SMTL ID : 6j5i.1

Cryo-EM structure of the mammalian DP-state ATP synthase

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-3-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-8-1-mer

Ligands

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

ATP.1: 15 residues within 4Å: Chain A: Q.171, T.172, G.173, K.174, T.175, S.176, F.356, R.361, P.362, Q.429, Q.431 Chain D: S.357, R.358, M.360 Ligands: MG.2 10 PLIP interactions: 1 interactions with chain D, 9 interactions with chain A Hydrogen bonds: D:S.357, A:Q.171, A:T.172, A:G.173, A:K.174, A:T.175, A:Q.429, A:Q.431 Salt bridges: A:K.174, A:K.174 ATP.3: 15 residues within 4Å: Chain B: R.170, Q.171, T.172, G.173, K.174, T.175, S.176, E.327, F.356, R.361, Q.429, Q.431 Chain E: R.358, D.361 Ligands: MG.4 16 PLIP interactions: 12 interactions with chain B, 4 interactions with chain E Hydrogen bonds: B:Q.171, B:T.172, B:G.173, B:K.174, B:T.175, B:T.175, B:S.176, B:E.327, B:R.361, B:Q.429, E:R.358, E:R.358, E:D.361 Salt bridges: B:K.174, B:K.174, E:R.358 ATP.5: 15 residues within 4Å: Chain C: D.169, R.170, Q.171, T.172, G.173, K.174, T.175, S.176, F.356, R.361, G.430, Q.431 Chain F: S.357, R.374 Ligands: MG.6 14 PLIP interactions: 13 interactions with chain C, 1 interactions with chain F Hydrogen bonds: C:Q.171, C:Q.171, C:Q.171, C:T.172, C:G.173, C:K.174, C:T.175, C:T.175, C:S.176, C:S.176, C:Q.431, F:R.374 Salt bridges: C:K.174, C:K.174

5 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 2 residues within 4Å: Chain A: T.175 Ligands: ATP.1 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:T.175 MG.4: 4 residues within 4Å: Chain B: T.175, Q.207, D.268 Ligands: ATP.3 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:T.175, B:D.268 MG.6: 3 residues within 4Å: Chain C: T.175, D.268 Ligands: ATP.5 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:T.175 MG.8: 3 residues within 4Å: Chain D: T.165, E.194 Ligands: ADP.7 1 PLIP interactions: 1 interactions with chain D Metal complexes: D:T.165 MG.10: 2 residues within 4Å: Chain F: T.165 Ligands: ADP.9 No protein-ligand interaction detected (PLIP)

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

ADP.7: 12 residues within 4Å: Chain C: R.372 Chain D: A.160, G.161, V.162, G.163, K.164, T.165, V.166, Y.347, A.423, F.426 Ligands: MG.8 9 PLIP interactions: 9 interactions with chain D Hydrogen bonds: D:G.161, D:V.162, D:G.163, D:K.164, D:T.165, D:V.166, D:E.194 Salt bridges: D:K.164 pi-Stacking: D:F.426 ADP.9: 11 residues within 4Å: Chain B: R.372 Chain F: G.161, V.162, G.163, K.164, T.165, V.166, E.194, Y.347, F.420 Ligands: MG.10 13 PLIP interactions: 3 interactions with chain B, 10 interactions with chain F Hydrogen bonds: B:R.372, B:R.372, F:G.161, F:V.162, F:G.163, F:K.164, F:T.165, F:V.166, F:E.194 Salt bridges: B:R.372, F:K.164 pi-Stacking: F:Y.347, F:Y.347

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Gu, J. et al., Cryo-EM structure of the mammalian ATP synthase tetramer bound with inhibitory protein IF1. Science (2019)

Release Date

2019-06-26

Peptides

ATP synthase subunit alpha, mitochondrial: ABC
ATP synthase subunit beta: DEF
ATPase inhibitor, mitochondrial: G
ATP synthase subunit gamma: H
ATP synthase subunit delta, mitochondrial: I
ATP synthase F1 subunit epsilon: J
ATP synthase subunit O, mitochondrial: K
ATP synthase peripheral stalk-membrane subunit b: L
ATP synthase-coupling factor 6, mitochondrial: M
ATP synthase subunit d, mitochondrial: N
ATP synthase subunit e: O
ATP synthase subunit f, mitochondrial: P
ATP synthase subunit g: Q
ATP synthase membrane subunit DAPIT: R
subunit k analog: S
ATP synthase protein 8: T
ATP synthase subunit a: U
Mitochondrial H+ transporting ATP synthase subunit c isoform 1: VWXYZ012
ATP synthase membrane subunit 6.8PL: 3

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

G
J

H
G

I
H

J
I

K
S

L
b

M
c

N
d

O
e

P
f

Q
g

R
i

S
k

T
8

U
a

V
K

W
L

X
M

Y
N

Z
O

0
P

1
Q

2
R

3
u

ATP synthase subunit alpha, mitochondrial

ATP synthase subunit beta

ATPase inhibitor, mitochondrial

ATP synthase subunit gamma

ATP synthase subunit delta, mitochondrial

ATP synthase F1 subunit epsilon

ATP synthase subunit O, mitochondrial

ATP synthase peripheral stalk-membrane subunit b

ATP synthase-coupling factor 6, mitochondrial

ATP synthase subunit d, mitochondrial

ATP synthase subunit e

ATP synthase subunit f, mitochondrial

ATP synthase subunit g

ATP synthase membrane subunit DAPIT

subunit k analog

ATP synthase protein 8

ATP synthase subunit a

Mitochondrial H+ transporting ATP synthase subunit c isoform 1

ATP synthase membrane subunit 6.8PL

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