5Y31

Crystal structure of human LGI1-ADAM22 complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 7.13 Å
  • R-Value Free: 
    0.316 (Depositor), 0.312 (DCC) 
  • R-Value Work: 
    0.265 (Depositor), 0.265 (DCC) 
  • R-Value Observed: 
    0.268 (Depositor) 

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Ligand Structure Quality Assessment 

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This is version 1.3 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: https://doi.org/10.1038/s41467-018-03947-w
  • Primary Citation of Related Structures:  
    5Y2Z, 5Y30, 5Y31

  • 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 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:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Disintegrin and metalloproteinase domain-containing protein 22
A, C
497Homo sapiensMutation(s): 0 
Gene Names: ADAM22MDC2
UniProt & NIH Common Fund Data Resources
Find proteins for Q9P0K1 (Homo sapiens)
Explore Q9P0K1 
Go to UniProtKB:  Q9P0K1
PHAROS:  Q9P0K1
GTEx:  ENSG00000008277 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9P0K1
Glycosylation
Glycosylation Sites: 2Go to GlyGen: Q9P0K1-1
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Leucine-rich glioma-inactivated protein 1
B, D
544Homo sapiensMutation(s): 1 
Gene Names: LGI1EPTUNQ775/PRO1569
UniProt & NIH Common Fund Data Resources
Find proteins for O95970 (Homo sapiens)
Explore O95970 
Go to UniProtKB:  O95970
PHAROS:  O95970
GTEx:  ENSG00000108231 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO95970
Glycosylation
Glycosylation Sites: 3Go to GlyGen: O95970-1
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG

Download Ideal Coordinates CCD File 
H [auth A]
I [auth A]
K [auth B]
L [auth B]
M [auth B]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
CA
Query on CA

Download Ideal Coordinates CCD File 
E [auth A]
F [auth A]
G [auth A]
J [auth B]
N [auth C]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 7.13 Å
  • R-Value Free:  0.316 (Depositor), 0.312 (DCC) 
  • R-Value Work:  0.265 (Depositor), 0.265 (DCC) 
  • R-Value Observed: 0.268 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 105.143α = 90
b = 124.324β = 104.8
c = 164.663γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted NAGClick on this verticalbar to view details

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2018-05-02
    Type: Initial release
  • Version 1.1: 2018-11-07
    Changes: Data collection, Structure summary
  • Version 1.2: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Derived calculations, Structure summary
  • Version 1.3: 2024-10-23
    Changes: Data collection, Database references, Derived calculations, Structure summary