9KZC | pdb_00009kzc

Cryo-EM structure of the LGI1 LRR-LGI1 EPTP-ADAM22 ECD complex


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.78 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Structural insights into heterohexameric assembly of epilepsy-related ligand-receptor complex LGI1-ADAM22.

Yamaguchi, T.Okatsu, K.Kubota, M.Mitsumori, A.Yamagata, A.Fukata, Y.Fukata, M.Shibata, M.Fukai, S.

(2025) Elife 14

  • DOI: https://doi.org/10.7554/eLife.105918
  • Primary Citation of Related Structures:  
    9KZC, 9KZT

  • PubMed Abstract: 

    Leucine-rich glioma-inactivated 1 protein (LGI1) is a secreted neuronal protein consisting of the N-terminal leucine-rich repeat (LRR) and C-terminal epitempin-repeat (EPTP) domains. LGI1 is linked to epilepsy, a neurological disorder that can be caused by genetic mutations of genes regulating neuronal excitability (e.g. voltage- or ligand-gated ion channels). ADAM22 is a membrane receptor that binds to LGI1 extracellularly and interacts with AMPA-type glutamate receptors via PSD-95 intracellularly to maintain normal synaptic signal transmission. Structural analysis of the LGI1-ADAM22 complex is important for understanding the molecular mechanism of epileptogenesis and developing new therapies against epilepsy. We previously reported the crystal structure of a 2:2 complex consisting of two molecules of LGI1 and two molecules of the ADAM22 ectodomain (ECD), which is suggested to bridge neurons across the synaptic cleft. On the other hand, multiangle light scattering, small-angle X-ray scattering, and cryo-electron microscopy (cryo-EM) analyses have suggested the existence of a 3:3 complex consisting of three molecules of LGI1 and three molecules of ADAM22. In the previous cryo-EM analysis, many observed particles were in a dissociated state, making it difficult to determine the three-dimensional (3D) structure of the 3:3 complex. In this study, we stabilized the 3:3 LGI1-ADAM22 ECD complex using chemical cross-linking and determined the cryo-EM structures of the LGI1 LRR -LGI1 EPTP -ADAM22 ECD and 3:3 LGI1-ADAM22 ECD complexes at 2.78 Å and 3.79 Å resolutions, respectively. Furthermore, high-speed atomic force microscopy (HS-AFM) visualized the structural features and flexibility of the 3:3 LGI1-ADAM22 ECD complex in solution. We discuss new insights into the interaction modes of the LGI1-ADAM22 higher-order complex and the structural properties of the 3:3 LGI1-ADAM22 complex.


  • Organizational Affiliation
    • Department of Chemistry, Graduate School of Science, Kyoto University, Kyoto, Japan.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Disintegrin and metalloproteinase domain-containing protein 22486Homo 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
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 1B,
C [auth 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
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.78 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Japan Society for the Promotion of Science (JSPS)Japan--

Revision History  (Full details and data files)

  • Version 1.0: 2025-06-25
    Type: Initial release
  • Version 1.1: 2025-07-16
    Changes: Data collection, Database references