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 
  • R-Value Observed: 0.246 

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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 22504Homo 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
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Leucine-rich glioma-inactivated protein 1347Homo sapiensMutation(s): 0 
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
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  • Reference Sequence
Oligosaccharides

Help

Entity ID: 3
MoleculeChains Length2D Diagram Glycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
M, O, Q, T
2N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT
GlyCosmos:  G42666HT
GlyGen:  G42666HT
Entity ID: 4
MoleculeChains Length2D Diagram Glycosylation3D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose
N, S
4N-Glycosylation
Glycosylation Resources
GlyTouCan:  G32152BH
GlyCosmos:  G32152BH
GlyGen:  G32152BH
Entity ID: 5
MoleculeChains Length2D Diagram Glycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose
P, U, V
3N-Glycosylation
Glycosylation Resources
GlyTouCan:  G21290RB
GlyCosmos:  G21290RB
GlyGen:  G21290RB
Entity ID: 6
MoleculeChains Length2D Diagram Glycosylation3D Interactions
alpha-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose
R
2N-Glycosylation
Glycosylation Resources
GlyTouCan:  G86851RC
GlyCosmos:  G86851RC
GlyGen:  G86851RC
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG

Download Ideal Coordinates CCD File 
SA [auth H],
VA [auth L]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
CA
Query on CA

Download Ideal Coordinates CCD File 
AA [auth C]
BA [auth C]
CA [auth E]
DA [auth E]
EA [auth E]
AA [auth C],
BA [auth C],
CA [auth E],
DA [auth E],
EA [auth E],
FA [auth G],
GA [auth G],
HA [auth G],
IA [auth I],
JA [auth I],
KA [auth I],
LA [auth K],
MA [auth K],
NA [auth K],
OA [auth B],
PA [auth D],
QA [auth F],
RA [auth H],
TA [auth J],
UA [auth L],
W [auth A],
X [auth A],
Y [auth A],
Z [auth C]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.67 Å
  • R-Value Free: 0.279 
  • R-Value Work: 0.244 
  • R-Value Observed: 0.246 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 83.579α = 86.4
b = 83.608β = 88.17
c = 293.543γ = 59.95
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
JST-CRESTJapan--
MEXTJapan16H04749

Revision History  (Full details and data files)

  • Version 1.0: 2018-05-02
    Type: Initial release
  • Version 1.1: 2018-10-31
    Changes: Data collection, Structure summary
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary
  • Version 2.1: 2023-11-22
    Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary