SMTL ID : 6te0.1

Cryo-EM structure of Euglena gracilis mitochondrial ATP synthase, OSCP/F1/c-ring, rotational state 3

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

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

Ligands

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

ATP.1: 21 residues within 4Å: Chain A: R.185, Q.186, T.187, G.188, K.189, T.190, S.191, Q.222, E.342, F.371, R.376, P.377, Q.441, K.442 Chain D: F.329, S.330, R.359, M.361, D.362, Y.371 Ligands: MG.2 13 PLIP interactions: 11 interactions with chain A, 2 interactions with chain D Hydrogen bonds: A:Q.186, A:T.187, A:G.188, A:K.189, A:T.190, A:Q.222, A:Q.222, A:R.376, A:K.442, D:D.362, D:Y.371 Salt bridges: A:K.189, A:K.189 ATP.3: 19 residues within 4Å: Chain B: Y.164, 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, M.361, D.362 Ligands: MG.4, TRT.9 15 PLIP interactions: 14 interactions with chain B, 1 interactions with chain E Hydrogen bonds: 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 ATP.5: 18 residues within 4Å: Chain C: 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 F: S.358, M.361, D.362, Y.371 Ligands: MG.6 13 PLIP interactions: 11 interactions with chain C, 2 interactions with chain F Hydrogen bonds: C:Q.186, 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:M.361, F:D.362 Salt bridges: C:K.189, C:K.189 ATP.10: 23 residues within 4Å: Chain B: S.358, V.385, R.387 Chain F: A.162, G.163, V.164, G.165, K.166, T.167, V.168, E.192, R.193, E.196, N.260, Y.314, Y.348, Q.419, P.420, F.421, A.424, F.427, T.428 Ligands: MG.11 19 PLIP interactions: 15 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, F:N.260, F:F.421, B:S.358, B:S.358 Salt bridges: F:K.166, F:K.166, F:R.193, F:R.193, B:R.387, B:R.387 pi-Stacking: 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: 3 residues within 4Å: Chain B: T.190, Q.222 Ligands: ATP.3 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:T.190 MG.6: 2 residues within 4Å: Chain C: T.190 Ligands: ATP.5 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:T.190 MG.8: 4 residues within 4Å: Chain D: T.167, R.193, E.196 Ligands: ADP.7 3 PLIP interactions: 3 interactions with chain D Metal complexes: D:T.167, D:E.196, D:E.196 MG.11: 5 residues within 4Å: Chain F: 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: 19 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, I.169, R.193, Y.348, F.421, A.424, F.427, T.428 Ligands: MG.8 13 PLIP interactions: 10 interactions with chain D, 3 interactions with chain C Hydrogen bonds: D:G.163, D:V.164, D:G.165, D:K.166, D:T.167, D:T.167, D:V.168, C:S.386 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: 19 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, V.337, E.355, A.357, S.358, R.359 Ligands: ATP.3 3 PLIP interactions: 1 interactions with chain B, 2 interactions with chain E Hydrogen bonds: B:R.185 Hydrophobic interactions: E:F.159, E:I.320

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
Ribonucleoprotein P18: GHI
oligomycin sensitivity conferring protein (OSCP): J
ATP synthase F1 subunit gamma protein: K
ATP synthase subunit delta: L
ATP synthase subunit epsilon: M
ATP synthase subunit c: NOPQRSTUVW

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

B
A

C
B

D
F

E
D

F
E

G
L

H
J

I
K

J
M

K
G

L
H

M
I

N
O

O
P

P
Q

Q
R

R
S

S
T

T
U

U
V

V
W

W
X

Membrane

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

ATP synthase subunit beta

Ribonucleoprotein P18

oligomycin sensitivity conferring protein (OSCP)

ATP synthase F1 subunit gamma protein

ATP synthase subunit delta

ATP synthase subunit epsilon

ATP synthase subunit c

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