› 5iry

X-ray diffraction
3.1Å resolution

Crystal structure of human Desmocollin-1 ectodomain

Released:
DOI: 10.2210/pdb5iry/pdb
PDB entry 5iry coloured by chain, front view.
PDB entry 5iry coloured by chain, side view.
PDB entry 5iry coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Structural basis of adhesive binding by desmocollins and desmogleins.
Harrison OJ, Brasch J, Lasso G, Katsamba PS, Ahlsen G, Honig B, Shapiro L
Proc Natl Acad Sci U S A 113 7160-5 (2016)
PMID: 27298358

Function and Biology Details

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

Structure analysis Details

Assembly composition:
homo dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-170662 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecules (2 distinct):
Desmocollin-1 Chains: A, B
Molecule details ›
Chains: A, B
Length: 548 amino acids
Theoretical weight: 61.9 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens
UniProt:
  • Canonical: Q08554 (Residues: 135-676; Coverage: 63%)
Gene names: CDHF1, DSC1
Sequence domains: Cadherin domain

Ligands and Environments

Carbohydrate polymer : NEW Components: NAG, BMA
Carbohydrate polymer
4 bound ligands:
Ligand NAG 1 x NAG
Ligand CA 24 x CA
Ligand MAN 9 x MAN
Ligand EDO 1 x EDO
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 24-ID-C
Spacegroup: C2
Unit cell:
a: 213.806Å b: 66.174Å c: 141.633Å
α: 90° β: 127.15° γ: 90°
R-values:
R R work R free
0.251 0.249 0.302
Expression system: Homo sapiens

Quick links

Citations

33 review citations

Pemphigus.
Kasperkiewicz et al. (2017)
32 more

8 mentions without citation

Structural origins of clustered protocadherin-mediated neuronal barcoding.
Rubinstein et al. (2017)
7 more