, R.414, P.415, Q.482, R.483, Q.484 Chain G: S.434, R.435, A.438, Y.447, R.451 Ligands: MG.6 15 PLIP interactions: 13 interactions with chain D, 2 interactions with chain G Hydrogen bonds: D:Q.223, D:Q.223, D:T.224, D:G.225, D:K.226, D:T.227, D:A.228, D:E.380, D:Q.482, D:Q.484, D:Q.484, G:R.435, G:Y.447 Salt bridges: D:K.226, D:K.226

5 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 2 residues within 4Å: Chain B: T.227 Ligands: ATP.1 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:T.227 MG.4: 3 residues within 4Å: Chain C: T.227, Q.260 Ligands: ATP.3 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:T.227 MG.6: 3 residues within 4Å: Chain D: T.227, D.321 Ligands: ATP.5 1 PLIP interactions: 1 interactions with chain D Metal complexes: D:T.227 MG.8: 4 residues within 4Å: Chain E: T.234, R.260, E.263 Ligands: ADP.7 1 PLIP interactions: 1 interactions with chain E Metal complexes: E:T.234 MG.10: 4 residues within 4Å: Chain G: K.233, T.234, N.336 Ligands: ADP.9 1 PLIP interactions: 1 interactions with chain G Metal complexes: G:T.234

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

ADP.7: 16 residues within 4Å: Chain D: R.425 Chain E: G.228, A.229, G.230, V.231, G.232, K.233, T.234, V.235, E.263, Y.424, F.497, A.500, F.503, T.504 Ligands: MG.8 13 PLIP interactions: 11 interactions with chain E, 2 interactions with chain D Hydrogen bonds: E:G.230, E:V.231, E:G.232, E:K.233, E:T.234, E:T.234, E:T.234, E:V.235 Salt bridges: E:K.233, D:R.425, D:R.425 pi-Stacking: E:Y.424, E:Y.424 ADP.9: 18 residues within 4Å: Chain C: V.423, R.425 Chain G: G.228, A.229, G.230, V.231, G.232, K.233, T.234, V.235, R.260, Y.424, F.497, A.500, F.503, T.504, M.538 Ligands: MG.10 13 PLIP interactions: 13 interactions with chain G Hydrogen bonds: G:G.230, G:V.231, G:G.232, G:K.233, G:T.234, G:T.234, G:T.234, G:V.235, G:R.260, G:T.504 Salt bridges: G:K.233 pi-Stacking: G:Y.424, G:Y.424

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Muhleip, A. et al., ATP synthase hexamer assemblies shape cristae of Toxoplasma mitochondria. Nat Commun (2021)

Release Date

2020-12-16

Peptides

Inhibitor of F1: A
ATP synthase subunit alpha,subunit alpha: BCD
ATP synthase subunit beta: EFG
ATP synthase subunit gamma: H
ATP synthase subunit delta: I
ATP synthase subunit epsilon: J
Oligomycin sensitivity conferring protein (OSCP): K
subunit c: LMNOPQRSTU

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
i

B
A

C
E

D
C

E
B

F
F

G
D

H
g

I
d

J
e

K
G

L
H

M
I

N
J

O
K

P
L

Q
M

R
N

S
O

T
P

U
Q

Membrane

We predict this structure to be a membrane protein.
Show / Hide

Inhibitor of F1

ATP synthase subunit alpha,subunit alpha

ATP synthase subunit beta

ATP synthase subunit gamma

ATP synthase subunit delta

ATP synthase subunit epsilon

Oligomycin sensitivity conferring protein (OSCP)

subunit c

Related Entries With Identical Sequence