› 5epp

X-ray diffraction
1.88Å resolution

Structural Insights into the Interaction of p97 N-terminus Domain and VBM Motif in Rhomboid Protease, RHBDL4

Released:
DOI: 10.2210/pdb5epp/pdb
PDB entry 5epp coloured by chain, front view.
PDB entry 5epp coloured by chain, side view.
PDB entry 5epp coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Structural insights into the interaction of p97 N-terminus domain and VBM in rhomboid protease, RHBDL4.
Lim JJ, Lee Y, Ly TT, Kang JY, Lee JG, An JY, Youn HS, Park KR, Kim TG, Yang JK, Jun Y, Eom SH
Biochem J 473 2863-80 (2016)
PMID: 27407164

Function and Biology Details

Reactions catalysed: 
ATP + H(2)O = ADP + phosphate
Cleaves type-1 transmembrane domains using a catalytic dyad composed of serine and histidine that are contributed by different transmembrane domains.
Biochemical function:
  • not assigned
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-157171 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (2 distinct):
Transitional endoplasmic reticulum ATPase Chain: A
Molecule details ›
Chain: A
Length: 184 amino acids
Theoretical weight: 20.86 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: P55072 (Residues: 21-199; Coverage: 22%)
Gene names: HEL-220, HEL-S-70, VCP
Sequence domains:
Structure domains:
Rhomboid-related protein 4 Chain: B
Molecule details ›
Chain: B
Length: 15 amino acids
Theoretical weight: 1.95 KDa
Source organism: Homo sapiens
Expression system: Not provided
UniProt:
  • Canonical: Q8TEB9 (Residues: 300-314; Coverage: 5%)
Gene names: HSD-50, HSD50, RHBDD1, RHBDL4

Ligands and Environments

No bound ligands
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: PAL/PLS BEAMLINE 5C (4A)
Spacegroup: P65
Unit cell:
a: 96.999Å b: 96.999Å c: 50.902Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.178 0.177 0.21
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

1 review citation

The role of rhomboid superfamily members in protein homeostasis: Mechanistic insight and physiological implications.
Kandel et al. (2020)
4 other articles

6 mentions without citation

The Interplay of Cofactor Interactions and Post-translational Modifications in the Regulation of the AAA+ ATPase p97.
Hänzelmann et al. (2017)
5 more