SMTL ID : 7uxh.1

cryo-EM structure of the mTORC1-TFEB-Rag-Ragulator complex

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

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

Ligands

2 x IHP: INOSITOL HEXAKISPHOSPHATE(Non-covalent)

IHP.1: 9 residues within 4Å: Chain A: K.1655, S.1658, K.1662, Y.1698, K.1702, R.1749, K.1753, W.1786, K.1788 13 PLIP interactions: 13 interactions with chain A Hydrogen bonds: A:S.1658, A:S.1658, A:K.1662, A:Y.1698 Salt bridges: A:K.1655, A:K.1662, A:K.1662, A:K.1702, A:K.1702, A:K.1706, A:R.1749, A:K.1753, A:K.1788 IHP.2: 9 residues within 4Å: Chain C: K.1655, S.1658, K.1662, Y.1698, K.1702, R.1749, K.1753, W.1786, K.1788 11 PLIP interactions: 11 interactions with chain C Hydrogen bonds: C:S.1658, C:S.1658, C:Y.1698 Salt bridges: C:K.1655, C:K.1662, C:K.1702, C:K.1702, C:K.1706, C:R.1749, C:K.1753, C:K.1788

4 x GTP: GUANOSINE-5'-TRIPHOSPHATE(Non-covalent)

GTP.3: 23 residues within 4Å: Chain F: K.15, S.16, G.17, S.18, G.19, K.20, T.21, S.22, T.36, R.37, L.39, A.41, T.42, G.64, G.65, H.127, K.128, D.130, L.131, S.163, I.164, W.165 Ligands: MG.4 20 PLIP interactions: 20 interactions with chain F Hydrogen bonds: F:G.17, F:S.18, F:G.19, F:K.20, F:T.21, F:S.22, F:S.22, F:T.42, F:T.42, F:T.42, F:G.65, F:K.128, F:S.163, F:S.163, F:I.164, F:W.165 Salt bridges: F:K.20, F:K.20, F:D.130 pi-Cation interactions: F:K.128 GTP.6: 28 residues within 4Å: Chain M: K.15, S.16, G.17, S.18, G.19, K.20, T.21, S.22, T.36, R.37, L.39, G.40, A.41, T.42, C.63, G.64, G.65, L.66, H.127, K.128, D.130, L.131, S.163, I.164, W.165 Chain T: R.13, Q.17 Ligands: MG.7 19 PLIP interactions: 19 interactions with chain M Hydrogen bonds: M:G.17, M:S.18, M:G.19, M:K.20, M:T.21, M:S.22, M:S.22, M:T.42, M:G.65, M:H.127, M:K.128, M:S.163, M:I.164, M:W.165 Salt bridges: M:K.20, M:K.20, M:D.130 pi-Stacking: M:W.165 pi-Cation interactions: M:K.128 GTP.9: 24 residues within 4Å: Chain V: K.15, S.16, G.17, S.18, G.19, K.20, T.21, S.22, T.36, R.37, L.39, G.40, A.41, T.42, G.64, G.65, H.127, K.128, D.130, L.131, S.163, I.164, W.165 Ligands: MG.10 18 PLIP interactions: 18 interactions with chain V Hydrogen bonds: V:S.16, V:G.17, V:S.18, V:G.19, V:K.20, V:T.21, V:S.22, V:S.22, V:T.42, V:G.65, V:K.128, V:S.163, V:S.163, V:I.164, V:W.165 Salt bridges: V:K.20, V:K.20, V:D.130 GTP.12: 27 residues within 4Å: Chain 2: K.15, S.16, G.17, S.18, G.19, K.20, T.21, S.22, T.36, R.37, L.39, G.40, A.41, T.42, C.63, G.64, G.65, H.127, K.128, D.130, L.131, S.163, I.164, W.165 Chain 9: R.13, Q.17 Ligands: MG.13 20 PLIP interactions: 20 interactions with chain 2 Hydrogen bonds: 2:G.17, 2:S.18, 2:G.19, 2:K.20, 2:T.21, 2:S.22, 2:S.22, 2:T.42, 2:G.65, 2:H.127, 2:K.128, 2:S.163, 2:S.163, 2:I.164, 2:W.165 Salt bridges: 2:K.20, 2:K.20, 2:D.130 pi-Stacking: 2:W.165 pi-Cation interactions: 2:K.128

4 x MG: MAGNESIUM ION(Non-covalent)

