› 7uxh

Electron Microscopy
3.2Å resolution

cryo-EM structure of the mTORC1-TFEB-Rag-Ragulator complex

Released:
DOI: 10.2210/pdb7uxh/pdb
PDB entry 7uxh coloured by chain, front view.
PDB entry 7uxh coloured by chain, side view.
PDB entry 7uxh coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Structure of the lysosomal mTORC1-TFEB-Rag-Ragulator megacomplex.
Cui Z, Napolitano G, de Araujo MEG, Esposito A, Monfregola J, Huber LA, Ballabio A, Hurley JH
Nature (2023)
PMID: 36697823
Related structures: EMD-26861

Function and Biology Details

Reaction catalysed: 
ATP + a protein = ADP + a phosphoprotein
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero 36-mer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-128953 (preferred)
Entry contents:
11 distinct polypeptide molecules
Macromolecules (11 distinct):
Serine/threonine-protein kinase mTOR Chains: A, C
Molecule details ›
Chains: A, C
Length: 2549 amino acids
Theoretical weight: 289.26 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens
UniProt:
  • Canonical: P42345 (Residues: 1-2549; Coverage: 100%)
Gene names: FRAP, FRAP1, FRAP2, MTOR, RAFT1, RAPT1
Sequence domains:
Target of rapamycin complex subunit LST8 Chains: B, D
Molecule details ›
Chains: B, D
Length: 326 amino acids
Theoretical weight: 35.91 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens
UniProt:
  • Canonical: Q9BVC4 (Residues: 1-326; Coverage: 100%)
Gene names: GBL, LST8, MLST8
Sequence domains: WD domain, G-beta repeat
Regulatory-associated protein of mTOR Chains: E, U
Molecule details ›
Chains: E, U
Length: 1335 amino acids
Theoretical weight: 149.2 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens
UniProt:
  • Canonical: Q8N122 (Residues: 1-1335; Coverage: 100%)
Gene names: KIAA1303, RAPTOR, RPTOR
Sequence domains:
Ras-related GTP-binding protein A Chains: F, M, V, c
Molecule details ›
Chains: F, M, V, c
Length: 313 amino acids
Theoretical weight: 36.6 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens
UniProt:
  • Canonical: Q7L523 (Residues: 1-313; Coverage: 100%)
Gene name: RRAGA
Sequence domains: Gtr1/RagA G protein conserved region
Ras-related GTP-binding protein C Chains: G, N, W, d
Molecule details ›
Chains: G, N, W, d
Length: 399 amino acids
Theoretical weight: 44.3 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens
UniProt:
  • Canonical: Q9HB90 (Residues: 1-399; Coverage: 100%)
Gene name: RRAGC
Sequence domains: Gtr1/RagA G protein conserved region
Ragulator complex protein LAMTOR1 Chains: H, O, X, e
Molecule details ›
Chains: H, O, X, e
Length: 161 amino acids
Theoretical weight: 17.76 KDa
Source organism: Homo sapiens
Expression system: Spodoptera frugiperda
UniProt:
  • Canonical: Q6IAA8 (Residues: 1-161; Coverage: 100%)
Gene names: C11orf59, LAMTOR1, PDRO, PP7157
Sequence domains: Late endosomal/lysosomal adaptor and MAPK and MTOR activator
Ragulator complex protein LAMTOR2 Chains: I, P, Y, f
Molecule details ›
Chains: I, P, Y, f
Length: 125 amino acids
Theoretical weight: 13.52 KDa
Source organism: Homo sapiens
Expression system: Spodoptera frugiperda
UniProt:
  • Canonical: Q9Y2Q5 (Residues: 1-125; Coverage: 100%)
Gene names: HSPC003, LAMTOR2, MAPBPIP, ROBLD3
Sequence domains: Roadblock/LC7 domain
Ragulator complex protein LAMTOR3 Chains: J, Q, Z, g
Molecule details ›
Chains: J, Q, Z, g
Length: 124 amino acids
Theoretical weight: 13.64 KDa
Source organism: Homo sapiens
Expression system: Spodoptera frugiperda
UniProt:
  • Canonical: Q9UHA4 (Residues: 1-124; Coverage: 100%)
Gene names: LAMTOR3, MAP2K1IP1, MAPKSP1, PRO2783
Sequence domains: Mitogen-activated protein kinase kinase 1 interacting
Ragulator complex protein LAMTOR4 Chains: K, R, a, h
Molecule details ›
Chains: K, R, a, h
Length: 99 amino acids
Theoretical weight: 10.75 KDa
Source organism: Homo sapiens
Expression system: Spodoptera frugiperda
UniProt:
  • Canonical: Q0VGL1 (Residues: 1-99; Coverage: 100%)
Gene names: C7orf59, LAMTOR4
Ragulator complex protein LAMTOR5 Chains: L, S, b, i
Molecule details ›
Chains: L, S, b, i
Length: 91 amino acids
Theoretical weight: 9.62 KDa
Source organism: Homo sapiens
Expression system: Spodoptera frugiperda
UniProt:
  • Canonical: O43504 (Residues: 1-91; Coverage: 100%)
Gene names: HBXIP, LAMTOR5, XIP
Sequence domains: Ragulator complex protein LAMTOR5
Transcription factor EB Chains: T, j
Molecule details ›
Chains: T, j
Length: 476 amino acids
Theoretical weight: 52.93 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens
UniProt:
  • Canonical: P19484 (Residues: 1-476; Coverage: 100%)
Gene names: BHLHE35, TFEB
Sequence domains:

Ligands and Environments

4 bound ligands:
Ligand IHP 2 x IHP
Ligand GTP 4 x GTP
Ligand MG 4 x MG
Ligand GDP 4 x GDP
No modified residues

Experiments and Validation Details

Entry percentile scores
Resolution: 3.2Å
Relevant EMDB volumes: EMD-26861
Expression systems:
  • Homo sapiens
  • Spodoptera frugiperda

Quick links

Citations

11 review citations

Lysosomes in senescence and aging.
Tan et al. (2023)
10 more