› 5y3a

X-ray diffraction
2.9Å resolution

Crystal structure of Ragulator complex (p18 49-161)

Released:
DOI: 10.2210/pdb5y3a/pdb
PDB entry 5y3a coloured by chain, front view.
PDB entry 5y3a coloured by chain, side view.
PDB entry 5y3a coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Structural basis for Ragulator functioning as a scaffold in membrane-anchoring of Rag GTPases and mTORC1.
Zhang T, Wang R, Wang Z, Wang X, Wang F, Ding J
Nat Commun 8 1394 (2017)
PMID: 29123114

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero pentamer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-128947 (preferred)
Entry contents:
5 distinct polypeptide molecules
Macromolecules (5 distinct):
Ragulator complex protein LAMTOR1 Chains: A, F
Molecule details ›
Chains: A, F
Length: 112 amino acids
Theoretical weight: 12.35 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: Q6IAA8 (Residues: 50-161; Coverage: 70%)
Gene names: C11orf59, LAMTOR1, PDRO, PP7157
Sequence domains: Late endosomal/lysosomal adaptor and MAPK and MTOR activator
Ragulator complex protein LAMTOR2 Chains: B, G
Molecule details ›
Chains: B, G
Length: 127 amino acids
Theoretical weight: 13.72 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: Q9Y2Q5 (Residues: 1-125; Coverage: 100%)
Gene names: HSPC003, LAMTOR2, MAPBPIP, ROBLD3
Sequence domains: Roadblock/LC7 domain
Structure domains: Dynein light chain 2a, cytoplasmic
Ragulator complex protein LAMTOR3 Chains: C, H
Molecule details ›
Chains: C, H
Length: 124 amino acids
Theoretical weight: 13.64 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: Q9UHA4 (Residues: 1-124; Coverage: 100%)
Gene names: LAMTOR3, MAP2K1IP1, MAPKSP1, PRO2783
Sequence domains: Mitogen-activated protein kinase kinase 1 interacting
Structure domains: Dynein light chain 2a, cytoplasmic
Ragulator complex protein LAMTOR4 Chains: D, I
Molecule details ›
Chains: D, I
Length: 101 amino acids
Theoretical weight: 10.94 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: Q0VGL1 (Residues: 1-99; Coverage: 100%)
Gene names: C7orf59, LAMTOR4
Ragulator complex protein LAMTOR5 Chains: E, J
Molecule details ›
Chains: E, J
Length: 93 amino acids
Theoretical weight: 9.83 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: O43504 (Residues: 1-91; Coverage: 100%)
Gene names: HBXIP, LAMTOR5, XIP
Sequence domains: Ragulator complex protein LAMTOR5
Structure domains: Dynein light chain 2a, cytoplasmic

Ligands and Environments

1 bound ligand:
Ligand SO4 8 x SO4
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SSRF BEAMLINE BL17U1
Spacegroup: P212121
Unit cell:
a: 71.341Å b: 89.626Å c: 232.173Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.248 0.246 0.288
Expression system: Escherichia coli

Quick links

Citations

11 review citations

Nutrient regulation of mTORC1 at a glance.
Condon et al. (2019)
10 more

2 mentions without citation

Structural basis for Ragulator functioning as a scaffold in membrane-anchoring of Rag GTPases and mTORC1.
Zhang et al. (2017)
1 more