SMTL ID : 4b2q.1

Model of the yeast F1Fo-ATP synthase dimer based on subtomogram average

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY 37.00 Å

Oligo State

hetero-4-2-2-4-2-2-2-20-2-2-2-2-mer

Ligands

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

ATP.1: 14 residues within 4Å: Chain A: Q.149, T.150, G.151, K.152, T.153, A.154, E.305, F.334, R.339, P.340, Q.407, Q.409 Chain D: S.350 Ligands: MG.2 12 PLIP interactions: 11 interactions with chain A, 1 interactions with chain D Hydrogen bonds: A:Q.149, A:T.150, A:G.151, A:K.152, A:T.153, A:A.154, A:Q.407, A:Q.409, D:S.350 Salt bridges: A:K.152, A:K.152 pi-Stacking: A:F.334 ATP.3: 13 residues within 4Å: Chain B: Q.150, T.151, G.152, K.153, T.154, A.155, F.335, R.340, P.341, Q.408, N.409, Q.410 Ligands: MG.4 10 PLIP interactions: 10 interactions with chain B Hydrogen bonds: B:T.151, B:G.152, B:K.153, B:T.154, B:A.155, B:R.340, B:Q.408, B:Q.410 Salt bridges: B:K.153, B:K.153 ATP.5: 13 residues within 4Å: Chain C: Q.149, T.150, G.151, K.152, T.153, A.154, F.334, R.339, Q.407, Q.409 Chain F: S.350, Y.363 Ligands: MG.6 12 PLIP interactions: 11 interactions with chain C, 1 interactions with chain F Hydrogen bonds: C:Q.149, C:Q.149, C:T.150, C:T.150, C:G.151, C:K.152, C:T.153, C:A.154, C:Q.407, F:S.350 Salt bridges: C:K.152, C:K.152 ATP.11: 13 residues within 4Å: Chain 0: S.350 Chain X: Q.149, T.150, G.151, K.152, T.153, A.154, E.305, F.334, P.340, Q.407, Q.409 Ligands: MG.12 12 PLIP interactions: 11 interactions with chain X, 1 interactions with chain 0 Hydrogen bonds: X:Q.149, X:T.150, X:G.151, X:K.152, X:T.153, X:A.154, X:Q.407, X:Q.409, 0:S.350 Salt bridges: X:K.152, X:K.152 pi-Stacking: X:F.334 ATP.13: 13 residues within 4Å: Chain Y: Q.150, T.151, G.152, K.153, T.154, A.155, F.335, R.340, P.341, Q.408, N.409, Q.410 Ligands: MG.14 10 PLIP interactions: 10 interactions with chain Y Hydrogen bonds: Y:T.151, Y:G.152, Y:K.153, Y:T.154, Y:A.155, Y:R.340, Y:Q.408, Y:Q.410 Salt bridges: Y:K.153, Y:K.153 ATP.15: 13 residues within 4Å: Chain 2: S.350, Y.363 Chain Z: Q.149, T.150, G.151, K.152, T.153, A.154, F.334, R.339, Q.407, Q.409 Ligands: MG.16 13 PLIP interactions: 12 interactions with chain Z, 1 interactions with chain 2 Hydrogen bonds: Z:Q.149, Z:Q.149, Z:T.150, Z:T.150, Z:G.151, Z:K.152, Z:T.153, Z:T.153, Z:A.154, Z:Q.407, 2:S.350 Salt bridges: Z:K.152, Z:K.152

10 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 4 residues within 4Å: Chain A: T.153, Q.185, D.246 Ligands: ATP.1 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:T.153 MG.4: 4 residues within 4Å: Chain B: K.153, T.154, D.247 Ligands: ATP.3 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:T.154 MG.6: 3 residues within 4Å: Chain C: T.153, D.246 Ligands: ATP.5 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:T.153 MG.8: 5 residues within 4Å: Chain D: T.159, E.184, R.185, E.188 Ligands: ADP.7 1 PLIP interactions: 1 interactions with chain D Metal complexes: D:T.159 MG.10: 4 residues within 4Å: Chain F: T.159, E.184, D.251 Ligands: ADP.9 2 PLIP interactions: 2 interactions with chain F Metal complexes: F:T.159, F:E.184 MG.12: 4 residues within 4Å: Chain X: T.153, Q.185, D.246 Ligands: ATP.11 1 PLIP interactions: 1 interactions with chain X Metal complexes: X:T.153 MG.14: 4 residues within 4Å: Chain Y: K.153, T.154, D.247 Ligands: ATP.13 1 PLIP interactions: 1 interactions with chain Y Metal complexes: Y:T.154 MG.16: 3 residues within 4Å: Chain Z: T.153, D.246 Ligands: ATP.15 1 PLIP interactions: 1 interactions with chain Z Metal complexes: Z:T.153 MG.18: 5 residues within 4Å: Chain 0: T.159, E.184, R.185, E.188 Ligands: ADP.17 1 PLIP interactions: 1 interactions with chain 0 Metal complexes: 0:T.159 MG.20: 4 residues within 4Å: Chain 2: T.159, E.184, D.251 Ligands: ADP.19 2 PLIP interactions: 2 interactions with chain 2 Metal complexes: 2:T.159, 2:E.184

