SMTL ID : 9ed4.1

A composite map of mTORC1-Rag-Ragultor-4EBP1 on membrane

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

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

Ligands

2 x GSP: 5'-GUANOSINE-DIPHOSPHATE-MONOTHIOPHOSPHATE(Non-covalent)

GSP.1: 24 residues within 4Å: Chain B: Y.14, R.15, S.16, V.17, G.18, K.19, S.20, S.21, F.31, D.33, Y.35, P.37, T.38, D.60, A.62, G.63, N.119, K.120, D.122, L.123, S.149, A.150, K.151 Ligands: MG.2 19 PLIP interactions: 19 interactions with chain B Hydrogen bonds: B:Y.14, B:S.16, B:V.17, B:K.19, B:K.19, B:S.20, B:S.20, B:S.21, B:D.33, B:Y.35, B:P.37, B:T.38, B:G.63, B:N.119, B:K.120, B:A.150 Salt bridges: B:K.19, B:D.122 pi-Cation interactions: B:K.120 GSP.10: 24 residues within 4Å: Chain N: Y.14, R.15, S.16, V.17, G.18, K.19, S.20, S.21, F.31, D.33, Y.35, P.37, T.38, D.60, A.62, G.63, N.119, K.120, D.122, L.123, S.149, A.150, K.151 Ligands: MG.11 17 PLIP interactions: 17 interactions with chain N Hydrogen bonds: N:S.16, N:V.17, N:K.19, N:K.19, N:S.20, N:S.20, N:S.21, N:D.33, N:Y.35, N:T.38, N:G.63, N:N.119, N:K.120, N:A.150 Salt bridges: N:K.19, N:D.122 pi-Cation interactions: N:K.120

8 x MG: MAGNESIUM ION(Non-covalent)(Non-functional Binders)

MG.2: 6 residues within 4Å: Chain B: K.19, S.20, P.37, T.38, D.60 Ligands: GSP.1 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:S.20, B:T.38 MG.4: 3 residues within 4Å: Chain C: S.2165 Ligands: ANP.3, MG.5 No protein-ligand interaction detected (PLIP) MG.5: 7 residues within 4Å: Chain C: K.2187, H.2340, N.2343, I.2356, D.2357 Ligands: ANP.3, MG.4 No protein-ligand interaction detected (PLIP) MG.8: 7 residues within 4Å: Chain D: K.20, T.21, A.41, T.42, D.62, G.64 Ligands: GTP.7 No protein-ligand interaction detected (PLIP) MG.11: 6 residues within 4Å: Chain N: K.19, S.20, P.37, T.38, D.60 Ligands: GSP.10 2 PLIP interactions: 2 interactions with chain N Metal complexes: N:S.20, N:T.38 MG.13: 3 residues within 4Å: Chain O: S.2165 Ligands: ANP.12, MG.14 No protein-ligand interaction detected (PLIP) MG.14: 7 residues within 4Å: Chain O: K.2187, H.2340, N.2343, I.2356, D.2357 Ligands: ANP.12, MG.13 No protein-ligand interaction detected (PLIP) MG.17: 7 residues within 4Å: Chain P: K.20, T.21, A.41, T.42, D.62, G.64 Ligands: GTP.16 No protein-ligand interaction detected (PLIP)

2 x ANP: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER(Non-covalent)

ANP.3: 21 residues within 4Å: Chain C: I.2163, S.2165, K.2166, Q.2167, P.2169, L.2185, K.2187, Y.2225, I.2237, G.2238, W.2239, V.2240, T.2245, H.2340, S.2342, N.2343, M.2345, I.2356, D.2357 Ligands: MG.4, MG.5 8 PLIP interactions: 8 interactions with chain C Hydrogen bonds: C:S.2165, C:Q.2167, C:K.2187, C:G.2238, C:V.2240, C:H.2340, C:D.2357 Salt bridges: C:K.2187 ANP.12: 21 residues within 4Å: Chain O: I.2163, S.2165, K.2166, Q.2167, P.2169, L.2185, K.2187, Y.2225, I.2237, G.2238, W.2239, V.2240, T.2245, H.2340, S.2342, N.2343, M.2345, I.2356, D.2357 Ligands: MG.13, MG.14 8 PLIP interactions: 8 interactions with chain O Hydrogen bonds: O:S.2165, O:Q.2167, O:K.2187, O:G.2238, O:V.2240, O:H.2340, O:D.2357 Salt bridges: O:K.2187

2 x IHP: INOSITOL HEXAKISPHOSPHATE(Non-covalent)

