SMTL ID : 6tdy.1

Cryo-EM structure of Euglena gracilis mitochondrial ATP synthase, OSCP/F1/c-ring in rotational state 1

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

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

Ligands

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

ATP.1: 18 residues within 4Å: Chain A: D.184, R.185, Q.186, T.187, G.188, K.189, T.190, S.191, Q.222, F.371, R.376, P.377, Q.441, K.442 Chain D: R.359, D.362, Y.371 Ligands: MG.2 16 PLIP interactions: 3 interactions with chain D, 13 interactions with chain A Hydrogen bonds: D:D.362, D:D.362, D:Y.371, A:Q.186, A:T.187, A:G.188, A:T.190, A:T.190, A:S.191, A:S.191, A:R.376, A:Q.441, A:K.442 Salt bridges: A:K.189, A:K.189 pi-Cation interactions: A:K.442 ATP.3: 17 residues within 4Å: Chain B: R.185, Q.186, T.187, G.188, K.189, T.190, S.191, Q.222, F.371, R.376, P.377, Q.441, K.442 Chain E: R.359, D.362 Ligands: MG.4, TRT.9 17 PLIP interactions: 16 interactions with chain B, 1 interactions with chain E Hydrogen bonds: B:Q.186, B:Q.186, B:T.187, B:G.188, B:K.189, B:T.190, B:T.190, B:S.191, B:S.191, B:Q.222, B:R.376, B:Q.441, B:K.442, E:D.362 Salt bridges: B:K.189, B:K.189 pi-Stacking: B:F.371 ATP.5: 17 residues within 4Å: Chain C: R.185, Q.186, T.187, G.188, K.189, T.190, S.191, F.371, R.376, P.377, Q.441, K.442, R.559 Chain F: R.359, D.362, Y.371 Ligands: MG.6 14 PLIP interactions: 12 interactions with chain C, 2 interactions with chain F Hydrogen bonds: C:Q.186, C:T.187, C:T.187, C:G.188, C:K.189, C:T.190, C:T.190, C:S.191, C:S.191, C:Q.441, F:D.362, F:D.362 Salt bridges: C:K.189, C:K.189 ATP.10: 24 residues within 4Å: Chain B: I.357, S.358, V.385, R.387 Chain F: G.161, A.162, G.163, V.164, G.165, K.166, T.167, V.168, E.192, R.193, Y.314, Y.348, P.349, Q.419, P.420, F.421, A.424, F.427, T.428 Ligands: MG.11 17 PLIP interactions: 13 interactions with chain F, 4 interactions with chain B Hydrogen bonds: F:G.163, F:V.164, F:G.165, F:K.166, F:T.167, F:T.167, F:V.168, F:E.192, B:S.358 Salt bridges: F:K.166, F:K.166, F:R.193, B:R.387, B:R.387, B:R.387 pi-Stacking: F:Y.348, F:Y.348

5 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 4 residues within 4Å: Chain A: T.190, Q.222, D.283 Ligands: ATP.1 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:T.190 MG.4: 4 residues within 4Å: Chain B: T.190, Q.222, D.283 Ligands: ATP.3 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:T.190 MG.6: 3 residues within 4Å: Chain C: T.190, D.283 Ligands: ATP.5 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:T.190 MG.8: 5 residues within 4Å: Chain D: K.166, T.167, R.193, E.196 Ligands: ADP.7 1 PLIP interactions: 1 interactions with chain D Metal complexes: D:T.167 MG.11: 6 residues within 4Å: Chain F: K.166, T.167, E.192, R.193, E.196 Ligands: ATP.10 1 PLIP interactions: 1 interactions with chain F Metal complexes: F:T.167

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

ADP.7: 20 residues within 4Å: Chain C: V.385, S.386, R.387 Chain D: G.161, A.162, G.163, V.164, G.165, K.166, T.167, V.168, R.193, Y.348, Q.419, P.420, F.421, A.424, F.427, T.428 Ligands: MG.8 11 PLIP interactions: 9 interactions with chain D, 2 interactions with chain C Hydrogen bonds: D:G.163, D:V.164, D:G.165, D:K.166, D:T.167, D:V.168 Salt bridges: D:K.166, C:R.387, C:R.387 pi-Stacking: D:Y.348, D:Y.348

1 x TRT: FRAGMENT OF TRITON X-100(Non-covalent)

TRT.9: 17 residues within 4Å: Chain B: R.185, Q.186, F.371, R.376 Chain E: F.159, V.315, D.318, I.320, F.329, L.332, D.333, A.334, T.335, A.357, S.358, R.359 Ligands: ATP.3 5 PLIP interactions: 3 interactions with chain E, 2 interactions with chain B Hydrophobic interactions: E:F.159, E:I.320, E:F.329 Hydrogen bonds: B:R.185, B:R.185

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Muhleip, A. et al., Structure of a mitochondrial ATP synthase with bound native cardiolipin. Elife (2019)

Release Date

2019-11-27

Peptides

ATP synthase subunit alpha: ABC
ATP synthase subunit beta: DEF
ATP synthase subunit gamma: G
ATP synthase subunit delta: H
ATP synthase subunit epsilon: I
p18: JKL
oligomycin sensitivity conferring protein (OSCP): M
inhibitor of F1 (IF1): N
ATP synthase subunit c: OPQRSTUVWX
ATP synthase subunit d: Y
ATPTB4: Z

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
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

U
U

V
V

W
W

X
X

Y
h

Z
c

Membrane

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

ATP synthase subunit beta

ATP synthase subunit gamma

ATP synthase subunit delta

ATP synthase subunit epsilon

p18

oligomycin sensitivity conferring protein (OSCP)

inhibitor of F1 (IF1)

ATP synthase subunit c

ATP synthase subunit d

ATPTB4

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