SMTL ID : 6rd4.1

CryoEM structure of Polytomella F-ATP synthase, Full dimer, composite map

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-2-2-2-2-2-2-2-2-2-2-20-2-2-2-2-2-6-6-mer

Ligands

2 x ZN: ZINC ION(Non-covalent)

ZN.1: 3 residues within 4Å: Chain G: L.105 Chain U: H.248, H.252 3 PLIP interactions: 1 interactions with chain U, 2 Ligand-Water interactions Metal complexes: U:H.248, H2O.1, H2O.1 ZN.12: 3 residues within 4Å: Chain b: L.105 Chain p: H.248, H.252 3 PLIP interactions: 1 interactions with chain p, 2 Ligand-Water interactions Metal complexes: p:H.248, H2O.2, H2O.2

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

ATP.2: 18 residues within 4Å: Chain 2: S.384, R.385, Y.397, R.401 Chain Z: R.227, Q.228, T.229, G.230, K.231, T.232, A.233, E.384, F.413, R.418, P.419, Q.486, Q.488 Ligands: MG.3 18 PLIP interactions: 14 interactions with chain Z, 4 interactions with chain 2 Hydrogen bonds: Z:Q.228, Z:Q.228, Z:T.229, Z:G.230, Z:K.231, Z:T.232, Z:A.233, Z:E.384, Z:E.384, Z:Q.486, Z:Q.488, 2:S.384, 2:R.385, 2:R.385, 2:R.401 Salt bridges: Z:K.231, Z:K.231 pi-Stacking: Z:F.413 ATP.4: 17 residues within 4Å: Chain 0: R.227, Q.228, T.229, G.230, K.231, T.232, A.233, E.384, F.413, R.418, P.419, Q.486, K.487, Q.488 Chain 4: R.385, N.388 Ligands: MG.5 18 PLIP interactions: 15 interactions with chain 0, 3 interactions with chain 4 Hydrogen bonds: 0:D.226, 0:Q.228, 0:T.229, 0:T.229, 0:G.230, 0:K.231, 0:T.232, 0:A.233, 0:R.418, 0:Q.486, 0:Q.488, 0:Q.488, 4:R.385 Salt bridges: 0:K.231, 0:K.231, 4:R.385, 4:R.385 pi-Stacking: 0:F.413 ATP.6: 18 residues within 4Å: Chain 1: D.226, 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: R.385, N.388, Y.397 Ligands: MG.7 19 PLIP interactions: 3 interactions with chain 3, 16 interactions with chain 1 Hydrogen bonds: 3:S.384, 3:N.388, 1:Q.228, 1:Q.228, 1:T.229, 1:T.229, 1:G.230, 1:K.231, 1:T.232, 1:A.233, 1:R.418, 1:Q.486, 1:K.487, 1:Q.488, 1:Q.488 Salt bridges: 3:R.385, 1:K.231, 1:K.231 pi-Stacking: 1:F.413 ATP.13: 18 residues within 4Å: Ligands: MG.14 Chain u: R.227, Q.228, T.229, G.230, K.231, T.232, A.233, E.384, F.413, R.418, P.419, Q.486, Q.488 Chain x: S.384, R.385, Y.397, R.401 18 PLIP interactions: 14 interactions with chain u, 4 interactions with chain x Hydrogen bonds: u:Q.228, u:Q.228, u:T.229, u:G.230, u:K.231, u:T.232, u:A.233, u:E.384, u:E.384, u:Q.486, u:Q.488, x:S.384, x:R.385, x:R.385, x:R.401 Salt bridges: u:K.231, u:K.231 pi-Stacking: u:F.413 ATP.15: 17 residues within 4Å: Ligands: MG.16 Chain v: R.227, Q.228, T.229, G.230, K.231, T.232, A.233, E.384, F.413, R.418, P.419, Q.486, K.487, Q.488 Chain z: R.385, N.388 19 PLIP interactions: 16 interactions with chain v, 3 interactions with chain z Hydrogen bonds: v:D.226, v:Q.228, v:T.229, v:T.229, v:G.230, v:K.231, v:T.232, v:T.232, v:A.233, v:R.418, v:Q.486, v:Q.488, v:Q.488, z:R.385 Salt bridges: v:K.231, v:K.231, z:R.385, z:R.385 pi-Stacking: v:F.413 ATP.17: 18 residues within 4Å: Ligands: MG.18 Chain w: D.226, 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 y: R.385, N.388, Y.397 19 PLIP interactions: 16 interactions with chain w, 3 interactions with chain y Hydrogen bonds: w:Q.228, w:Q.228, w:T.229, w:T.229, w:G.230, w:K.231, w:T.232, w:A.233, w:R.418, w:Q.486, w:K.487, w:Q.488, w:Q.488, y:S.384, y:N.388 Salt bridges: w:K.231, w:K.231, y:R.385 pi-Stacking: w:F.413