IHP.6: 10 residues within 4Å: Chain C: K.1655, S.1658, K.1662, Y.1698, K.1702, R.1749, K.1753, W.1786, K.1788, P.2213 13 PLIP interactions: 13 interactions with chain C Hydrogen bonds: C:Y.1698 Salt bridges: C:R.1628, C:K.1655, C:K.1655, C:K.1655, C:K.1702, C:K.1702, C:K.1702, C:R.1749, C:R.1749, C:K.1753, C:K.1753, C:K.1788 IHP.15: 10 residues within 4Å: Chain O: K.1655, S.1658, K.1662, Y.1698, K.1702, R.1749, K.1753, W.1786, K.1788, P.2213 13 PLIP interactions: 13 interactions with chain O Hydrogen bonds: O:Y.1698 Salt bridges: O:R.1628, O:K.1655, O:K.1655, O:K.1655, O:K.1702, O:K.1702, O:K.1702, O:R.1749, O:R.1749, O:K.1753, O:K.1753, O:K.1788

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

GTP.7: 24 residues within 4Å: Chain D: 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.8 20 PLIP interactions: 20 interactions with chain D Hydrogen bonds: D:K.15, D:G.17, D:S.18, D:G.19, D:K.20, D:T.21, D:S.22, D:S.22, D:G.40, D:T.42, D:G.65, D:H.127, D:K.128, D:K.128, D:S.163, D:I.164, D:W.165 Salt bridges: D:K.20, D:K.20, D:D.130 GTP.16: 24 residues within 4Å: Chain P: 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.17 20 PLIP interactions: 20 interactions with chain P Hydrogen bonds: P:K.15, P:G.17, P:S.18, P:G.19, P:K.20, P:T.21, P:S.22, P:S.22, P:G.40, P:T.42, P:G.65, P:H.127, P:K.128, P:K.128, P:S.163, P:I.164, P:W.165 Salt bridges: P:K.20, P:K.20, P:D.130

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

GDP.9: 16 residues within 4Å: Chain I: P.934, E.935 Chain J: 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 22 PLIP interactions: 21 interactions with chain J, 1 interactions with chain I Hydrogen bonds: J:L.69, J:R.71, J:R.71, J:R.71, J:S.72, J:S.72, J:G.73, J:K.74, J:N.75, J:S.76, J:S.76, J:K.179, J:K.179, J:I.220, J:Y.221, J:Y.221 Salt bridges: J:R.71, J:K.74, J:D.181, I:E.935 pi-Stacking: J:Y.221 pi-Cation interactions: J:K.179 GDP.18: 16 residues within 4Å: Chain U: P.934, E.935 Chain V: 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 22 PLIP interactions: 21 interactions with chain V, 1 interactions with chain U Hydrogen bonds: V:L.69, V:R.71, V:R.71, V:S.72, V:S.72, V:G.73, V:K.74, V:N.75, V:S.76, V:S.76, V:K.179, V:K.179, V:I.220, V:Y.221, V:Y.221 Salt bridges: V:R.71, V:R.71, V:K.74, V:D.181, U:E.935 pi-Stacking: V:Y.221 pi-Cation interactions: V:K.179

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Cui, Z. et al., Structural basis for growth factor and nutrient signal integration on the lysosomal membrane by mTORC1. To Be Published

Release Date

2025-09-10

Peptides

Target of rapamycin complex subunit LST8: AM
GTP-binding protein Rheb: BN
Serine/threonine-protein kinase mTOR: CO
Ras-related GTP-binding protein A: DP
Ragulator complex protein LAMTOR2: EQ
Ragulator complex protein LAMTOR3: FR
Ragulator complex protein LAMTOR5: GS
Eukaryotic translation initiation factor 4E-binding protein 1: HT
Regulatory-associated protein of mTOR: IU
Ras-related GTP-binding protein C: JV
Ragulator complex protein LAMTOR1: KW
Ragulator complex protein LAMTOR4: LX

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

M
M

B
L

N
N

C
A

O
O

D
D

P
P

E
G

Q
Q

F
H

R
R

G
J

S
S

H
K

T
T

I
C

U
U

J
E

V
V

K
F

W
W

L
I

X
X

Target of rapamycin complex subunit LST8

GTP-binding protein Rheb

Serine/threonine-protein kinase mTOR

Ras-related GTP-binding protein A

Ragulator complex protein LAMTOR2

Ragulator complex protein LAMTOR3

Ragulator complex protein LAMTOR5

Eukaryotic translation initiation factor 4E-binding protein 1

Regulatory-associated protein of mTOR

Ras-related GTP-binding protein C

Ragulator complex protein LAMTOR1

Ragulator complex protein LAMTOR4

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