› 4iru

X-ray diffraction
3.2Å resolution

Crystal Structure of lepB GAP core in a transition state mimetic complex with Rab1A and ALF3

Released:
DOI: 10.2210/pdb4iru/pdb
PDB entry 4iru coloured by chain, front view.
PDB entry 4iru coloured by chain, side view.
PDB entry 4iru coloured by chain, top view.
Source organisms:
Primary publication:
The Legionella pneumophila GTPase activating protein LepB accelerates Rab1 deactivation by a non-canonical hydrolytic mechanism.
Mishra AK, Del Campo CM, Collins RE, Roy CR, Lambright DG
J Biol Chem 288 24000-11 (2013)
PMID: 23821544

Function and Biology Details

Reaction catalysed: 
GTP + H(2)O = GDP + phosphate
Biochemical function:
Biological process:
  • not assigned
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
hetero dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-158708 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (2 distinct):
LepB Chains: A, C, E
Molecule details ›
Chains: A, C, E
Length: 299 amino acids
Theoretical weight: 33.92 KDa
Source organism: Legionella pneumophila subsp. pneumophila str. Philadelphia 1
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q5ZSM7 (Residues: 326-623; Coverage: 23%)
Gene names: lepB, lpg2490
Sequence domains:
Structure domains:
Ras-related protein Rab-1A Chains: B, D, F
Molecule details ›
Chains: B, D, F
Length: 184 amino acids
Theoretical weight: 21.18 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P62820 (Residues: 4-177; Coverage: 85%)
Gene names: RAB1, RAB1A
Sequence domains: Ras family
Structure domains: P-loop containing nucleotide triphosphate hydrolases

Ligands and Environments

6 bound ligands:
Ligand ACT 12 x ACT
Ligand GOL 8 x GOL
Ligand K 6 x K
Ligand MG 3 x MG
Ligand GDP 3 x GDP
Ligand AF3 3 x AF3
1 modified residue:
Ligand MSE 24 x MSE

Experiments and Validation Details

Entry percentile scores
X-ray source: NSLS BEAMLINE X29A
Spacegroup: I4122
Unit cell:
a: 139.404Å b: 139.404Å c: 384.519Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.232 0.23 0.288
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

3 review citations

Formation of the Legionella-containing vacuole: phosphoinositide conversion, GTPase modulation and ER dynamics.
Steiner et al. (2018)
2 more

6 mentions without citation

Rab GTPases and their interacting protein partners: Structural insights into Rab functional diversity.
Pylypenko et al. (2018)
5 more