SMTL ID : 7ux2.1

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

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

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

Ligands

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

GTP.1: 26 residues within 4Å: Chain A: K.932 Chain B: 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, L.66, H.127, K.128, D.130, L.131, S.163, I.164, W.165 Ligands: MG.2 19 PLIP interactions: 19 interactions with chain B Hydrogen bonds: B:S.16, B:G.17, B:S.18, B:G.19, B:K.20, B:T.21, B:S.22, B:S.22, B:R.37, B:T.42, B:G.65, B:H.127, B:K.128, B:K.128, B:I.164, B:W.165 Salt bridges: B:K.20, B:K.20, B:D.130 GTP.4: 27 residues within 4Å: Chain I: 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, L.66, H.127, K.128, D.130, L.131, S.163, I.164, W.165 Chain P: R.13, Q.17 Ligands: MG.5 17 PLIP interactions: 17 interactions with chain I Hydrogen bonds: I:K.15, I:G.17, I:S.18, I:S.18, I:G.19, I:K.20, I:T.21, I:S.22, I:T.42, I:G.65, I:H.127, I:K.128, I:K.128, I:I.164 Salt bridges: I:K.20, I:K.20, I:D.130

2 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 5 residues within 4Å: Chain B: T.21, G.40, T.42, D.62 Ligands: GTP.1 No protein-ligand interaction detected (PLIP) MG.5: 5 residues within 4Å: Chain I: T.21, G.40, T.42, D.62 Ligands: GTP.4 No protein-ligand interaction detected (PLIP)

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

GDP.3: 18 residues within 4Å: Chain A: P.934, E.935 Chain C: L.69, R.70, R.71, S.72, G.73, K.74, N.75, S.76, Q.147, H.178, K.179, D.181, G.182, S.219, I.220, Y.221 18 PLIP interactions: 17 interactions with chain C, 1 interactions with chain A Hydrogen bonds: C:R.71, C:S.72, C:S.72, C:G.73, C:K.74, C:N.75, C:S.76, C:S.76, C:Q.147, C:K.179, C:K.179, C:S.219, C:I.220, C:Y.221 Salt bridges: C:K.74, C:D.181, A:E.935 pi-Stacking: C:Y.221 GDP.6: 19 residues within 4Å: Chain J: L.69, R.70, R.71, S.72, G.73, K.74, N.75, S.76, Q.147, H.178, K.179, D.181, G.182, S.219, I.220, Y.221 Chain P: E.14, Q.18, R.22 21 PLIP interactions: 19 interactions with chain J, 2 interactions with chain P Hydrogen bonds: J:L.69, J:R.70, 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:Q.147, J:H.178, J:K.179, J:K.179, J:I.220, J:Y.221, P:Q.18, P:Q.18 Salt bridges: J:R.70, J:D.181 pi-Stacking: J:Y.221

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

Regulatory-associated protein of mTOR: A
Ras-related GTP-binding protein A: BI
Ras-related GTP-binding protein C: CJ
Ragulator complex protein LAMTOR1: DK
Ragulator complex protein LAMTOR2: EL
Ragulator complex protein LAMTOR3: FM
Ragulator complex protein LAMTOR4: GN
Ragulator complex protein LAMTOR5: HO
Transcription factor EB: P

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

I
I

C
C

J
J

D
D

K
K

E
E

L
L

F
F

M
M

G
G

N
N

H
H

O
O

P
P

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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