10EN | pdb_000010en

SK3D-Matured in complex with GluN1-GluN2B, full refinement


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.70 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

Validation slider image for 10EN

This is version 1.1 of the entry. See complete history

Literature

Ectopic NMDAR expression in cancer unmasks germline-encoded autoimmunity.

Kleeman, S.O.Michalski, K.Zhao, X.Steigerwald, R.Ferrer, M.Levett, L.Ertel, E.Schultz, A.Simorowski, N.Moody, P.Wee, T.L.Valente, C.Fox, S.Makuch, M.Thomsen, S.Harrison, R.Regan, C.Preall, J.Gao, Q.Thomas, D.Habel, J.Rubino, R.Irani, S.Furukawa, H.Janowitz, T.

(2026) Nature 

  • DOI: https://doi.org/10.1038/s41586-026-10278-0
  • Primary Citation Related Structures: 
    10EN, 10EV, 10EX, 10EY, 10EZ, 10FD, 10FE, 10FF, 10FL, 10FN, 10FO

  • PubMed Abstract: 

    Autoimmunity and anti-cancer immunity lie on the same biological continuum 1,2 , but their link remains obscure. The paraneoplastic neurological syndrome ANRE (anti-NMDA receptor (NMDAR) encephalitis) is a paradigm for their connectivity 3 , given that intratumoural NMDAR expression is correlated with the generation of anti-NMDAR antibodies 4,5 . Here we verify ectopic expression of GluN1 and GluN2B NMDAR subunits in triple-negative breast cancer (TNBC) 6 and model this using orthotopic TNBC tumours with inducible expression of GluN1-GluN2B NMDARs. We show that NMDAR expression is sufficient to induce the recruitment of B cells and their affinity maturation, consistent with an integrated adaptive immune response. Reconstruction of extended intratumoural B cell phylogenies and cryogenic electron microscopy structural analyses demonstrate that affinity-matured hypermutated and class-switched antibodies emerged from pre-existing germline-configuration lower-affinity anti-NMDAR antibodies. Distinct matured antibodies targeted specific epitopes and induced conformational rearrangements within the NMDAR amino-terminal domain, predictive of their functional effects, ranging from inhibition to potentiation. Passive transfer of an NMDAR-potentiating antibody caused autonomic dysregulation and lowered the seizure threshold in healthy female mice, recapitulating key diagnostic criteria of ANRE 4,5 . We further identify a correlation between intratumoural NMDAR expression and anti-NMDAR antibody titres in patients with TNBC. Taken together, our data establish a direct connection between intratumoural NMDAR expression, antibody maturation and the onset of autoimmunity. These findings suggest that germline-encoded anti-NMDAR antibodies contribute to immune surveillance but can also trigger autoimmune disease after maturation, revealing a mechanistic trade-off between cancer immunity and neurotoxicity.


  • Organizational Affiliation
    • Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA.

Macromolecule Content 

  • Total Structure Weight: 411.26 kDa 
  • Atom Count: 26,125 
  • Modeled Residue Count: 3,553 
  • Deposited Residue Count: 3,670 
  • Unique protein chains: 4

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Isoform 4 of Glutamate receptor ionotropic, NMDA 1
A, C
817Homo sapiensMutation(s): 0 
Gene Names: GRIN1NMDAR1
UniProt
Find proteins for Q5R1P0 (Canis lupus familiaris)
Go to UniProtKB:  Q5R1P0
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ5R1P0-4
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Glutamate receptor
B, D
787Homo sapiensMutation(s): 0 
Gene Names: GRIN2B
UniProt
Find proteins for A0A8B7RCM5 (Hipposideros armiger)
Explore A0A8B7RCM5 
Go to UniProtKB:  A0A8B7RCM5
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A8B7RCM5
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
SK3D Light chainE,
G [auth I]
111Mus musculusMutation(s): 0 
Find similar proteins by:|  3D Structure
Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
SK3D Heavy chainF,
H [auth J]
120Mus musculusMutation(s): 0 

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.70 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONcryoSPARC

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of Mental Health (NIH/NIMH)United StatesMH085926

Revision History  (Full details and data files)

  • Version 1.0: 2026-03-25
    Type: Initial release
  • Version 1.1: 2026-04-08
    Changes: Data collection, Database references