› 6amb

X-ray diffraction
2.5Å resolution

Crystal Structure of the Afadin RA1 domain in complex with HRAS

Released:
DOI: 10.2210/pdb6amb/pdb
PDB entry 6amb coloured by chain, front view.
PDB entry 6amb coloured by chain, side view.
PDB entry 6amb coloured by chain, top view.
Source organisms:
Primary publication:
Evolution of AF6-RAS association and its implications in mixed-lineage leukemia.
Smith MJ, Ottoni E, Ishiyama N, Goudreault M, Haman A, Meyer C, Tucholska M, Gasmi-Seabrook G, Menezes S, Laister RC, Minden MD, Marschalek R, Gingras AC, Hoang T, Ikura M
Nat Commun 8 1099 (2017)
PMID: 29062045

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-133973 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (2 distinct):
GTPase HRas, N-terminally processed Chain: A
Molecule details ›
Chain: A
Length: 170 amino acids
Theoretical weight: 19.39 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21
UniProt:
  • Canonical: P01112 (Residues: 1-168; Coverage: 89%)
Gene names: HRAS, HRAS1
Sequence domains: Ras family
Structure domains: P-loop containing nucleotide triphosphate hydrolases
Afadin Chain: B
Molecule details ›
Chain: B
Length: 99 amino acids
Theoretical weight: 11.53 KDa
Source organism: Mus musculus
Expression system: Escherichia coli BL21
UniProt:
  • Canonical: Q9QZQ1 (Residues: 38-136; Coverage: 5%)
Gene names: Af6, Afdn, Mllt4
Sequence domains: Ras association (RalGDS/AF-6) domain

Ligands and Environments

2 bound ligands:
Ligand GNP 1 x GNP
Ligand MG 1 x MG
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 19-ID
Spacegroup: P212121
Unit cell:
a: 48.239Å b: 57.152Å c: 73.329Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.223 0.218 0.266
Expression system: Escherichia coli BL21

Quick links

Citations

1 review citation

New insights into RAS biology reinvigorate interest in mathematical modeling of RAS signaling.
Erickson et al. (2019)
9 other articles

5 mentions without citation

Assessment of mutation probabilities of KRAS G12 missense mutants and their long-timescale dynamics by atomistic molecular simulations and Markov state modeling.
Pantsar et al. (2018)
4 more