› 5zhx

X-ray diffraction
3.5Å resolution

Crystal structure of SmgGDS-558 and farnesylated RhoA complex

Released:
DOI: 10.2210/pdb5zhx/pdb
PDB entry 5zhx coloured by chain, front view.
PDB entry 5zhx coloured by chain, side view.
PDB entry 5zhx coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
GEF mechanism revealed by the structure of SmgGDS-558 and farnesylated RhoA complex and its implication for a chaperone mechanism.
Shimizu H, Toma-Fukai S, Kontani K, Katada T, Shimizu T
Proc Natl Acad Sci U S A 115 9563-9568 (2018)
PMID: 30190425

Function and Biology Details

Reaction catalysed: 
GTP + H(2)O = GDP + phosphate
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-156546 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (2 distinct):
Rap1 GTPase-GDP dissociation stimulator 1 Chains: A, B, C, D
Molecule details ›
Chains: A, B, C, D
Length: 487 amino acids
Theoretical weight: 53.42 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: P52306 (Residues: 77-607; Coverage: 79%)
Gene names: RAP1GDS1, SMGGDS
Sequence domains: Armadillo/beta-catenin-like repeat
Transforming protein RhoA Chains: e, f, g, h
Molecule details ›
Chains: e, f, g, h
Length: 198 amino acids
Theoretical weight: 22.17 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: P61586 (Residues: 1-193; Coverage: 100%)
Gene names: ARH12, ARHA, RHO12, RHOA
Sequence domains: Ras family

Ligands and Environments

1 bound ligand:
Ligand FAR 4 x FAR
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SPRING-8 BEAMLINE BL44XU
Spacegroup: P212121
Unit cell:
a: 93.32Å b: 181.77Å c: 205.31Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.253 0.25 0.306
Expression system: Escherichia coli

Quick links

Citations

3 review citations

The Cys Sense: Thiol Redox Switches Mediate Life Cycles of Cellular Proteins.
Radzinski et al. (2021)
2 more

4 mentions without citation

Structural Insights into the Regulation Mechanism of Small GTPases by GEFs.
Toma-Fukai et al. (2019)
3 more