5XEQ

Crystal Structure of human MDGA1 and human neuroligin-2 complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.136 Å
  • R-Value Free: 0.278 
  • R-Value Work: 0.234 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structural Insights into Modulation of Neurexin-Neuroligin Trans-synaptic Adhesion by MDGA1/Neuroligin-2 Complex

Kim, J.A.Kim, D.Won, S.Y.Han, K.A.Park, D.Cho, E.Yun, N.An, H.J.Um, J.W.Kim, E.Lee, J.O.Ko, J.Kim, H.M.

(2017) Neuron 94: 1121-1131.e6

  • DOI: 10.1016/j.neuron.2017.05.034

  • PubMed Abstract: 
  • Membrane-associated mucin domain-containing glycosylphosphatidylinositol anchor proteins (MDGAs) bind directly to neuroligin-1 (NL1) and neuroligin-2 (NL2), thereby respectively regulating excitatory and inhibitory synapse development. However, the m ...

    Membrane-associated mucin domain-containing glycosylphosphatidylinositol anchor proteins (MDGAs) bind directly to neuroligin-1 (NL1) and neuroligin-2 (NL2), thereby respectively regulating excitatory and inhibitory synapse development. However, the mechanisms by which MDGAs modulate NL activity to specify development of the two synapse types remain unclear. Here, we determined the crystal structures of human NL2/MDGA1 Ig1-3 complex, revealing their stable 2:2 arrangement with three interaction interfaces. Cell-based assays using structure-guided, site-directed MDGA1 mutants showed that all three contact patches were required for the MDGA's negative regulation of NL2-mediated synaptogenic activity. Furthermore, MDGA1 competed with neurexins for NL2 via its Ig1 domain. The binding affinities of both MDGA1 and MDGA2 for NL1 and NL2 were similar, consistent with the structural prediction of similar binding interfaces. However, MDGA1 selectively associated with NL2, but not NL1, in vivo. These findings collectively provide structural insights into the mechanism by which MDGAs negatively modulate synapse development governed by NLs/neurexins.


    Organizational Affiliation

    Center for Synaptic Brain Dysfunctions, Institute for Basic Science, Daejeon 34141, Korea; Graduate School of Medical Science & Engineering, KAIST, Daejeon 34141, Korea. Electronic address: hm_kim@kaist.ac.kr.,Department of Brain & Cognitive Sciences, Daegu Gyeongbuk Institute of Science and Technology (DGIST), Daegu 42988, Korea. Electronic address: jaewonko@dgist.ac.kr.,Center for Synaptic Brain Dysfunctions, Institute for Basic Science, Daejeon 34141, Korea.,Department of Brain & Cognitive Sciences, Daegu Gyeongbuk Institute of Science and Technology (DGIST), Daegu 42988, Korea.,Graduate School of Analytical Science and Technology, Chungnam National University, Daejeon 305-764, Korea.,Center for Synaptic Brain Dysfunctions, Institute for Basic Science, Daejeon 34141, Korea; Department of Biological Sciences, KAIST, Daejeon 34141, Korea.,Graduate School of Nanoscience and Technology, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Korea.,Department of Chemistry, KAIST, Daejeon 34141, Korea.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Neuroligin-2
A
576Homo sapiensMutation(s): 1 
Gene Names: NLGN2 (KIAA1366)
Find proteins for Q8NFZ4 (Homo sapiens)
Go to Gene View: NLGN2
Go to UniProtKB:  Q8NFZ4
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
MAM domain-containing glycosylphosphatidylinositol anchor protein 1
B
319Homo sapiensMutation(s): 0 
Gene Names: MDGA1 (MAMDC3)
Find proteins for Q8NFP4 (Homo sapiens)
Go to Gene View: MDGA1
Go to UniProtKB:  Q8NFP4
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG

Download SDF File 
Download CCD File 
A, B
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.136 Å
  • R-Value Free: 0.278 
  • R-Value Work: 0.234 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 154.875α = 90.00
b = 69.134β = 115.31
c = 108.843γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
PDB_EXTRACTdata extraction
PHASERphasing
HKL-2000data reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2017-07-12
    Type: Initial release
  • Version 1.1: 2017-08-30
    Type: Data collection