› 4yh7

X-ray diffraction
4.4Å resolution

Crystal structure of PTPdelta ectodomain in complex with IL1RAPL1

Released:
DOI: 10.2210/pdb4yh7/pdb
PDB entry 4yh7 coloured by chain, front view.
PDB entry 4yh7 coloured by chain, side view.
PDB entry 4yh7 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
OpenAccess logo Nat Commun 6 6926 (2015)
PMID: 25908590

Function and Biology Details

Reactions catalysed: 
Protein tyrosine phosphate + H(2)O = protein tyrosine + phosphate
(1a) NAD(+) = cyclic ADP-ribose + nicotinamide
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-157923 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (4 distinct):
Receptor-type tyrosine-protein phosphatase delta Chain: A
Molecule details ›
Chain: A
Length: 841 amino acids
Theoretical weight: 93.56 KDa
Source organism: Mus musculus
Expression system: Homo sapiens
UniProt:
  • Canonical: Q64487 (Residues: 21-1265; Coverage: 44%)
  • Best match: Q64487-12 (Residues: 21-854)
Gene name: Ptprd
Sequence domains:
Interleukin-1 receptor accessory protein-like 1 Chain: B
Molecule details ›
Chain: B
Length: 348 amino acids
Theoretical weight: 39.82 KDa
Source organism: Mus musculus
Expression system: Homo sapiens
UniProt:
  • Canonical: P59823 (Residues: 19-352; Coverage: 49%)
Gene name: Il1rapl1
Sequence domains:

Ligands and Environments

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

Experiments and Validation Details

Entry percentile scores
X-ray source: SPRING-8 BEAMLINE BL41XU
Spacegroup: I41
Unit cell:
a: 286.295Å b: 286.295Å c: 70.183Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.292 0.29 0.325
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