SMTL ID : 9io5.1

Cryo-EM structure of G1-ATPase dimer from Mycoplasma mobile gliding machinery

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-6-6-2-3-6-1-1-mer

Ligands

1 x UNK- UNK- UNK- UNK- UNK- UNK- UNK- UNK- UNK: UNKNOWN HELIX(Non-covalent)

UNK-UNK-UNK-UNK-UNK-UNK-UNK-UNK-UNK.1: 9 residues within 4Å: Chain J: H.217, L.220, F.221, L.262, Q.263, S.265, Y.266, E.267, F.268 9 PLIP interactions: 9 interactions with chain J Hydrophobic interactions: J:L.220, J:L.220, J:F.221, J:Y.266, J:Y.266, J:F.268, J:F.268 Hydrogen bonds: J:H.217, J:E.267

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

ATP.2: 20 residues within 4Å: Chain A: G.453, A.454, G.455, V.456, G.457, K.458, T.459, V.460, E.484, R.485, E.488, Y.635, F.708, A.711, F.714 Chain D: I.314, S.315, V.342, R.344 Ligands: MG.3 15 PLIP interactions: 12 interactions with chain A, 3 interactions with chain D Hydrogen bonds: A:G.455, A:V.456, A:G.457, A:K.458, A:T.459, A:V.460, A:E.484 Salt bridges: A:K.458, A:K.458, A:R.485, D:R.344, D:R.344, D:R.344 pi-Stacking: A:Y.635, A:Y.635 ATP.7: 16 residues within 4Å: Chain C: K.646, S.649, K.651 Chain D: R.150, G.151, T.152, G.153, K.154, T.155, A.156, F.328, R.333, Q.401, A.402, E.403 Ligands: MG.8 18 PLIP interactions: 11 interactions with chain D, 7 interactions with chain C Hydrogen bonds: D:G.151, D:T.152, D:T.152, D:G.153, D:K.154, D:T.155, D:A.156, D:Q.299, D:Q.401, C:K.646, C:S.649, C:K.651, C:K.651 Salt bridges: D:K.154, D:K.154, C:K.646, C:K.646, C:K.646 ATP.9: 16 residues within 4Å: Chain A: S.645, K.646 Chain E: R.150, G.151, T.152, G.153, K.154, T.155, A.156, Q.299, F.328, R.333, Q.401, A.402, E.403 Ligands: MG.10 14 PLIP interactions: 10 interactions with chain E, 4 interactions with chain A Hydrogen bonds: E:G.151, E:T.152, E:G.153, E:K.154, E:T.155, E:A.156, E:Q.299, E:Q.401, A:S.645 Salt bridges: E:K.154, E:K.154, A:K.646, A:K.646, A:K.646 ATP.11: 15 residues within 4Å: Chain B: K.646 Chain F: D.149, R.150, G.151, T.152, G.153, K.154, T.155, A.156, F.328, R.333, Q.401, A.402, E.403 Ligands: MG.12 14 PLIP interactions: 11 interactions with chain F, 3 interactions with chain B Hydrogen bonds: F:G.151, F:T.152, F:G.153, F:K.154, F:T.155, F:T.155, F:A.156, F:Q.401, F:E.403, B:K.646 Salt bridges: F:K.154, F:K.154, B:K.646, B:K.646 ATP.13: 17 residues within 4Å: Chain H: G.453, A.454, G.455, V.456, G.457, K.458, T.459, V.460, R.485, Y.635, P.636, F.708, F.714 Chain K: I.314, S.315, R.344 Ligands: MG.14 16 PLIP interactions: 13 interactions with chain H, 3 interactions with chain K Hydrogen bonds: H:G.455, H:V.456, H:G.457, H:K.458, H:T.459, H:T.459, H:T.459, H:V.460 Salt bridges: H:K.458, H:K.458, H:R.485, K:R.344, K:R.344, K:R.344 pi-Stacking: H:Y.635, H:Y.635 ATP.18: 16 residues within 4Å: Chain J: K.646, S.649 Chain K: R.150, G.151, T.152, G.153, K.154, T.155, A.156, Q.299, F.328, R.333, Q.401, A.402, E.403 Ligands: MG.19 14 PLIP interactions: 10 interactions with chain K, 4 interactions with chain J Hydrogen bonds: K:G.151, K:T.152, K:G.153, K:K.154, K:T.155, K:A.156, K:Q.299, K:Q.401, J:S.649 Salt bridges: K:K.154, K:K.154, J:K.646, J:K.646, J:K.646 ATP.20: 18 residues within 4Å: Chain H: S.645, K.646 Chain L: D.149, R.150, G.151, T.152, G.153, K.154, T.155, A.156, Q.299, F.328, R.333, P.334, Q.401, A.402, E.403 Ligands: MG.21 15 PLIP interactions: 4 interactions with chain H, 11 interactions with chain L Hydrogen bonds: H:S.645, L:G.151, L:T.152, L:T.152, L:G.153, L:K.154, L:T.155, L:A.156, L:Q.299, L:Q.401 Salt bridges: H:K.646, H:K.646, H:K.646, L:K.154, L:K.154 ATP.22: 13 residues within 4Å: Chain M: R.150, G.151, T.152, G.153, K.154, T.155, A.156, F.328, R.333, Q.401, A.402, E.403 Ligands: MG.23 11 PLIP interactions: 10 interactions with chain M, 1 interactions with chain I Hydrogen bonds: M:G.151, M:T.152, M:G.153, M:K.154, M:T.155, M:A.156, M:Q.401, I:K.646 Salt bridges: M:K.154, M:K.154 pi-Cation interactions: M:R.333

