SMTL ID : 6bcu.1

Cryo-EM structure of the activated RHEB-mTORC1 refined to 3.4 angstrom

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY 3.80 Å

Oligo State

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

Ligands

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

ATP.1: 22 residues within 4Å: Chain A: I.2163, S.2165, K.2166, Q.2167, P.2169, L.2185, K.2187, Y.2225, I.2237, G.2238, W.2239, V.2240, C.2243, T.2245, H.2340, S.2342, N.2343, M.2345, I.2356, D.2357 Ligands: MG.2, MG.3 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:S.2165, A:Q.2167, A:G.2238, A:V.2240 Salt bridges: A:K.2187, A:K.2187 ATP.6: 22 residues within 4Å: Chain F: I.2163, S.2165, K.2166, Q.2167, P.2169, L.2185, K.2187, Y.2225, I.2237, G.2238, W.2239, V.2240, C.2243, T.2245, H.2340, S.2342, N.2343, M.2345, I.2356, D.2357 Ligands: MG.7, MG.8 5 PLIP interactions: 5 interactions with chain F Hydrogen bonds: F:Q.2167, F:G.2238, F:V.2240 Salt bridges: F:K.2187, F:K.2187

6 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 3 residues within 4Å: Chain A: N.2343, D.2357 Ligands: ATP.1 No protein-ligand interaction detected (PLIP) MG.3: 5 residues within 4Å: Chain A: Q.2167, K.2187, E.2190, D.2357 Ligands: ATP.1 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:D.2357 MG.5: 4 residues within 4Å: Chain E: S.24, T.42, D.64 Ligands: GTP.4 2 PLIP interactions: 2 interactions with chain E Metal complexes: E:S.24, E:T.42 MG.7: 3 residues within 4Å: Chain F: N.2343, D.2357 Ligands: ATP.6 No protein-ligand interaction detected (PLIP) MG.8: 5 residues within 4Å: Chain F: Q.2167, K.2187, E.2190, D.2357 Ligands: ATP.6 1 PLIP interactions: 1 interactions with chain F Metal complexes: F:D.2357 MG.10: 4 residues within 4Å: Chain J: S.24, T.42, D.64 Ligands: GTP.9 2 PLIP interactions: 2 interactions with chain J Metal complexes: J:S.24, J:T.42

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

GTP.4: 21 residues within 4Å: Chain E: R.19, S.20, V.21, G.22, K.23, S.24, S.25, S.38, Y.39, P.41, T.42, A.66, G.67, N.123, K.124, D.126, L.127, S.153, A.154, K.155 Ligands: MG.5 18 PLIP interactions: 18 interactions with chain E Hydrogen bonds: E:S.20, E:V.21, E:G.22, E:K.23, E:S.24, E:S.24, E:S.25, E:S.25, E:T.42, E:G.67, E:N.123, E:K.124, E:A.154, E:K.155, E:K.155 Salt bridges: E:K.23, E:K.23, E:D.126 GTP.9: 21 residues within 4Å: Chain J: R.19, S.20, V.21, G.22, K.23, S.24, S.25, S.38, Y.39, P.41, T.42, A.66, G.67, N.123, K.124, D.126, L.127, S.153, A.154, K.155 Ligands: MG.10 18 PLIP interactions: 18 interactions with chain J Hydrogen bonds: J:S.20, J:V.21, J:G.22, J:K.23, J:S.24, J:S.24, J:S.25, J:S.25, J:T.42, J:G.67, J:N.123, J:K.124, J:A.154, J:K.155, J:K.155 Salt bridges: J:K.23, J:K.23, J:D.126

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Yang, H. et al., Mechanisms of mTORC1 activation by RHEB and inhibition by PRAS40. Nature (2017)

Release Date

2017-12-20

Peptides

Serine/threonine-protein kinase mTOR,Serine/threonine-protein kinase mTOR: AF
Target of rapamycin complex subunit LST8: BG
Regulatory-associated protein of mTOR,Regulatory-associated protein of mTOR: CH
Eukaryotic translation initiation factor 4E-binding protein 1: DI
GTP-binding protein Rheb: EJ

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

F
B

B
D

G
E

C
W

H
Y

D
X

I
Z

E
S

J
R

Serine/threonine-protein kinase mTOR,Serine/threonine-protein kinase mTOR

Target of rapamycin complex subunit LST8

Regulatory-associated protein of mTOR,Regulatory-associated protein of mTOR

Eukaryotic translation initiation factor 4E-binding protein 1

GTP-binding protein Rheb

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