› 7ux2

Electron Microscopy
2.9Å resolution

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

Released:
DOI: 10.2210/pdb7ux2/pdb
PDB entry 7ux2 coloured by chain, front view.
PDB entry 7ux2 coloured by chain, side view.
PDB entry 7ux2 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-26846

Function and Biology Details

Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero hexadecamer (preferred)
PDBe Complex ID:
PDB-CPX-128951 (preferred)
Entry contents:
9 distinct polypeptide molecules
Macromolecules (9 distinct):
Regulatory-associated protein of mTOR Chain: A
Molecule details ›
Chain: A
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: B, I
Molecule details ›
Chains: B, I
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: C, J
Molecule details ›
Chains: C, J
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: D, K
Molecule details ›
Chains: D, K
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: E, L
Molecule details ›
Chains: E, L
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: F, M
Molecule details ›
Chains: F, M
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: G, N
Molecule details ›
Chains: G, N
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: H, O
Molecule details ›
Chains: H, O
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 Chain: P
Molecule details ›
Chain: P
Length: 476 amino acids
Theoretical weight: 52.93 KDa
Source organism: Homo sapiens
Expression system: Spodoptera frugiperda
UniProt:
  • Canonical: P19484 (Residues: 1-476; Coverage: 100%)
Gene names: BHLHE35, TFEB
Sequence domains:

Ligands and Environments

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

Experiments and Validation Details

Entry percentile scores
Resolution: 2.9Å
Relevant EMDB volumes: EMD-26846
Expression systems:
  • Homo sapiens
  • Spodoptera frugiperda

Quick links

Citations

11 review citations

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