2RCB

Crystal structure of the NR3B ligand binding core complex with D-serine at 1.62 Angstrom resolution


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.62 Å
  • R-Value Free: 0.228 
  • R-Value Work: 0.192 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Molecular mechanism of ligand recognition by NR3 subtype glutamate receptors.

Yao, Y.Harrison, C.B.Freddolino, P.L.Schulten, K.Mayer, M.L.

(2008) Embo J. 27: 2158-2170

  • DOI: 10.1038/emboj.2008.140
  • Primary Citation of Related Structures:  2RC7, 2RC8, 2RC9, 2RCA

  • PubMed Abstract: 
  • NR3 subtype glutamate receptors have a unique developmental expression profile, but are the least well-characterized members of the NMDA receptor gene family, which have key roles in synaptic plasticity and brain development. Using ligand binding ass ...

    NR3 subtype glutamate receptors have a unique developmental expression profile, but are the least well-characterized members of the NMDA receptor gene family, which have key roles in synaptic plasticity and brain development. Using ligand binding assays, crystallographic analysis, and all atom MD simulations, we investigate mechanisms underlying the binding by NR3A and NR3B of glycine and D-serine, which are candidate neurotransmitters for NMDA receptors containing NR3 subunits. The ligand binding domains of both NR3 subunits adopt a similar extent of domain closure as found in the corresponding NR1 complexes, but have a unique loop 1 structure distinct from that in all other glutamate receptor ion channels. Within their ligand binding pockets, NR3A and NR3B have strikingly different hydrogen bonding networks and solvent structures from those found in NR1, and fail to undergo a conformational rearrangement observed in NR1 upon binding the partial agonist ACPC. MD simulations revealed numerous interdomain contacts, which stabilize the agonist-bound closed-cleft conformation, and a novel twisting motion for the loop 1 helix that is unique in NR3 subunits.


    Related Citations: 
    • Characterization of a soluble ligand binding domain of the NMDA receptor regulatory subunit NR3A
      Yao, Y.,Mayer, M.L.
      (2006) J.NEUROSCI. 26: 4559


    Organizational Affiliation

    Laboratory of Cellular and Molecular Neurophysiology, Porter Neuroscience Research Center, NICHD, NIH, DHHS, Bethesda, MD, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Glutamate [NMDA] receptor subunit 3B
A, B
292Rattus norvegicusGene Names: Grin3b
Find proteins for Q8VHN2 (Rattus norvegicus)
Go to UniProtKB:  Q8VHN2
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
DSN
Query on DSN

Download SDF File 
Download CCD File 
A, B
D-SERINE
C3 H7 N O3
MTCFGRXMJLQNBG-UWTATZPHSA-N
 Ligand Interaction
GOL
Query on GOL

Download SDF File 
Download CCD File 
A
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
DSNKd: 163 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.62 Å
  • R-Value Free: 0.228 
  • R-Value Work: 0.192 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 45.779α = 90.00
b = 83.521β = 90.00
c = 144.959γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data collection
HKL-2000data scaling
HKL-2000data reduction
PHASERphasing
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2007-09-19 
  • Released Date: 2008-08-05 
  • Deposition Author(s): Yao, Y., Mayer, M.L.

Revision History 

  • Version 1.0: 2008-08-05
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Advisory, Version format compliance
  • Version 1.2: 2017-08-23
    Type: Source and taxonomy