SMTL ID : 7uxc.1

cryo-EM structure of the mTORC1-TFEB-Rag-Ragulator complex with symmetry expansion

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-1-1-2-2-2-2-2-2-2-1-mer

Ligands

1 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 11 PLIP interactions: 11 interactions with chain A Hydrogen bonds: A:S.1658, A:Y.1698, A:W.1786 Salt bridges: A:K.1655, A:K.1662, A:K.1702, A:K.1702, A:R.1749, A:K.1753, A:K.1788, A:K.1788

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

GTP.2: 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.3 18 PLIP interactions: 18 interactions with chain D Hydrogen bonds: D:S.16, D:G.17, D:S.18, D:G.19, D:K.20, D:T.21, D:S.22, D:S.22, D:T.42, D:G.65, D:K.128, D:S.163, D:S.163, D:I.164, D:W.165 Salt bridges: D:K.20, D:K.20, D:D.130 GTP.5: 27 residues within 4Å: Chain K: K.15, S.16, G.17, S.18, G.19, K.20, T.21, S.22, T.36, R.37, 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 R: R.13, Q.17 Ligands: MG.6 21 PLIP interactions: 20 interactions with chain K, 1 interactions with chain R Hydrogen bonds: K:G.17, K:S.18, K:G.19, K:K.20, K:T.21, K:S.22, K:S.22, K:T.42, K:G.65, K:H.127, K:K.128, K:S.163, K:S.163, K:I.164, K:W.165, R:Q.17 Salt bridges: K:K.20, K:K.20, K:D.130 pi-Stacking: K:W.165 pi-Cation interactions: K:K.128

2 x MG: MAGNESIUM ION(Non-covalent)

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

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

GDP.4: 17 residues within 4Å: Chain C: P.934, E.935 Chain E: 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 17 PLIP interactions: 16 interactions with chain E, 1 interactions with chain C Hydrogen bonds: E:R.71, E:R.71, E:S.72, E:S.72, E:G.73, E:K.74, E:N.75, E:S.76, E:Q.147, E:K.179, E:I.220, E:Y.221 Salt bridges: E:K.74, E:D.181, C:E.935 pi-Stacking: E:Y.221 pi-Cation interactions: E:K.179 GDP.7: 18 residues within 4Å: Chain L: 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 R: E.14, Q.18, R.22 22 PLIP interactions: 3 interactions with chain R, 19 interactions with chain L Hydrogen bonds: R:E.14, R:Q.18, R:Q.18, L:L.69, L:R.71, L:R.71, L:R.71, L:S.72, L:S.72, L:G.73, L:K.74, L:N.75, L:S.76, L:Q.147, L:K.179, L:I.220 Salt bridges: L:R.71, L:R.71, L:K.74, L:D.181 pi-Stacking: L:Y.221 pi-Cation interactions: L: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: A
Target of rapamycin complex subunit LST8: B
Regulatory-associated protein of mTOR: C
Ras-related GTP-binding protein A: DK
Ras-related GTP-binding protein C: EL
Ragulator complex protein LAMTOR1: FM
Ragulator complex protein LAMTOR2: GN
Ragulator complex protein LAMTOR3: HO
Ragulator complex protein LAMTOR4: IP
Ragulator complex protein LAMTOR5: JQ
Transcription factor EB: R

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

K
K

E
E

L
L

F
F

M
M

G
G

N
N

H
H

O
O

I
I

P
P

J
J

Q
Q

R
R

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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