10 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 3 residues within 4Å: Chain Z: T.232, D.325 Ligands: ATP.2 1 PLIP interactions: 1 interactions with chain Z Metal complexes: Z:T.232 MG.5: 3 residues within 4Å: Chain 0: T.232, 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: 6 residues within 4Å: Chain 3: T.190, E.215, R.216, E.219, D.285 Ligands: ADP.10 1 PLIP interactions: 1 interactions with chain 3 Metal complexes: 3:T.190 MG.14: 3 residues within 4Å: Ligands: ATP.13 Chain u: T.232, D.325 1 PLIP interactions: 1 interactions with chain u Metal complexes: u:T.232 MG.16: 3 residues within 4Å: Ligands: ATP.15 Chain v: T.232, D.325 1 PLIP interactions: 1 interactions with chain v Metal complexes: v:T.232 MG.18: 3 residues within 4Å: Ligands: ATP.17 Chain w: T.232, D.325 1 PLIP interactions: 1 interactions with chain w Metal complexes: w:T.232 MG.20: 5 residues within 4Å: Ligands: ADP.19 Chain x: T.190, E.215, R.216, E.219 2 PLIP interactions: 2 interactions with chain x Metal complexes: x:T.190, x:E.215 MG.22: 6 residues within 4Å: Ligands: ADP.21 Chain y: T.190, E.215, R.216, E.219, D.285 1 PLIP interactions: 1 interactions with chain y Metal complexes: y:T.190

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

ADP.8: 16 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, E.219, Y.374, F.447, A.450, F.453, T.454 Ligands: MG.9 12 PLIP interactions: 10 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:V.191, 0:R.429, 0:R.429 Salt bridges: 2:K.189 pi-Stacking: 2:Y.374, 2:Y.374 ADP.10: 14 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, T.454 Chain Z: R.429 Ligands: MG.11 11 PLIP interactions: 9 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:V.191 Salt bridges: 3:K.189, Z:R.429, Z:R.429 pi-Stacking: 3:Y.374, 3:Y.374 ADP.19: 16 residues within 4Å: Ligands: MG.20 Chain v: V.427, R.429 Chain x: A.185, G.186, V.187, G.188, K.189, T.190, V.191, E.219, Y.374, F.447, A.450, F.453, T.454 12 PLIP interactions: 10 interactions with chain x, 2 interactions with chain v Hydrogen bonds: x:G.186, x:V.187, x:G.188, x:K.189, x:T.190, x:T.190, x:V.191, v:R.429, v:R.429 Salt bridges: x:K.189 pi-Stacking: x:Y.374, x:Y.374 ADP.21: 14 residues within 4Å: Ligands: MG.22 Chain u: R.429 Chain y: G.184, G.186, V.187, G.188, K.189, T.190, V.191, Y.374, F.447, A.450, F.453, T.454 11 PLIP interactions: 9 interactions with chain y, 2 interactions with chain u Hydrogen bonds: y:G.186, y:V.187, y:G.188, y:K.189, y:T.190, y:V.191 Salt bridges: y:K.189, u:R.429, u:R.429 pi-Stacking: y:Y.374, y: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: A5
ATP synthase associated protein ASA1: B6
Mitochondrial ATP synthase subunit ASA2: C7
Mitochondrial F1F0 ATP synthase associated 32 kDa protein: D8
Mitochondrial ATP synthase associated protein ASA4: E9
Mitochondrial F1F0 ATP synthase associated 14 kDa protein: Fa
Mitochondrial ATP synthase subunit ASA6: Gb
Mitochondrial ATP synthase associated protein ASA7: Hc
Mitochondrial ATP synthase subunit ASA8: Id
Mitochondrial ATP synthase subunit ASA9: Je
Mitochondrial ATP synthase subunit c: KLMNOPQRSTfghijklmno
Mitochondrial ATP synthase subunit 6: Up
Mitochondrial ATP synthase subunit OSCP: Vq
epsilon: Polytomella F-ATP synthase epsilon subunit: Wr
Mitochondrial ATP synthase subunit delta: Xs
ATP synthase gamma chain, mitochondrial: Yt
ATP synthase subunit alpha: Z01uvw
ATP synthase subunit beta: 234xyz

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
0

5
0

B
1

6
1

C
2

7
2

D
3

8
3

E
4

9
4

F
5

a
5

G
6

b
6

H
7

c
7

I
8

d
8

J
9

e
9

K
A

L
B

M
C

N
D

O
E

P
F

Q
G

R
H

S
I

T
J

f
A

g
B

h
C

i
D

j
E

k
F

l
G

m
H

n
I

o
J

U
M

p
M

V
P

q
P

W
Q

r
Q

X
R

s
R

Y
S

t
S

Z
T

0
U

1
V

u
T

v
U

w
V

2
X

3
Y

4
Z

x
X

y
Y

z
Z

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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