› 6wcw

X-ray diffraction
2.8Å resolution

Structure of human Rubicon RH domain in complex with GTP-bound Rab7

Released:
DOI: 10.2210/pdb6wcw/pdb
PDB entry 6wcw coloured by chain, front view.
PDB entry 6wcw coloured by chain, side view.
PDB entry 6wcw coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Structural basis for autophagy inhibition by the human Rubicon-Rab7 complex.
Bhargava HK, Tabata K, Byck JM, Hamasaki M, Farrell DP, Anishchenko I, DiMaio F, Im YJ, Yoshimori T, Hurley JH
Proc Natl Acad Sci U S A 117 17003-17010 (2020)
PMID: 32632011

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-156305 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (2 distinct):
Ras-related protein Rab-7a Chain: B
Molecule details ›
Chain: B
Length: 184 amino acids
Theoretical weight: 20.84 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21
UniProt:
  • Canonical: P51149 (Residues: 2-182; Coverage: 87%)
Gene names: RAB7, RAB7A
Sequence domains: Ras family
Run domain Beclin-1-interacting and cysteine-rich domain-containing protein Chain: A
Molecule details ›
Chain: A
Length: 254 amino acids
Theoretical weight: 29.54 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21
UniProt:
  • Canonical: Q92622 (Residues: 699-949; Coverage: 26%)
Gene names: KIAA0226, RUBCN
Sequence domains: Rubicon Homology Domain

Ligands and Environments

3 bound ligands:
Ligand GTP 1 x GTP
Ligand MG 1 x MG
Ligand ZN 4 x ZN
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: ALS BEAMLINE 8.3.1
Unit cell:
a: 60.04Å b: 45.33Å c: 186.277Å
α: 90° β: 98.507° γ: 90°
R-values:
R R work R free
0.202 0.2 0.258
Expression system: Escherichia coli BL21

Quick links

Citations

7 review citations

Targeting Autophagy to Treat Cancer: Challenges and Opportunities.
Lim et al. (2020)
6 more

2 mentions without citation

Structural basis for autophagy inhibition by the human Rubicon-Rab7 complex.
Bhargava et al. (2020)
1 more