SMTL ID : 6rdp.1

Cryo-EM structure of Polytomella F-ATP synthase, Rotary substate 1C, focussed refinement of F1 head and rotor

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

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

Ligands

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

ATP.1: 20 residues within 4Å: Chain O: 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 R: S.384, R.385, L.387, Y.397, R.401 Ligands: MG.2 14 PLIP interactions: 4 interactions with chain R, 10 interactions with chain O Hydrogen bonds: R:R.385, R:R.385, R:R.401, O:Q.228, O:T.229, O:K.231, O:T.232, O:A.233, O:Q.486, O:Q.488 Salt bridges: R:R.385, O:K.231, O:K.231 pi-Stacking: O:F.413 ATP.3: 15 residues within 4Å: Chain P: R.227, Q.228, T.229, G.230, K.231, T.232, A.233, F.413, R.418, P.419, Q.486, Q.488 Chain T: R.385, N.388 Ligands: MG.4 16 PLIP interactions: 13 interactions with chain P, 3 interactions with chain T Hydrogen bonds: P:Q.228, P:T.229, P:T.229, P:G.230, P:K.231, P:T.232, P:A.233, P:R.418, P:Q.486, P:Q.488, T:R.385, T:N.388 Salt bridges: P:K.231, P:K.231, T:R.385 pi-Stacking: P:F.413 ATP.5: 17 residues within 4Å: Chain Q: D.226, Q.228, T.229, G.230, K.231, T.232, A.233, F.413, R.418, P.419, Q.486, Q.488 Chain S: S.384, R.385, N.388, Y.397 Ligands: MG.6 18 PLIP interactions: 4 interactions with chain S, 14 interactions with chain Q Hydrogen bonds: S:S.384, S:R.385, S:N.388, Q:Q.228, Q:Q.228, Q:T.229, Q:T.229, Q:G.230, Q:K.231, Q:T.232, Q:A.233, Q:R.418, Q:Q.486, Q:Q.488 Salt bridges: S:R.385, Q:K.231, Q:K.231 pi-Stacking: Q:F.413

5 x MG: MAGNESIUM ION(Non-covalent)

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

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

ADP.7: 15 residues within 4Å: Chain P: V.427, R.429 Chain R: A.185, G.186, V.187, G.188, K.189, T.190, V.191, Y.374, F.447, A.450, F.453, T.454 Ligands: MG.8 12 PLIP interactions: 10 interactions with chain R, 2 interactions with chain P Hydrogen bonds: R:G.186, R:V.187, R:G.188, R:K.189, R:T.190, R:T.190, R:V.191, P:R.429, P:R.429 Salt bridges: R:K.189 pi-Stacking: R:Y.374, R:Y.374 ADP.9: 14 residues within 4Å: Chain O: S.428, R.429 Chain S: G.184, A.185, G.186, G.188, K.189, T.190, V.191, Y.374, F.447, A.450, F.453 Ligands: MG.10 10 PLIP interactions: 8 interactions with chain S, 2 interactions with chain O Hydrogen bonds: S:G.186, S:G.188, S:K.189, S:T.190, S:V.191 Salt bridges: S:K.189, O:R.429, O:R.429 pi-Stacking: S:Y.374, S: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

Mitochondrial ATP synthase subunit c: ABCDEFGHIJ
Mitochondrial ATP synthase subunit OSCP: K
epsilon: Polytomella F-ATP synthase epsilon subunit: L
Mitochondrial ATP synthase subunit delta: M
ATP synthase gamma chain, mitochondrial: N
ATP synthase subunit alpha: OPQ
ATP synthase subunit beta: RST

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

G
G

H
H

I
I

J
J

K
P

L
Q

M
R

N
S

O
T

P
U

Q
V

R
X

S
Y

T
Z

Membrane

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

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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