› 5y39

X-ray diffraction
2.65Å resolution

Crystal structure of Ragulator complex (p18 76-145)

Released:
DOI: 10.2210/pdb5y39/pdb
PDB entry 5y39 coloured by chain, front view.
PDB entry 5y39 coloured by chain, side view.
PDB entry 5y39 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: 70 amino acids
Theoretical weight: 7.97 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: Q6IAA8 (Residues: 76-145; Coverage: 44%)
Gene names: C11orf59, LAMTOR1, PDRO, PP7157
Ragulator complex protein LAMTOR2 Chains: B, G
Molecule details ›
Chains: B, G
Length: 125 amino acids
Theoretical weight: 13.52 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: 90 amino acids
Theoretical weight: 9.54 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: O43504 (Residues: 1-90; Coverage: 99%)
Gene names: HBXIP, LAMTOR5, XIP
Sequence domains: Ragulator complex protein LAMTOR5
Structure domains: Dynein light chain 2a, cytoplasmic

Ligands and Environments

No bound ligands
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SSRF BEAMLINE BL17U1
Spacegroup: C2221
Unit cell:
a: 110.659Å b: 117.854Å c: 157.805Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.218 0.216 0.263
Expression system: Escherichia coli

Quick links

Citations

11 review citations

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

3 mentions without citation

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