8ZH7 | pdb_00008zh7

Crystal structure of N-terminal domain of N-methyl-D-aspartate receptor subunit NR1 in complex with patient-derived antibody


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.50 Å
  • R-Value Free: 
    0.227 (Depositor), 0.208 (DCC) 
  • R-Value Work: 
    0.186 (Depositor), 0.170 (DCC) 
  • R-Value Observed: 
    0.188 (Depositor) 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Monoclonal humanized monovalent antibody blocking therapy for anti-NMDA receptor encephalitis.

Kanno, A.Kito, T.Maeda, M.Yamaki, S.Amano, Y.Shimomura, T.Anisimova, M.Kanazawa, N.Suzuki, K.Razai, A.Mihara, T.Kubo, K.Shimada, T.Nakamura, K.Nomura, N.Kondo, Y.Okimoto, A.Sugiyama, A.Park, D.Stein, I.Petshow, S.Vandendoren, V.Bilic, S.Kazimi, R.Eastman, V.Snipas, S.J.Mitchell, M.Maurer, M.Jefson, M.Lichter, J.Yamajuku, D.Shirai, H.Adachi, M.Hoeppner, D.J.Kubo, S.Zito, K.Iizuka, T.Flynn, P.Matsumoto, M.

(2025) Nat Commun 16: 5292-5292

  • DOI: https://doi.org/10.1038/s41467-025-60628-1
  • Primary Citation of Related Structures:  
    8ZH7

  • PubMed Abstract: 

    Anti-NMDA receptor (NMDAR) encephalitis is a devastating disease with severe psychiatric and neurological symptoms believed to be caused by pathogenic autoantibodies that bind to the N-terminal domain (NTD) of the NMDAR GluN1 subunit (GluN1-NTD) crosslinking adjacent NMDARs and driving their internalization. Here we describe ART5803, a humanized monovalent antibody, as a potential therapy for anti-NMDAR encephalitis. ART5803 binds with a high affinity (K D  = 0.69 nM) to GluN1-NTD without affecting NMDAR activity or inducing internalization. ART5803 blocks NMDAR internalization induced by patients' pathogenic autoantibodies, and restores NMDAR function. A marmoset animal model was developed using sustained intracerebroventricular (ICV) administration of a human pathogenic autoantibody to evoke behavioral and motor abnormalities. ART5803 ICV infusion or peripheral injections rapidly reversed these abnormalities. These data, together with the pharmacokinetic profile in cynomolgus monkeys, indicate a therapeutic potential for intravenous (IV)-administered ART5803 as a fast-acting and efficacious option for anti-NMDAR encephalitis.


  • Organizational Affiliation
    • Arialys Therapeutics, Inc., La Jolla, CA, USA.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Glutamate receptor ionotropic, NMDA 1
A, D, G, J
384Homo sapiensMutation(s): 0 
Gene Names: GRIN1NMDAR1
UniProt & NIH Common Fund Data Resources
Find proteins for Q05586 (Homo sapiens)
Explore Q05586 
Go to UniProtKB:  Q05586
PHAROS:  Q05586
GTEx:  ENSG00000176884 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ05586
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Antibody #003-102 heavy chain
B, E, H, K
250Homo sapiensMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Antibody #003-102 light chain
C, F, I, L
236Homo sapiensMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.50 Å
  • R-Value Free:  0.227 (Depositor), 0.208 (DCC) 
  • R-Value Work:  0.186 (Depositor), 0.170 (DCC) 
  • R-Value Observed: 0.188 (Depositor) 
Space Group: P 31
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 287.01α = 90
b = 287.01β = 90
c = 53.87γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
XSCALEdata scaling
XDSdata reduction
PHASERphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2025-05-14
    Type: Initial release
  • Version 1.1: 2025-07-02
    Changes: Database references