› 7t3c

Electron Microscopy
4Å resolution

GATOR1-RAG-RAGULATOR - Dual Complex

Released:
DOI: 10.2210/pdb7t3c/pdb
PDB entry 7t3c coloured by chain, front view.
PDB entry 7t3c coloured by chain, side view.
PDB entry 7t3c coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Cryo-EM structures of the human GATOR1-Rag-Ragulator complex reveal a spatial-constraint regulated GAP mechanism.
Egri SB, Ouch C, Chou HT, Yu Z, Song K, Xu C, Shen K
Mol Cell 82 1836-1849.e5 (2022)
PMID: 35338845
Related structures: EMD-25654

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero heptadecamer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-128949 (preferred)
Entry contents:
11 distinct polypeptide molecules
Macromolecules (11 distinct):
GATOR1 complex protein NPRL2 Chain: B
Molecule details ›
Chain: B
Length: 380 amino acids
Theoretical weight: 43.71 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens
UniProt:
  • Canonical: Q8WTW4 (Residues: 1-380; Coverage: 100%)
Gene names: NPRL2, TUSC4
Sequence domains: Nitrogen permease regulator 2
GATOR1 complex protein DEPDC5 Chain: A
Molecule details ›
Chain: A
Length: 1603 amino acids
Theoretical weight: 181.48 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens
UniProt:
  • Canonical: O75140 (Residues: 1-1603; Coverage: 100%)
Gene names: DEPDC5, KIAA0645
Sequence domains:
Ragulator complex protein LAMTOR3 Chains: H, O
Molecule details ›
Chains: H, O
Length: 124 amino acids
Theoretical weight: 13.64 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens
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 LAMTOR2 Chains: G, N
Molecule details ›
Chains: G, N
Length: 125 amino acids
Theoretical weight: 13.52 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens
UniProt:
  • Canonical: Q9Y2Q5 (Residues: 1-125; Coverage: 100%)
Gene names: HSPC003, LAMTOR2, MAPBPIP, ROBLD3
Sequence domains: Roadblock/LC7 domain
Ragulator complex protein LAMTOR5 Chains: J, Q
Molecule details ›
Chains: J, Q
Length: 91 amino acids
Theoretical weight: 9.62 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens
UniProt:
  • Canonical: O43504 (Residues: 1-91; Coverage: 100%)
Gene names: HBXIP, LAMTOR5, XIP
Sequence domains: Ragulator complex protein LAMTOR5
Ragulator complex protein LAMTOR4 Chains: I, P
Molecule details ›
Chains: I, P
Length: 99 amino acids
Theoretical weight: 10.75 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens
UniProt:
  • Canonical: Q0VGL1 (Residues: 1-99; Coverage: 100%)
Gene names: C7orf59, LAMTOR4
Ragulator complex protein LAMTOR1 Chains: F, M
Molecule details ›
Chains: F, M
Length: 161 amino acids
Theoretical weight: 17.76 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens
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
GATOR1 complex protein NPRL3 Chain: C
Molecule details ›
Chain: C
Length: 569 amino acids
Theoretical weight: 63.68 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens
UniProt:
  • Canonical: Q12980 (Residues: 1-569; Coverage: 100%)
Gene names: C16orf35, CGTHBA, MARE, NPRL3
Sequence domains: Nitrogen Permease regulator of amino acid transport activity 3
Ras-related GTP-binding protein A Chains: D, K
Molecule details ›
Chains: D, K
Length: 313 amino acids
Theoretical weight: 36.62 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 Chain: E
Molecule details ›
Chain: E
Length: 399 amino acids
Theoretical weight: 44.2 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
Ras-related GTP-binding protein C Chain: L
Molecule details ›
Chain: L
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

Ligands and Environments

2 bound ligands:
Ligand GDP 3 x GDP
Ligand AF3 3 x AF3
No modified residues

Experiments and Validation Details

Entry percentile scores
Resolution: 4Å
Relevant EMDB volumes: EMD-25654
Expression system: Homo sapiens

Quick links

Citations

3 review citations

Longin domain GAP complexes in nutrient signalling, membrane traffic and neurodegeneration.
Jansen et al. (2023)
2 more

4 mentions without citation

Cryo-EM structures of the human GATOR1-Rag-Ragulator complex reveal a spatial-constraint regulated GAP mechanism.
Egri et al. (2022)
3 more