PDBsum entry 1m5d

Membrane protein

PDB id: 1m5d

Contents

Protein chain

258 a.a. *

Ligands

SO4 ×2

BRH

Waters ×326

* Residue conservation analysis

PDB id:

1m5d

Name:

Membrane protein

Title:

X-ray structure of the glur2 ligand binding core (s1s2j-y702f) in complex with br-hibo at 1.73 a resolution

Structure:

Glutamate receptor 2. Chain: a. Fragment: flop ligand binding core (s1s2j-y702f). Synonym: glur-2, glur-b, glur-k2, glutamate receptor ionotropic ampa 2. Engineered: yes. Mutation: yes

Source:

Rattus norvegicus. Norway rat. Organism_taxid: 10116. Gene: glur-2. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.

Biol. unit:

Dimer (from PDB file)

Resolution:

1.73Å R-factor: 0.186 R-free: 0.215

Authors:

A.Hogner,J.S.Kastrup,R.Jin,T.Liljefors,M.L.Mayer,J.Egebjerg, I.K.Larsen,E.Gouaux

Key ref:

A.Hogner et al. (2002). Structural basis for AMPA receptor activation and ligand selectivity: crystal structures of five agonist complexes with the GluR2 ligand-binding core. J Mol Biol, 322, 93. PubMed id: 12215417 DOI: 10.1016/S0022-2836(02)00650-2

Date:

09-Jul-02 Release date: 18-Sep-02

Protein chain

P19491  (GRIA2_RAT) -  Glutamate receptor 2 from Rattus norvegicus

Seq: 883 a.a.

Struc: 258 a.a.*

* PDB and UniProt seqs differ at 3 residue positions (black crosses)

DOI no: 10.1016/S0022-2836(02)00650-2

J Mol Biol 322:93 (2002)

PubMed id: 12215417

Structural basis for AMPA receptor activation and ligand selectivity: crystal structures of five agonist complexes with the GluR2 ligand-binding core.

A.Hogner, J.S.Kastrup, R.Jin, T.Liljefors, M.L.Mayer, J.Egebjerg, I.K.Larsen, E.Gouaux.

ABSTRACT

Glutamate is the principal excitatory neurotransmitter within the mammalian CNS, playing an important role in many different functions in the brain such as learning and memory. In this study, a combination of molecular biology, X-ray structure determinations, as well as electrophysiology and binding experiments, has been used to increase our knowledge concerning the ionotropic glutamate receptor GluR2 at the molecular level. Five high-resolution X-ray structures of the ligand-binding domain of GluR2 (S1S2J) complexed with the three agonists (S)-2-amino-3-[3-hydroxy-5-(2-methyl-2H-tetrazol-5-yl)isoxazol-4-yl]propionic acid (2-Me-Tet-AMPA), (S)-2-amino-3-(3-carboxy-5-methylisoxazol-4-yl)propionic acid (ACPA), and (S)-2-amino-3-(4-bromo-3-hydroxy-isoxazol-5-yl)propionic acid (Br-HIBO), as well as of a mutant thereof (S1S2J-Y702F) in complex with ACPA and Br-HIBO, have been determined. The structures reveal that AMPA agonists with an isoxazole moiety adopt different binding modes in the receptor, dependent on the substituents of the isoxazole. Br-HIBO displays selectivity among different AMPA receptor subunits, and the design and structure determination of the S1S2J-Y702F mutant in complex with Br-HIBO and ACPA have allowed us to explain the molecular mechanism behind this selectivity and to identify key residues for ligand recognition. The agonists induce the same degree of domain closure as AMPA, except for Br-HIBO, which shows a slightly lower degree of domain closure. An excellent correlation between domain closure and efficacy has been obtained from electrophysiology experiments undertaken on non-desensitising GluR2i(Q)-L483Y receptors expressed in oocytes, providing strong evidence that receptor activation occurs as a result of domain closure. The structural results, combined with the functional studies on the full-length receptor, form a powerful platform for the design of new selective agonists.

Selected figure(s)

Figure 3.
Figure 3. Drawings showing the three agonists and their interactions with the S1S2J protein. (a) 2-Me-Tet-AMPA, (b) ACPA, and (c) Br-HIBO. The bonds of the protein are displayed in yellow and the bound agonists bonds are in blue. Water molecules are shown as red spheres, while remaining atoms are in standard atomic colours (carbon is black, oxygen is red, nitrogen is blue, and bromine is green). Broken lines indicate all potential hydrogen bonds or ionic interactions within 3.3 Å. Radiating spheres indicate hydrophobic contacts within 3.9 Å between carbon atoms in the agonist and neighbouring residues. The only exception is in (c), where hydrophobic contacts between the bromine atom and neighbouring residues are displayed. The binding site of protomer A was employed for (a) and (b), and the binding sites for protomers B and C have similar structures. This Figure was prepared with the program Ligplot.[55.] (d) F[o]−F[c] omit electron density map contoured at 3.0σ for S1S2J:2-Me-Tet-AMPA, S1S2J:ACPA, S1S2J:Br-HIBO, and S1S2J-Y702F:Br-HIBO was prepared by BOBSCRIPT.[56.]

Figure 4.
Figure 4. Surface electrostatic potential of part of the binding site of 2-Me-Tet-AMPA in complex with S1S2J. Positive potential is coloured in blue and negative potential in red, as indicated by the coloured bar to the left. The labelled residues form a well-defined partly hydrophobic and partly polar cavity within the binding site of S1S2J. These residues are within 3.9 Å from the 2-methyltetrazole ring, except from residues Thr686 and Leu704, which are at a distance of 4.2 Å and 4.7 Å, respectively. The ligand 2-Me-Tet-AMPA is shown in ball-and-stick representation, coloured as follows: carbon is white, oxygen is red, and nitrogen is blue. The Figure was prepared with the program Sybyl (Tripos Assoc. Inc.).

The above figures are reprinted by permission from Elsevier: J Mol Biol (2002, 322, 93-0) copyright 2002.

Figures were selected by an automated process.