› 4kgq

X-ray diffraction
2.27Å resolution

Crystal structure of a human light loop mutant in complex with dcr3

Released:
DOI: 10.2210/pdb4kgq/pdb
PDB entry 4kgq coloured by chain, front view.
PDB entry 4kgq coloured by chain, side view.
PDB entry 4kgq coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Mechanistic basis for functional promiscuity in the TNF and TNF receptor superfamilies: structure of the LIGHT:DcR3 assembly.
Liu W, Zhan C, Cheng H, Kumar PR, Bonanno JB, Nathenson SG, Almo SC
Structure 22 1252-1262 (2014)
PMID: 25087510

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero dodecamer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-128994 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (4 distinct):
Tumor necrosis factor receptor superfamily member 6B Chains: C, D
Molecule details ›
Chains: C, D
Length: 174 amino acids
Theoretical weight: 19.04 KDa
Source organism: Homo sapiens
Expression system: Drosophila
UniProt:
  • Canonical: O95407 (Residues: 30-195; Coverage: 61%)
Gene names: DCR3, TNFRSF6B, TR6, UNQ186/PRO212
Sequence domains: TNFR/NGFR cysteine-rich region
Structure domains: Tumor Necrosis Factor Receptor, subunit A, domain 2
Tumor necrosis factor ligand superfamily member 14, soluble form Chains: A, B
Molecule details ›
Chains: A, B
Length: 158 amino acids
Theoretical weight: 17.35 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: O43557 (Residues: 83-240; Coverage: 66%)
Gene names: HVEML, LIGHT, TNFSF14, UNQ391/PRO726
Sequence domains: TNF(Tumour Necrosis Factor) family
Structure domains: Jelly Rolls

Ligands and Environments

Carbohydrate polymer : NEW Components: NAG, BMA, MAN
Carbohydrate polymer
Carbohydrate polymer : NEW Components: NAG
Carbohydrate polymer
1 bound ligand:
Ligand MG 2 x MG
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: NSLS BEAMLINE X29A
Spacegroup: P213
Unit cell:
a: 149.269Å b: 149.269Å c: 149.269Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.197 0.195 0.238
Expression systems:
  • Drosophila
  • Escherichia coli

Quick links

Citations

5 review citations

The TNF Receptor Superfamily in Co-stimulating and Co-inhibitory Responses.
Ward-Kavanagh et al. (2016)
4 more

1 mention without citation

Mechanistic basis for functional promiscuity in the TNF and TNF receptor superfamilies: structure of the LIGHT:DcR3 assembly.
Liu et al. (2014)