5UP2

Triheteromeric NMDA receptor GluN1/GluN2A/GluN2B in complex with glycine, glutamate, Ro 25-6981, MK-801 and a GluN2B-specific Fab, at pH 6.5


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 6 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history

Literature

Cryo-EM structures of the triheteromeric NMDA receptor and its allosteric modulation.

Lu, W.Du, J.Goehring, A.Gouaux, E.

(2017) Science 355: --

  • DOI: 10.1126/science.aal3729

  • PubMed Abstract: 
  • N-methyl-d-aspartate receptors (NMDARs) are heterotetrameric ion channels assembled as diheteromeric or triheteromeric complexes. Here, we report structures of the triheteromeric GluN1/GluN2A/GluN2B receptor in the absence or presence of the GluN2B-s ...

    N-methyl-d-aspartate receptors (NMDARs) are heterotetrameric ion channels assembled as diheteromeric or triheteromeric complexes. Here, we report structures of the triheteromeric GluN1/GluN2A/GluN2B receptor in the absence or presence of the GluN2B-specific allosteric modulator Ro 25-6981 (Ro), determined by cryogenic electron microscopy (cryo-EM). In the absence of Ro, the GluN2A and GluN2B amino-terminal domains (ATDs) adopt "closed" and "open" clefts, respectively. Upon binding Ro, the GluN2B ATD clamshell transitions from an open to a closed conformation. Consistent with a predominance of the GluN2A subunit in ion channel gating, the GluN2A subunit interacts more extensively with GluN1 subunits throughout the receptor, in comparison with the GluN2B subunit. Differences in the conformation of the pseudo-2-fold-related GluN1 subunits further reflect receptor asymmetry. The triheteromeric NMDAR structures provide the first view of the most common NMDA receptor assembly and show how incorporation of two different GluN2 subunits modifies receptor symmetry and subunit interactions, allowing each subunit to uniquely influence receptor structure and function, thus increasing receptor complexity.


    Organizational Affiliation

    Vollum Institute, Oregon Health and Science University, 3181 Southwest Sam Jackson Park Road, Portland, OR 97239, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
N-methyl-D-aspartate receptor subunit NR1-8a
A, C
836Xenopus laevisMutation(s): 0 
Gene Names: grin1
Membrane protein
mpstruct
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Channels: Other Ion Channels
Protein: 
GluN1a/GluN2B NMDA receptor
Find proteins for A0A1L8F5J9 (Xenopus laevis)
Go to UniProtKB:  A0A1L8F5J9
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
N-methyl-D-aspartate receptor subunit NR2A
B
831Xenopus laevisMutation(s): 0 
Gene Names: grin2a
Membrane protein
mpstruct
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Channels: Other Ion Channels
Protein: 
GluN1a/GluN2B NMDA receptor
Find proteins for B7ZSK1 (Xenopus laevis)
Go to UniProtKB:  B7ZSK1
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Ionotropic glutamate receptor subunit NR2B
D
837Xenopus laevisMutation(s): 0 
Gene Names: grin2b
Membrane protein
mpstruct
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Channels: Other Ion Channels
Protein: 
GluN1a/GluN2B NMDA receptor
Find proteins for A7XY94 (Xenopus laevis)
Go to UniProtKB:  A7XY94
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
GluN2B-specific Fab, termed 11D1
F, G
216N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG

Download SDF File 
Download CCD File 
A, C, D
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
UNK
Query on UNK
F, G
L-PEPTIDE LINKINGC4 H9 N O2

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Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 6 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2017-03-22
    Type: Initial release
  • Version 1.1: 2017-03-29
    Type: Non-polymer description
  • Version 1.2: 2017-04-05
    Type: Database references
  • Version 1.3: 2017-04-26
    Type: Other
  • Version 1.4: 2017-11-08
    Type: Advisory, Data collection, Derived calculations