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

ADP.7: 14 residues within 4Å: Chain C: S.349, R.350 Chain D: G.153, A.154, G.155, V.156, G.157, K.158, T.159, V.160, Y.340, F.413, T.420 Ligands: MG.8 12 PLIP interactions: 9 interactions with chain D, 3 interactions with chain C Hydrogen bonds: D:G.153, D:G.155, D:V.156, D:G.157, D:K.158, D:T.159, D:T.159, D:V.160, C:R.350 Salt bridges: D:K.158, C:R.350, C:R.350 ADP.9: 14 residues within 4Å: Chain B: V.349, S.350, R.351 Chain F: G.155, V.156, G.157, K.158, T.159, V.160, Y.340, F.413, F.419, T.420 Ligands: MG.10 10 PLIP interactions: 3 interactions with chain B, 7 interactions with chain F Hydrogen bonds: B:S.350, F:G.155, F:V.156, F:G.157, F:K.158, F:T.159, F:V.160 Salt bridges: B:R.351, B:R.351, F:K.158 ADP.17: 14 residues within 4Å: Chain 0: G.153, A.154, G.155, V.156, G.157, K.158, T.159, V.160, Y.340, F.413, T.420 Chain Z: S.349, R.350 Ligands: MG.18 12 PLIP interactions: 9 interactions with chain 0, 3 interactions with chain Z Hydrogen bonds: 0:G.153, 0:G.155, 0:V.156, 0:G.157, 0:K.158, 0:T.159, 0:T.159, 0:V.160, Z:R.350 Salt bridges: 0:K.158, Z:R.350, Z:R.350 ADP.19: 14 residues within 4Å: Chain 2: G.155, V.156, G.157, K.158, T.159, V.160, Y.340, F.413, F.419, T.420 Chain Y: V.349, S.350, R.351 Ligands: MG.20 10 PLIP interactions: 3 interactions with chain Y, 7 interactions with chain 2 Hydrogen bonds: Y:S.350, 2:G.155, 2:V.156, 2:G.157, 2:K.158, 2:T.159, 2:V.160 Salt bridges: Y:R.351, Y:R.351, 2:K.158

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Davies, K.M. et al., Structure of the Yeast F1Fo-ATP Synthase Dimer and its Role in Shaping the Mitochondrial Cristae. Proc.Natl.Acad.Sci.USA (2012)

Release Date

2012-08-29

Peptides

ATP SYNTHASE SUBUNIT ALPHA, MITOCHONDRIAL: ACXZ
ATP SYNTHASE SUBUNIT ALPHA, MITOCHONDRIAL: BY
ATP SYNTHASE SUBUNIT BETA, MITOCHONDRIAL: D0
ATP SYNTHASE SUBUNIT BETA, MITOCHONDRIAL: EF12
ATP SYNTHASE SUBUNIT GAMMA, MITOCHONDRIAL: G3
ATP SYNTHASE SUBUNIT DELTA, MITOCHONDRIAL: H4
ATP SYNTHASE SUBUNIT EPSILON, MITOCHONDRIAL: I5
ATP SYNTHASE SUBUNIT 9, MITOCHONDRIAL: JKLMNOPQRS6789abcdef
ATP SYNTHASE SUBUNIT B, MITOCHONDRIAL: Tg
ATP SYNTHASE SUBUNIT D, MITOCHONDRIAL: Uh
ATP SYNTHASE-COUPLING FACTOR 6, MITOCHONDRIAL: Vi
ATP SYNTHASE SUBUNIT O, MITOCHONDRIAL: Wj

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
C

X
a

Z
c

B
B

Y
b

D
D

0
d

E
E

F
F

1
e

2
f

G
G

3
g

H
H

4
h

I
I

5
i

J
J

K
K

L
L

M
M

N
N

O
O

P
P

Q
Q

R
R

S
S

6
j

7
k

8
l

9
m

a
n

b
o

c
p

d
q

e
r

f
s

T
T

g
t

U
U

h
u

V
V

i
v

W
W

j
w

Membrane

We predict this structure to be a membrane protein.
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ATP SYNTHASE SUBUNIT ALPHA, MITOCHONDRIAL

ATP SYNTHASE SUBUNIT ALPHA, MITOCHONDRIAL

ATP SYNTHASE SUBUNIT BETA, MITOCHONDRIAL

ATP SYNTHASE SUBUNIT BETA, MITOCHONDRIAL

ATP SYNTHASE SUBUNIT GAMMA, MITOCHONDRIAL

ATP SYNTHASE SUBUNIT DELTA, MITOCHONDRIAL

ATP SYNTHASE SUBUNIT EPSILON, MITOCHONDRIAL

ATP SYNTHASE SUBUNIT 9, MITOCHONDRIAL

ATP SYNTHASE SUBUNIT B, MITOCHONDRIAL

ATP SYNTHASE SUBUNIT D, MITOCHONDRIAL

ATP SYNTHASE-COUPLING FACTOR 6, MITOCHONDRIAL

ATP SYNTHASE SUBUNIT O, MITOCHONDRIAL

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