SMTL ID : 6tdz.1

Cryo-EM structure of Euglena gracilis mitochondrial ATP synthase, OSCP/F1/c-ring, rotational state 2

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

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

Ligands

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

ATP.1: 19 residues within 4Å: Chain Q: Y.164, D.184, R.185, Q.186, T.187, G.188, K.189, T.190, S.191, F.371, R.376, P.377, Q.441, K.442 Chain T: R.359, M.361, D.362, Y.371 Ligands: MG.2 14 PLIP interactions: 13 interactions with chain Q, 1 interactions with chain T Hydrogen bonds: Q:Q.186, Q:T.187, Q:G.188, Q:K.189, Q:T.190, Q:S.191, Q:S.191, Q:R.376, Q:Q.441, Q:K.442, T:D.362 Salt bridges: Q:K.189 pi-Stacking: Q:F.371 pi-Cation interactions: Q:K.442 ATP.3: 16 residues within 4Å: Chain R: R.185, Q.186, T.187, G.188, K.189, T.190, S.191, F.371, R.376, P.377, Q.441, K.442 Chain U: R.359, D.362 Ligands: MG.4, TRT.9 15 PLIP interactions: 15 interactions with chain R Hydrogen bonds: R:Q.186, R:Q.186, R:T.187, R:G.188, R:K.189, R:T.190, R:S.191, R:S.191, R:Q.222, R:R.376, R:Q.441, R:K.442 Salt bridges: R:K.189, R:K.189 pi-Stacking: R:F.371 ATP.5: 18 residues within 4Å: Chain S: Y.164, R.185, Q.186, T.187, G.188, K.189, T.190, S.191, F.371, R.376, P.377, Q.441, K.442 Chain V: R.359, M.361, D.362, Y.371 Ligands: MG.6 13 PLIP interactions: 11 interactions with chain S, 2 interactions with chain V Hydrogen bonds: S:Q.186, S:Q.186, S:T.187, S:G.188, S:K.189, S:T.190, S:S.191, S:S.191, S:Q.441, V:D.362, V:D.362 Salt bridges: S:K.189, S:K.189 ATP.10: 23 residues within 4Å: Chain R: I.357, S.358, V.385, R.387 Chain V: G.161, A.162, G.163, V.164, G.165, K.166, T.167, V.168, E.192, R.193, Y.348, P.349, Q.419, P.420, F.421, A.424, F.427, T.428 Ligands: MG.11 17 PLIP interactions: 12 interactions with chain V, 5 interactions with chain R Hydrogen bonds: V:G.163, V:V.164, V:G.165, V:K.166, V:T.167, V:T.167, V:V.168, R:I.357, R:S.358 Salt bridges: V:K.166, V:K.166, V:R.193, R:R.387, R:R.387, R:R.387 pi-Stacking: V:Y.348, V:Y.348

5 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 3 residues within 4Å: Chain Q: T.190, D.283 Ligands: ATP.1 1 PLIP interactions: 1 interactions with chain Q Metal complexes: Q:T.190 MG.4: 4 residues within 4Å: Chain R: K.189, T.190, D.283 Ligands: ATP.3 1 PLIP interactions: 1 interactions with chain R Metal complexes: R:T.190 MG.6: 4 residues within 4Å: Chain S: K.189, T.190, D.283 Ligands: ATP.5 1 PLIP interactions: 1 interactions with chain S Metal complexes: S:T.190 MG.8: 5 residues within 4Å: Chain T: K.166, T.167, R.193, E.196 Ligands: ADP.7 1 PLIP interactions: 1 interactions with chain T Metal complexes: T:T.167 MG.11: 5 residues within 4Å: Chain V: T.167, E.192, R.193, E.196 Ligands: ATP.10 1 PLIP interactions: 1 interactions with chain V Metal complexes: V:T.167

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

ADP.7: 20 residues within 4Å: Chain S: V.385, S.386, R.387 Chain T: 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 14 PLIP interactions: 11 interactions with chain T, 3 interactions with chain S Hydrogen bonds: T:G.161, T:G.163, T:V.164, T:G.165, T:K.166, T:T.167, T:T.167, T:V.168, S:S.386 Salt bridges: T:K.166, S:R.387, S:R.387 pi-Stacking: T:Y.348, T:Y.348

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

TRT.9: 17 residues within 4Å: Chain R: R.185, Q.186, F.371, R.376 Chain U: 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 4 PLIP interactions: 2 interactions with chain U, 2 interactions with chain R Hydrophobic interactions: U:F.159, U:F.329 Hydrogen bonds: R:R.185, R: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

oligomycin sensitivity conferring protein (OSCP): A
subunit d: B
subunit c: C
subunit gamma: D
subunit delta: E
subunit epsilon: F
subunit c: GHIJKLMNOP
subunit alpha: QRS
subunit beta: TUV
p18: WXY
inhibitor of F1 (IF1): Z

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
M

B
h

C
c

D
G

E
H

F
I

G
O

H
P

I
Q

J
R

K
S

L
T

M
U

N
V

O
W

P
X

Q
B

R
C

S
A

T
E

U
F

V
D

W
K

X
L

Y
J

Z
N

Membrane

We predict this structure to be a membrane protein.
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oligomycin sensitivity conferring protein (OSCP)

subunit d

subunit c

subunit gamma

subunit delta

subunit epsilon

subunit c

subunit alpha

subunit beta

p18

inhibitor of F1 (IF1)

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