MG.4: 5 residues within 4Å: Chain F: K.20, T.21, T.42, D.62 Ligands: GTP.3 1 PLIP interactions: 1 interactions with chain F Metal complexes: F:D.62 MG.7: 5 residues within 4Å: Chain M: K.20, T.21, T.42, D.62 Ligands: GTP.6 No protein-ligand interaction detected (PLIP) MG.10: 5 residues within 4Å: Chain V: K.20, T.21, T.42, D.62 Ligands: GTP.9 No protein-ligand interaction detected (PLIP) MG.13: 5 residues within 4Å: Chain 2: K.20, T.21, T.42, D.62 Ligands: GTP.12 1 PLIP interactions: 1 interactions with chain 2 Metal complexes: 2:T.42

4 x GDP: GUANOSINE-5'-DIPHOSPHATE(Non-covalent)

GDP.5: 16 residues within 4Å: Chain E: P.934, E.935 Chain G: L.69, R.70, R.71, S.72, G.73, K.74, N.75, S.76, H.178, K.179, D.181, S.219, I.220, Y.221 17 PLIP interactions: 16 interactions with chain G, 1 interactions with chain E Hydrogen bonds: G:L.69, G:R.71, G:R.71, G:S.72, G:S.72, G:G.73, G:K.74, G:N.75, G:S.76, G:S.76, G:K.179, G:K.179, G:I.220, G:Y.221 Salt bridges: G:K.74, G:D.181, E:E.935 GDP.8: 17 residues within 4Å: Chain N: L.69, R.70, R.71, S.72, G.73, K.74, N.75, S.76, Q.147, H.178, K.179, D.181, S.219, I.220, Y.221 Chain T: Q.18, R.22 20 PLIP interactions: 18 interactions with chain N, 2 interactions with chain T Hydrogen bonds: N:L.69, N:R.71, N:S.72, N:S.72, N:G.73, N:K.74, N:N.75, N:S.76, N:S.76, N:Q.147, N:H.178, N:K.179, N:I.220, T:Q.18, T:Q.18 Salt bridges: N:R.70, N:R.71, N:R.71, N:K.74, N:D.181 GDP.11: 17 residues within 4Å: Chain U: P.934, E.935 Chain W: L.69, R.70, R.71, S.72, G.73, K.74, N.75, S.76, Q.147, H.178, K.179, D.181, S.219, I.220, Y.221 15 PLIP interactions: 14 interactions with chain W, 1 interactions with chain U Hydrogen bonds: W:R.71, W:R.71, W:S.72, W:S.72, W:G.73, W:K.74, W:N.75, W:S.76, W:K.179, W:I.220, W:Y.221 Salt bridges: W:K.74, W:D.181, U:E.935 pi-Stacking: W:Y.221 GDP.14: 18 residues within 4Å: Chain 3: L.69, R.70, R.71, S.72, G.73, K.74, N.75, S.76, Q.147, H.178, K.179, D.181, S.219, I.220, Y.221 Chain 9: E.14, Q.18, R.22 23 PLIP interactions: 20 interactions with chain 3, 3 interactions with chain 9 Hydrogen bonds: 3:L.69, 3:R.71, 3:R.71, 3:R.71, 3:S.72, 3:S.72, 3:G.73, 3:K.74, 3:N.75, 3:S.76, 3:Q.147, 3:K.179, 3:I.220, 3:Y.221, 9:E.14, 9:Q.18, 9:Q.18 Salt bridges: 3:R.71, 3:R.71, 3:K.74, 3:D.181 pi-Stacking: 3:Y.221 pi-Cation interactions: 3:K.179

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Cui, Z. et al., Structure of the lysosomal mTORC1-TFEB-Rag-Ragulator megacomplex. Nature (2023)

Release Date

2022-11-30

Peptides

Serine/threonine-protein kinase mTOR: AC
Target of rapamycin complex subunit LST8: BD
Regulatory-associated protein of mTOR: EU
Ras-related GTP-binding protein A: FMV2
Ras-related GTP-binding protein C: GNW3
Ragulator complex protein LAMTOR1: HOX4
Ragulator complex protein LAMTOR2: IPY5
Ragulator complex protein LAMTOR3: JQZ6
Ragulator complex protein LAMTOR4: KR07
Ragulator complex protein LAMTOR5: LS18
Transcription factor EB: T9

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
C

B
B

D
D

E
E

U
U

F
F

M
M

V
V

2
c

G
G

N
N

W
W

3
d

H
H

O
O

X
X

4
e

I
I

P
P

Y
Y

5
f

J
J

Q
Q

Z
Z

6
g

K
K

R
R

0
a

7
h

L
L

S
S

1
b

8
i

T
T

9
j

Serine/threonine-protein kinase mTOR

Target of rapamycin complex subunit LST8

Regulatory-associated protein of mTOR

Ras-related GTP-binding protein A

Ras-related GTP-binding protein C

Ragulator complex protein LAMTOR1

Ragulator complex protein LAMTOR2

Ragulator complex protein LAMTOR3

Ragulator complex protein LAMTOR4

Ragulator complex protein LAMTOR5

Transcription factor EB

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