7TE4

Crystal structure of Fab2 anti-GluN2B antibody

  • Classification: IMMUNE SYSTEM
  • Organism(s): Mus musculus
  • Mutation(s): No 

  • Deposited: 2022-01-04 Released: 2022-03-02 
  • Deposition Author(s): Tajima, N., Furukawa, H.
  • Funding Organization(s): National Institutes of Health/National Institute of Mental Health (NIH/NIMH), National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.46 Å
  • R-Value Free: 0.297 
  • R-Value Work: 0.261 
  • R-Value Observed: 0.263 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Development and characterization of functional antibodies targeting NMDA receptors.

Tajima, N.Simorowski, N.Yovanno, R.A.Regan, M.C.Michalski, K.Gomez, R.Lau, A.Y.Furukawa, H.

(2022) Nat Commun 13: 923-923

  • DOI: https://doi.org/10.1038/s41467-022-28559-3
  • Primary Citation of Related Structures:  
    7TE4, 7TE6, 7TE9, 7TEB, 7TEE, 7TEQ, 7TER, 7TES, 7TET

  • PubMed Abstract: 

    N-methyl-D-aspartate receptors (NMDARs) are critically involved in basic brain functions and neurodegeneration as well as tumor invasiveness. Targeting specific subtypes of NMDARs with distinct activities has been considered an effective therapeutic strategy for neurological disorders and diseases. However, complete elimination of off-target effects of small chemical compounds has been challenging and thus, there is a need to explore alternative strategies for targeting NMDAR subtypes. Here we report identification of a functional antibody that specifically targets the GluN1-GluN2B NMDAR subtype and allosterically down-regulates ion channel activity as assessed by electrophysiology. Through biochemical analysis, x-ray crystallography, single-particle electron cryomicroscopy, and molecular dynamics simulations, we show that this inhibitory antibody recognizes the amino terminal domain of the GluN2B subunit and increases the population of the non-active conformational state. The current study demonstrates that antibodies may serve as specific reagents to regulate NMDAR functions for basic research and therapeutic objectives.


  • Organizational Affiliation

    W.M. Keck Structural Biology Laboratory, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, NY, 11724, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Fab2 anti-GluN2B antibody, light chainA [auth L],
C [auth A]
213Mus musculusMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Fab anti-GluN2B antibody, heavy chainB [auth H],
D [auth B]
223Mus musculusMutation(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: 2.46 Å
  • R-Value Free: 0.297 
  • R-Value Work: 0.261 
  • R-Value Observed: 0.263 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 54.744α = 90
b = 66.901β = 90
c = 240.417γ = 90
Software Package:
Software NamePurpose
HKL-2000data scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
PHASERphasing

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
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)United StatesNS111745

Revision History  (Full details and data files)

  • Version 1.0: 2022-03-02
    Type: Initial release
  • Version 1.1: 2023-10-18
    Changes: Data collection, Refinement description