5Y2Z

Crystal structure of human LGI1 EPTP-ADAM22 complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.67 Å
  • R-Value Free: 0.279 
  • R-Value Work: 0.244 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structural basis of epilepsy-related ligand-receptor complex LGI1-ADAM22.

Yamagata, A.Miyazaki, Y.Yokoi, N.Shigematsu, H.Sato, Y.Goto-Ito, S.Maeda, A.Goto, T.Sanbo, M.Hirabayashi, M.Shirouzu, M.Fukata, Y.Fukata, M.Fukai, S.

(2018) Nat Commun 9: 1546-1546

  • DOI: 10.1038/s41467-018-03947-w
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Epilepsy is a common brain disorder throughout history. Epilepsy-related ligand-receptor complex, LGI1-ADAM22, regulates synaptic transmission and has emerged as a determinant of brain excitability, as their mutations and acquired LGI1 autoantibodies ...

    Epilepsy is a common brain disorder throughout history. Epilepsy-related ligand-receptor complex, LGI1-ADAM22, regulates synaptic transmission and has emerged as a determinant of brain excitability, as their mutations and acquired LGI1 autoantibodies cause epileptic disorders in human. Here, we report the crystal structure of human LGI1-ADAM22 complex, revealing a 2:2 heterotetrameric assembly. The hydrophobic pocket of the C-terminal epitempin-repeat (EPTP) domain of LGI1 binds to the metalloprotease-like domain of ADAM22. The N-terminal leucine-rich repeat and EPTP domains of LGI1 mediate the intermolecular LGI1-LGI1 interaction. A pathogenic R474Q mutation of LGI1, which does not exceptionally affect either the secretion or the ADAM22 binding, is located in the LGI1-LGI1 interface and disrupts the higher-order assembly of the LGI1-ADAM22 complex in vitro and in a mouse model for familial epilepsy. These studies support the notion that the LGI1-ADAM22 complex functions as the trans-synaptic machinery for precise synaptic transmission.


    Organizational Affiliation

    Institute for Quantitative Biosciences, The University of Tokyo, Tokyo, 113-0032, Japan.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Disintegrin and metalloproteinase domain-containing protein 22
A, C, E, G, I, K
504Homo sapiensMutation(s): 0 
Gene Names: ADAM22 (MDC2)
Find proteins for Q9P0K1 (Homo sapiens)
Go to Gene View: ADAM22
Go to UniProtKB:  Q9P0K1
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Leucine-rich glioma-inactivated protein 1
B, D, F, H, J, L
347Homo sapiensMutation(s): 0 
Gene Names: LGI1 (EPT)
Find proteins for O95970 (Homo sapiens)
Go to Gene View: LGI1
Go to UniProtKB:  O95970
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CA
Query on CA

Download SDF File 
Download CCD File 
A, B, C, D, E, F, G, H, I, J, K, L
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
FUC
Query on FUC

Download SDF File 
Download CCD File 
B, D, F, H, J, L
ALPHA-L-FUCOSE
C6 H12 O5
SHZGCJCMOBCMKK-SXUWKVJYSA-N
 Ligand Interaction
BMA
Query on BMA

Download SDF File 
Download CCD File 
B, H
BETA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-RWOPYEJCSA-N
 Ligand Interaction
NAG
Query on NAG

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.67 Å
  • R-Value Free: 0.279 
  • R-Value Work: 0.244 
  • Space Group: P 1
Unit Cell:
Length (Å)Angle (°)
a = 83.579α = 86.40
b = 83.608β = 88.17
c = 293.543γ = 59.95
Software Package:
Software NamePurpose
HKL-2000data reduction
PHENIXrefinement
HKL-2000data scaling
MOLREPphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
JST-CRESTJapan--
MEXTJapan16H04749

Revision History 

  • Version 1.0: 2018-05-02
    Type: Initial release
  • Version 1.1: 2018-10-31
    Type: Data collection, Structure summary