› 5x6v

X-ray diffraction
2.02Å resolution

Crystal structure of human heteroheptameric complex

Released:
DOI: 10.2210/pdb5x6v/pdb
PDB entry 5x6v coloured by chain, front view.
PDB entry 5x6v coloured by chain, side view.
PDB entry 5x6v coloured by chain, top view.
Source organisms:
Primary publication:
Structural basis for the assembly of the Ragulator-Rag GTPase complex.
Yonehara R, Nada S, Nakai T, Nakai M, Kitamura A, Ogawa A, Nakatsumi H, Nakayama KI, Li S, Standley DM, Yamashita E, Nakagawa A, Okada M
Nat Commun 8 1625 (2017)
PMID: 29158492

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero heptamer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-128945 (preferred)
Entry contents:
7 distinct polypeptide molecules
Macromolecules (7 distinct):
Ragulator complex protein LAMTOR3 Chain: A
Molecule details ›
Chain: A
Length: 127 amino acids
Theoretical weight: 13.87 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: Q9UHA4 (Residues: 2-124; Coverage: 99%)
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 LAMTOR2 Chain: B
Molecule details ›
Chain: B
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 LAMTOR5 Chain: C
Molecule details ›
Chain: C
Length: 91 amino acids
Theoretical weight: 9.62 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
Ragulator complex protein LAMTOR4 Chain: D
Molecule details ›
Chain: D
Length: 99 amino acids
Theoretical weight: 10.75 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: Q0VGL1 (Residues: 1-99; Coverage: 100%)
Gene names: C7orf59, LAMTOR4
Ragulator complex protein LAMTOR1 Chain: E
Molecule details ›
Chain: E
Length: 123 amino acids
Theoretical weight: 13.41 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: Q6IAA8 (Residues: 42-161; Coverage: 75%)
Gene names: C11orf59, LAMTOR1, PDRO, PP7157
Sequence domains: Late endosomal/lysosomal adaptor and MAPK and MTOR activator
Ras-related GTP-binding protein A Chain: F
Molecule details ›
Chain: F
Length: 135 amino acids
Theoretical weight: 15.66 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: Q7L523 (Residues: 183-313; Coverage: 42%)
Gene name: RRAGA
Structure domains: Beta-Lactamase
Ras-related GTP-binding protein C Chain: G
Molecule details ›
Chain: G
Length: 139 amino acids
Theoretical weight: 15.76 KDa
Source organism: Mus musculus
Expression system: Escherichia coli
UniProt:
  • Canonical: Q99K70 (Residues: 238-375; Coverage: 35%)
Gene name: Rragc
Structure domains: Beta-Lactamase

Ligands and Environments

2 bound ligands:
Ligand NA 1 x NA
Ligand ACT 1 x ACT
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SPRING-8 BEAMLINE BL44XU
Spacegroup: P212121
Unit cell:
a: 74.099Å b: 93.476Å c: 125.452Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.195 0.193 0.243
Expression system: Escherichia coli

Quick links

Citations

9 review citations

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

2 mentions without citation

Structural basis for the assembly of the Ragulator-Rag GTPase complex.
Yonehara et al. (2017)
1 more