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› 5lpn

X-ray diffraction
2.8Å resolution

Structure of human Rab10 in complex with the bMERB domain of Mical-1

Released:
DOI: 10.2210/pdb5lpn/pdb
Model geometry
Fit model/data
PDB entry 5lpn coloured by chain, front view.
PDB entry 5lpn coloured by chain, side view.
PDB entry 5lpn coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
bMERB domains are bivalent Rab8 family effectors evolved by gene duplication.
Rai A, Oprisko A, Campos J, Fu Y, Friese T, Itzen A, Goody RS, Gazdag EM, Müller MP
OpenAccess logo Elife 5 (2016)
PMID: 27552051

Function and Biology Details

Reactions catalysed: 
GTP + H2O = GDP + phosphate + H(+).
L-methionyl-[F-actin] + NADPH + O2 + H(+) = L-methionyl-(R)-S-oxide-[F-actin] + NADP(+) + H2O.
(1) NADPH + O2 + H(+) = H2O2 + NADP(+).
Biochemical function:
Biological process:
  • not assigned
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
hetero trimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-158188 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (2 distinct):
Ras-related protein Rab-10 Chains: A, C
Molecule details ›
Chains: A, C
Length: 177 amino acids
Theoretical weight: 20.2 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: P61026 (Residues: 1-175; Coverage: 88%)
Gene name: RAB10
Sequence domains: Ras family
Structure domains: P-loop containing nucleotide triphosphate hydrolases
[F-actin]-monooxygenase MICAL1 Chain: B
Molecule details ›
Chain: B
Length: 153 amino acids
Theoretical weight: 17.85 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: Q8TDZ2 (Residues: 918-1067; Coverage: 14%)
Gene names: MICAL, MICAL1, NICAL
Sequence domains: Bivalent Mical/EHBP Rab binding domain

Ligands and Environments

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

Experiments and Validation Details

wwPDB Validation report is not available for this entry.
X-ray source: SLS BEAMLINE X10SA
Spacegroup: P212121
Unit cell:
a: 58.39Å b: 59Å c: 198.18Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.246 0.244 0.287
Expression system: Escherichia coli

Quick links

Citations

5 review citations

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

9 mentions without citation

Regulated methionine oxidation by monooxygenases.
Manta et al. (2017)
8 more