SMTL ID : 6rdk.1

Cryo-EM structure of Polytomella F-ATP synthase, Rotary substate 1B, composite map

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

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

Ligands

1 x ZN: ZINC ION(Non-covalent)

ZN.1: 2 residues within 4Å: Chain U: H.248, H.252 2 PLIP interactions: 2 interactions with chain U Metal complexes: U:H.248, U:H.252

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

ATP.2: 20 residues within 4Å: Chain 2: S.384, R.385, L.387, N.388, Y.397 Chain Z: R.227, Q.228, T.229, G.230, K.231, T.232, A.233, D.326, F.413, R.418, P.419, Q.486, K.487, Q.488 Ligands: MG.3 13 PLIP interactions: 9 interactions with chain Z, 4 interactions with chain 2 Hydrogen bonds: Z:Q.228, Z:K.231, Z:T.232, Z:A.233, Z:Q.486, 2:S.384, 2:R.385, 2:N.388 Salt bridges: Z:K.231, Z:K.231, Z:K.329, 2:R.385 pi-Stacking: Z:F.413 ATP.4: 15 residues within 4Å: Chain 0: R.227, Q.228, T.229, G.230, K.231, T.232, A.233, F.413, R.418, Q.486, K.487, Q.488 Chain 4: R.385, N.388 Ligands: MG.5 14 PLIP interactions: 12 interactions with chain 0, 2 interactions with chain 4 Hydrogen bonds: 0:Q.228, 0:Q.228, 0:T.229, 0:G.230, 0:K.231, 0:T.232, 0:A.233, 0:R.418, 0:Q.486, 0:Q.488, 4:R.385 Salt bridges: 0:K.231, 0:K.231, 4:R.385 ATP.6: 18 residues within 4Å: Chain 1: R.227, Q.228, T.229, G.230, K.231, T.232, A.233, F.413, R.418, P.419, Q.486, K.487, Q.488 Chain 3: S.384, R.385, N.388, Y.397 Ligands: MG.7 14 PLIP interactions: 10 interactions with chain 1, 4 interactions with chain 3 Hydrogen bonds: 1:Q.228, 1:G.230, 1:K.231, 1:T.232, 1:A.233, 1:R.418, 1:Q.486, 1:Q.488, 3:S.384, 3:R.385, 3:N.388 Salt bridges: 1:K.231, 1:K.231, 3:R.385

5 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 2 residues within 4Å: Chain Z: T.232 Ligands: ATP.2 1 PLIP interactions: 1 interactions with chain Z Metal complexes: Z:T.232 MG.5: 4 residues within 4Å: Chain 0: T.232, Q.264, D.325 Ligands: ATP.4 1 PLIP interactions: 1 interactions with chain 0 Metal complexes: 0:T.232 MG.7: 3 residues within 4Å: Chain 1: T.232, D.325 Ligands: ATP.6 1 PLIP interactions: 1 interactions with chain 1 Metal complexes: 1:T.232 MG.9: 5 residues within 4Å: Chain 2: T.190, E.215, R.216, E.219 Ligands: ADP.8 2 PLIP interactions: 2 interactions with chain 2 Metal complexes: 2:T.190, 2:E.215 MG.11: 4 residues within 4Å: Chain 3: T.190, E.215, R.216 Ligands: ADP.10 2 PLIP interactions: 2 interactions with chain 3 Metal complexes: 3:T.190, 3:E.215

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

ADP.8: 17 residues within 4Å: Chain 0: V.427, R.429 Chain 2: A.185, G.186, V.187, G.188, K.189, T.190, V.191, R.216, E.219, Y.374, F.447, A.450, F.453, T.454 Ligands: MG.9 14 PLIP interactions: 12 interactions with chain 2, 2 interactions with chain 0 Hydrogen bonds: 2:G.186, 2:V.187, 2:G.188, 2:K.189, 2:T.190, 2:T.190, 2:T.190, 2:V.191, 2:R.216, 0:R.429, 0:R.429 Salt bridges: 2:K.189 pi-Stacking: 2:Y.374, 2:Y.374 ADP.10: 15 residues within 4Å: Chain 3: G.184, G.186, V.187, G.188, K.189, T.190, V.191, Y.374, F.447, A.450, F.453 Chain Z: V.427, S.428, R.429 Ligands: MG.11 13 PLIP interactions: 11 interactions with chain 3, 2 interactions with chain Z Hydrogen bonds: 3:G.186, 3:V.187, 3:G.188, 3:K.189, 3:T.190, 3:T.190, 3:T.190, 3:V.191, Z:R.429 Salt bridges: 3:K.189, Z:R.429 pi-Stacking: 3:Y.374, 3:Y.374

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Murphy, B.J. et al., Rotary substates of mitochondrial ATP synthase reveal the basis of flexible F 1 -F o coupling. Science (2019)

Release Date

2019-07-03

Peptides

ASA-10: Polytomella F-ATP synthase associated subunit 10: A
ATP synthase associated protein ASA1: B
Mitochondrial ATP synthase subunit ASA2: C
Mitochondrial F1F0 ATP synthase associated 32 kDa protein: D
Mitochondrial ATP synthase associated protein ASA4: E
Mitochondrial F1F0 ATP synthase associated 14 kDa protein: F
Mitochondrial ATP synthase subunit ASA6: G
Mitochondrial ATP synthase associated protein ASA7: H
Mitochondrial ATP synthase subunit ASA8: I
Mitochondrial ATP synthase subunit ASA9: J
Mitochondrial ATP synthase subunit c: KLMNOPQRST
Mitochondrial ATP synthase subunit 6: U
Mitochondrial ATP synthase subunit OSCP: V
epsilon: Polytomella F-ATP synthase epsilon subunit: W
Mitochondrial ATP synthase subunit delta: X
ATP synthase gamma chain, mitochondrial: Y
ATP synthase subunit alpha: Z01
ATP synthase subunit beta: 234

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
0

B
1

C
2

D
3

E
4

F
5

G
6

H
7

I
8

J
9

K
A

L
B

M
C

N
D

O
E

P
F

Q
G

R
H

S
I

T
J

U
M

V
P

W
Q

X
R

Y
S

Z
T

0
U

1
V

2
X

3
Y

4
Z

Membrane

We predict this structure to be a membrane protein.
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ASA-10: Polytomella F-ATP synthase associated subunit 10

ATP synthase associated protein ASA1

Mitochondrial ATP synthase subunit ASA2

Mitochondrial F1F0 ATP synthase associated 32 kDa protein

Mitochondrial ATP synthase associated protein ASA4

Mitochondrial F1F0 ATP synthase associated 14 kDa protein

Mitochondrial ATP synthase subunit ASA6

Mitochondrial ATP synthase associated protein ASA7

Mitochondrial ATP synthase subunit ASA8

Mitochondrial ATP synthase subunit ASA9

Mitochondrial ATP synthase subunit c

Mitochondrial ATP synthase subunit 6

Mitochondrial ATP synthase subunit OSCP

epsilon: Polytomella F-ATP synthase epsilon subunit

Mitochondrial ATP synthase subunit delta

ATP synthase gamma chain, mitochondrial

ATP synthase subunit alpha

ATP synthase subunit beta

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