› 5ygp

X-ray diffraction
2.09Å resolution

Human TNFRSF25 death domain mutant-D412E

Released:
DOI: 10.2210/pdb5ygp/pdb
PDB entry 5ygp coloured by chain, front view.
PDB entry 5ygp coloured by chain, side view.
PDB entry 5ygp coloured by chain, top view.
Source organisms:
Primary publication:
Crystal structure and activation mechanism of DR3 death domain.
Yin X, Li W, Ma H, Zeng W, Peng C, Li Y, Liu M, Chen Q, Zhou R, Jin T
FEBS J 286 2593-2610 (2019)
PMID: 30941855

Function and Biology Details

Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-142592 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecules (2 distinct):
Maltose/maltodextrin-binding periplasmic protein; Tumor necrosis factor receptor superfamily member 25 Chains: A, B, C, D
Molecule details ›
Chains: A, B, C, D
Length: 463 amino acids
Theoretical weight: 51.18 KDa
Source organisms: Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P0AEX9 (Residues: 27-392; Coverage: 99%)
  • Canonical: Q93038 (Residues: 328-415; Coverage: 22%)
Gene names: APO3, DDR3, DR3, JW3994, TNFRSF12, TNFRSF25, UNQ455/PRO779, WSL, WSL1, b4034, malE
Sequence domains:

Ligands and Environments

Carbohydrate polymer : NEW Components: GLC
Carbohydrate polymer
1 bound ligand:
Ligand SO4 7 x SO4
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SSRF BEAMLINE BL19U1
Spacegroup: P21
Unit cell:
a: 97.62Å b: 155.02Å c: 74.03Å
α: 90° β: 90.18° γ: 90°
R-values:
R R work R free
0.218 0.218 0.246
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

1 review citation

The Role of TNFR2 and DR3 in the In Vivo Expansion of Tregs in T Cell Depleting Transplantation Regimens.
Rodriguez-Barbosa et al. (2020)
3 other articles

1 mention without citation

Crystal structure and activation mechanism of DR3 death domain.
Yin et al. (2019)