› 4yfd

X-ray diffraction
3.25Å resolution

Crystal structure PTP delta Ig1-Fn2 in complex with IL-1RAcP

Released:
DOI: 10.2210/pdb4yfd/pdb
PDB entry 4yfd coloured by chain, front view.
PDB entry 4yfd coloured by chain, side view.
PDB entry 4yfd coloured by chain, top view.
Source organism: Mus musculus
Primary publication:
Mechanisms of splicing-dependent trans-synaptic adhesion by PTPĪ“-IL1RAPL1/IL-1RAcP for synaptic differentiation.
Yamagata A, Yoshida T, Sato Y, Goto-Ito S, Uemura T, Maeda A, Shiroshima T, Iwasawa-Okamoto S, Mori H, Mishina M, Fukai S
Nat Commun 6 6926 (2015)
PMID: 25908590

Function and Biology Details

Reactions catalysed: 
(1a) NAD(+) = cyclic ADP-ribose + nicotinamide
Protein tyrosine phosphate + H(2)O = protein tyrosine + 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-178898 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (2 distinct):
Interleukin-1 receptor accessory protein Chain: B
Molecule details ›
Chain: B
Length: 339 amino acids
Theoretical weight: 39.37 KDa
Source organism: Mus musculus
Expression system: Homo sapiens
UniProt:
  • Canonical: Q61730 (Residues: 21-351; Coverage: 60%)
Gene name: Il1rap
Sequence domains:
Structure domains: Immunoglobulins
Receptor-type tyrosine-protein phosphatase delta Chain: A
Molecule details ›
Chain: A
Length: 491 amino acids
Theoretical weight: 53.91 KDa
Source organism: Mus musculus
Expression system: Homo sapiens
UniProt:
  • Canonical: Q64487 (Residues: 21-511; Coverage: 26%)
Gene name: Ptprd
Sequence domains:

Ligands and Environments

1 bound ligand:
Ligand NAG 7 x NAG
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SPRING-8 BEAMLINE BL41XU
Spacegroup: P2
Unit cell:
a: 77.497Å b: 63.306Å c: 169.35Å
α: 90° β: 94.23° γ: 90°
R-values:
R R work R free
0.257 0.256 0.287
Expression system: Homo sapiens

Quick links

Citations

8 review citations

Structural Basis of IL-1 Family Cytokine Signaling.
Fields et al. (2019)
7 more

6 mentions without citation

Structural Basis for LAR-RPTP-Mediated Synaptogenesis.
Won et al. (2018)
5 more