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Cryo-EM structure of MTORC1 bound to PRAS40-fused active RAGA/C gtpases

Analyse Cryo-EM structure of MTORC1 bound to PRAS40-fused active RAGA/C gtpases in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6SB0
Type: protein
Length: 8,305 residues
Chains: 12
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: MTOR,SERINE/THREONINE-protein kinase MTOR,MTOR, SERINE/THREONINE-protein kinase mtor…
EC: 2.7.11.1
UniProt: P42345, Q9BVC4, Q7L523, Q9HB90, Q8N122, Q96B36
Ligands: GTP, GDP
Pockets: 20 · best druggability 0.85

Structure

electron microscopy · 7 distinct chains · 54% helix, 12% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	MTOR,SERINE/THREONINE-protein kinase MTOR,MTOR, SERINE/THREONINE-protein kinase mtor (EC 2.7.11.1)	protein	2178	72% helix, 2% strand	P42345
E, H	Target of rapamycin complex subunit LST8	protein	317	0% helix, 43% strand	Q9BVC4
C, I	RAS-related GTP-binding protein a	protein	298	41% helix, 26% strand	Q7L523
D	RAS-related GTP-binding protein C	protein	272	42% helix, 22% strand	Q9HB90
Y, N	Regulatory-associated protein of mtor	protein	1052	41% helix, 15% strand	Q8N122
T, O	Proline-rich AKT1 substrate 1	protein	35	40% helix, 0% strand	Q96B36
J	RAS-related GTP-binding protein C	protein	273	41% helix, 22% strand	Q9HB90

Ligands and binding sites

GTP · Guanosine-5'-triphosphate · ligand · 2 copies · chains C, I
GDP · Guanosine-5'-diphosphate · ligand · 2 copies · chains D, J

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1074	0.85	0.86	177	empty
2	1051	0.85	0.86	151	empty
3	971	0.85	0.86	146	empty
4	1169	0.84	0.85	142	empty
5	1130	0.84	0.85	144	empty

Interfaces

17 interfaces between chains.

I–J · 687 Å² buried · 9 hydrogen bonds · protein-protein
C–D · 685 Å² buried · 9 hydrogen bonds · protein-protein
A–B · 511 Å² buried · 0 hydrogen bonds · protein-protein
I–N · 404 Å² buried · 0 hydrogen bonds · protein-protein
C–Y · 404 Å² buried · 0 hydrogen bonds · protein-protein

Compared structures

Q8N122 · AlphaFold monomer V2.0 prediction for regulatory-associated protein of mtor (Q8N122) · a predicted model of the same protein · chain Y against A, TM-score 0.98
Q9BVC4 · AlphaFold monomer V2.0 prediction for target of rapamycin complex subunit LST8 (Q9BVC4) · a predicted model of the same protein · chain E against A, TM-score 0.97
Q7L523 · AlphaFold monomer V2.0 prediction for RAS-related GTP-binding protein a (Q7L523) · a predicted model of the same protein · chain C against A, TM-score 0.97
Q9HB90 · AlphaFold monomer V2.0 prediction for RAS-related GTP-binding protein C (Q9HB90) · a predicted model of the same protein · chain D against A, TM-score 0.90
P42345 · AlphaFold monomer V2.0 prediction for SERINE/THREONINE-protein kinase mtor (P42345) · a predicted model of the same protein · chain A against A, TM-score 0.85
Q96B36 · AlphaFold monomer V2.0 prediction for proline-rich AKT1 substrate 1 (Q96B36) · a predicted model of the same protein · chain T against A, TM-score 0.49

Analyse

Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
Every structure of UniProt P42345
Every structure of UniProt Q9BVC4
Every structure of UniProt Q7L523
Every structure of UniProt Q9HB90
Every structure of UniProt Q8N122
Every structure of UniProt Q96B36
Elsewhere: RCSB PDB 6SB0 · PDBe 6SB0 · UniProt P42345 · UniProt Q9BVC4 · UniProt Q7L523 · UniProt Q9HB90 · UniProt Q8N122 · UniProt Q96B36

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