SMTL ID : 6j5j.1

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

Coordinates

PDB Format Compare

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: R.170, Q.171, T.172, G.173, K.174, T.175, S.176, F.356, R.361, Q.429, Q.431 Chain D: S.347, R.348, Y.360 Ligands: MG.2 14 PLIP interactions: 3 interactions with chain D, 11 interactions with chain A Hydrogen bonds: D:S.347, D:R.348, A:Q.171, A:Q.171, A:T.172, A:G.173, A:K.174, A:T.175, A:S.176, A:S.176, A:Q.429 Salt bridges: D:R.348, A:K.174, A:K.174 ATP.3: 12 residues within 4Å: Chain B: Q.171, T.172, G.173, K.174, T.175, S.176, F.356, R.361, Q.429, Q.431 Chain E: D.351 Ligands: MG.4 12 PLIP interactions: 10 interactions with chain B, 2 interactions with chain E Hydrogen bonds: B:Q.171, B:T.172, B:G.173, B:K.174, B:T.175, B:S.176, B:S.176, B:Q.429, E:D.351 Salt bridges: B:K.174, B:K.174, E:R.348 ATP.5: 16 residues within 4Å: Chain C: R.170, Q.171, T.172, G.173, K.174, T.175, S.176, F.356, R.361, P.362, Q.429, G.430, Q.431 Chain F: S.347, M.350 Ligands: MG.6 13 PLIP interactions: 11 interactions with chain C, 2 interactions with chain F Hydrogen bonds: C:Q.171, C:Q.171, C:T.172, C:G.173, C:K.174, C:T.175, C:S.176, C:S.176, C:Q.429, F:S.347, F:M.350 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: 2 residues within 4Å: Chain B: T.175 Ligands: ATP.3 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:T.175 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: 5 residues within 4Å: Chain D: T.155, E.180, R.181, E.184 Ligands: ADP.7 2 PLIP interactions: 2 interactions with chain D Metal complexes: D:T.155, D:E.180 MG.10: 2 residues within 4Å: Chain F: T.155 Ligands: ADP.9 1 PLIP interactions: 1 interactions with chain F Metal complexes: F:T.155

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

ADP.7: 12 residues within 4Å: Chain D: A.150, G.151, V.152, G.153, K.154, T.155, V.156, E.184, Y.337, F.410, A.413 Ligands: MG.8 8 PLIP interactions: 8 interactions with chain D Hydrogen bonds: D:G.151, D:V.152, D:G.153, D:K.154, D:T.155, D:T.155, D:V.156 Salt bridges: D:K.154 ADP.9: 14 residues within 4Å: Chain B: R.372 Chain F: A.150, G.151, V.152, G.153, K.154, T.155, V.156, E.184, Y.337, F.410, A.413, F.416 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.151, F:V.152, F:G.153, F:K.154, F:T.155, F:V.156, F:E.184 Salt bridges: B:R.372, F:K.154 pi-Stacking: F:Y.337, F:Y.337

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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