› 5xeq

X-ray diffraction
3.14Å resolution

Crystal Structure of human MDGA1 and human neuroligin-2 complex

Released:
DOI: 10.2210/pdb5xeq/pdb
PDB entry 5xeq coloured by chain, front view.
PDB entry 5xeq coloured by chain, side view.
PDB entry 5xeq coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Structural Insights into Modulation of Neurexin-Neuroligin Trans-synaptic Adhesion by MDGA1/Neuroligin-2 Complex.
Kim JA, Kim D, Won SY, Han KA, Park D, Cho E, Yun N, An HJ, Um JW, Kim E, Lee JO, Ko J, Kim HM
Neuron 94 1121-1131.e6 (2017)
PMID: 28641111

Function and Biology Details

Biochemical function:
Biological process:
  • not assigned
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero tetramer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-185533 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (3 distinct):
Neuroligin-2 Chain: A
Molecule details ›
Chain: A
Length: 576 amino acids
Theoretical weight: 64.1 KDa
Source organism: Homo sapiens
Expression system: Spodoptera frugiperda
UniProt:
  • Canonical: Q8NFZ4 (Residues: 42-611; Coverage: 69%)
Gene names: KIAA1366, NLGN2
Sequence domains: Carboxylesterase family
Structure domains: alpha/beta hydrolase
MAM domain-containing glycosylphosphatidylinositol anchor protein 1 Chain: B
Molecule details ›
Chain: B
Length: 319 amino acids
Theoretical weight: 35.04 KDa
Source organism: Homo sapiens
Expression system: Spodoptera frugiperda
UniProt:
  • Canonical: Q8NFP4 (Residues: 19-330; Coverage: 33%)
Gene names: MAMDC3, MDGA1
Sequence domains: Immunoglobulin domain

Ligands and Environments

Carbohydrate polymer : NEW Components: NAG
Carbohydrate polymer
1 bound ligand:
Ligand NAG 3 x NAG
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: PAL/PLS BEAMLINE 5C (4A)
Spacegroup: C2
Unit cell:
a: 154.875Å b: 69.134Å c: 108.843Å
α: 90° β: 115.31° γ: 90°
R-values:
R R work R free
0.238 0.234 0.278
Expression system: Spodoptera frugiperda

Quick links

Citations

11 review citations

Synaptic Neurexin Complexes: A Molecular Code for the Logic of Neural Circuits.
Südhof TC. (2017)
10 more

2 mentions without citation

Hot Spots for Protein Partnerships at the Surface of Cholinesterases and Related α/β Hydrolase Fold Proteins or Domains-A Structural Perspective.
Bourne et al. (2017)
1 more