10 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 4 residues within 4Å: Chain A: T.459, E.484, E.488 Ligands: ATP.2 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:T.459 MG.4: 4 residues within 4Å: Chain B: T.459, D.546 Ligands: ADP.5, PO4.6 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:T.459 MG.8: 3 residues within 4Å: Chain D: T.155, E.183 Ligands: ATP.7 1 PLIP interactions: 1 interactions with chain D Metal complexes: D:T.155 MG.10: 3 residues within 4Å: Chain E: T.155, D.240 Ligands: ATP.9 1 PLIP interactions: 1 interactions with chain E Metal complexes: E:T.155 MG.12: 3 residues within 4Å: Chain F: T.155, E.183 Ligands: ATP.11 1 PLIP interactions: 1 interactions with chain F Metal complexes: F:T.155 MG.14: 3 residues within 4Å: Chain H: T.459, E.484 Ligands: ATP.13 2 PLIP interactions: 2 interactions with chain H Metal complexes: H:T.459, H:E.484 MG.15: 4 residues within 4Å: Chain I: K.458, E.488 Ligands: ADP.16, PO4.17 No protein-ligand interaction detected (PLIP) MG.19: 3 residues within 4Å: Chain K: T.155, D.240 Ligands: ATP.18 1 PLIP interactions: 1 interactions with chain K Metal complexes: K:T.155 MG.21: 2 residues within 4Å: Chain L: T.155 Ligands: ATP.20 1 PLIP interactions: 1 interactions with chain L Metal complexes: L:T.155 MG.23: 4 residues within 4Å: Chain M: T.155, K.179, D.240 Ligands: ATP.22 1 PLIP interactions: 1 interactions with chain M Metal complexes: M:T.155

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

ADP.5: 15 residues within 4Å: Chain B: A.454, G.455, V.456, G.457, K.458, T.459, V.460, Y.635, F.708, A.711, F.714 Chain E: R.344, L.345 Ligands: MG.4, PO4.6 12 PLIP interactions: 10 interactions with chain B, 2 interactions with chain E Hydrogen bonds: B:G.453, B:G.455, B:V.456, B:G.457, B:K.458, B:T.459, B:T.459, B:V.460, E:R.344 Salt bridges: B:K.458, E:R.344 pi-Stacking: B:Y.635 ADP.16: 14 residues within 4Å: Chain I: G.452, G.453, A.454, G.455, V.456, G.457, K.458, T.459, V.460, E.488, Y.635 Chain L: R.344 Ligands: MG.15, PO4.17 9 PLIP interactions: 8 interactions with chain I, 1 interactions with chain L Hydrogen bonds: I:A.454, I:G.455, I:G.457, I:K.458, I:T.459, I:T.459 Salt bridges: I:K.458, L:R.344 pi-Stacking: I:Y.635

2 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.6: 8 residues within 4Å: Chain B: G.453, K.458, R.485, N.547, R.550 Chain E: R.344 Ligands: MG.4, ADP.5 6 PLIP interactions: 5 interactions with chain B, 1 interactions with chain E Hydrogen bonds: B:D.546, B:N.547 Salt bridges: B:K.458, B:R.485, B:R.550, E:R.344 PO4.17: 7 residues within 4Å: Chain I: R.485, D.546, N.547, R.550 Chain L: R.344 Ligands: MG.15, ADP.16 5 PLIP interactions: 4 interactions with chain I, 1 interactions with chain L Hydrogen bonds: I:N.547 Salt bridges: I:K.458, I:R.485, I:R.550, L:R.344

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Toyonaga, T. et al., Dimeric assembly of F 1 -like ATPase for the gliding motility of Mycoplasma. Sci Adv (2025)

Release Date

2025-03-12

Peptides

G1-ATPase subunit beta: ABCHIJ
G1-ATPase subunit alpha: DEFKLM
G1-ATPase subunit gamma: GN
Phosphoglycerate kinase: OPQ
G1-ATPase subunit D: RSTUVW
G1-ATPase subunit E: X
UNKNOWN HELIX: Y

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

H
H

I
I

J
J

D
D

E
E

F
F

K
K

L
L

M
M

G
G

N
N

O
O

P
P

Q
Q

R
R

S
S

T
T

U
U

V
V

W
W

X
X

Y
Y

G1-ATPase subunit beta

G1-ATPase subunit alpha

G1-ATPase subunit gamma

Phosphoglycerate kinase

G1-ATPase subunit D

G1-ATPase subunit E

UNKNOWN HELIX

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