PDBsum entry 4kcd

Membrane protein

PDB id: 4kcd

Contents

Protein chains

290 a.a.

Ligands

GOL ×2

Waters ×584

PDB id:

4kcd

Name:

Membrane protein

Title:

Crystal structure of the nmda receptor glun3a ligand binding domain apo state

Structure:

Glutamate receptor ionotropic, nmda 3a. Chain: a, b. Fragment: ligand binding domain (unp residues 511-660, 776-915). Synonym: glun3a, glutamate receptor chi-1, n-methyl-d-aspartate receptor, n-methyl-d-aspartate receptor subtype 3a, nmdar3a, nr3a, nmdar-l, nmdar-l1. Engineered: yes

Source:

Rattus norvegicus. Brown rat,rat,rats. Organism_taxid: 10116. Gene: grin3a. Expressed in: escherichia coli. Expression_system_taxid: 562.

Resolution:

1.68Å R-factor: 0.156 R-free: 0.184

Authors:

Y.Yao,A.Y.Lau,M.L.Mayer

Key ref:

Y.Yao et al. (2013). Conformational analysis of NMDA receptor GluN1, GluN2, and GluN3 ligand-binding domains reveals subtype-specific characteristics. Structure, 21, 1788-1799. PubMed id: 23972471 DOI: 10.1016/j.str.2013.07.011

Date:

24-Apr-13 Release date: 31-Jul-13

Protein chains

Q9R1M7  (NMD3A_RAT) -  Glutamate receptor ionotropic, NMDA 3A from Rattus norvegicus

Seq: 1135 a.a.

Struc: 290 a.a.*

* PDB and UniProt seqs differ at 1 residue position (black cross)

DOI no: 10.1016/j.str.2013.07.011

Structure 21:1788-1799 (2013)

PubMed id: 23972471

Conformational analysis of NMDA receptor GluN1, GluN2, and GluN3 ligand-binding domains reveals subtype-specific characteristics.

Y.Yao, J.Belcher, A.J.Berger, M.L.Mayer, A.Y.Lau.

ABSTRACT

The NMDA receptor family of glutamate receptor ion channels is formed by obligate heteromeric assemblies of GluN1, GluN2, and GluN3 subunits. GluN1 and GluN3 bind glycine, whereas GluN2 binds glutamate. Crystal structures of the GluN1 and GluN3A ligand-binding domains (LBDs) in their apo states unexpectedly reveal open- and closed-cleft conformations, respectively, with water molecules filling the binding pockets. Computed conformational free energy landscapes for GluN1, GluN2A, and GluN3A LBDs reveal that the apo-state LBDs sample closed-cleft conformations, suggesting that their agonists bind via a conformational selection mechanism. By contrast, free energy landscapes for the AMPA receptor GluA2 LBD suggest binding of glutamate via an induced-fit mechanism. Principal component analysis reveals a rich spectrum of hinge bending, rocking, twisting, and sweeping motions that are different for the GluN1, GluN2A, GluN3A, and GluA2 LBDs. This variation highlights the structural complexity of signaling by glutamate receptor ion channels.