PDBsum entry 1lbc

Membrane protein

PDB id: 1lbc

Contents

Protein chains

259 a.a. *

Ligands

GLU ×3

CYZ ×3

Metals

_ZN ×5

Waters ×319

* Residue conservation analysis

References listed in PDB file

Key reference

Title

Mechanism of glutamate receptor desensitization.

Authors

Y.Sun, R.Olson, M.Horning, N.Armstrong, M.Mayer, E.Gouaux.

Ref.

Nature, 2002, 417, 245-253. [DOI no: 10.1038/417245a]

PubMed id

12015593

Abstract

Ligand-gated ion channels transduce chemical signals into electrical impulses by opening a transmembrane pore in response to binding one or more neurotransmitter molecules. After activation, many ligand-gated ion channels enter a desensitized state in which the neurotransmitter remains bound but the ion channel is closed. Although receptor desensitization is crucial to the functioning of many ligand-gated ion channels in vivo, the molecular basis of this important process has until now defied analysis. Using the GluR2 AMPA-sensitive glutamate receptor, we show here that the ligand-binding cores form dimers and that stabilization of the intradimer interface by either mutations or allosteric modulators reduces desensitization. Perturbations that destabilize the interface enhance desensitization. Receptor activation involves conformational changes within each subunit that result in an increase in the separation of portions of the receptor that are linked to the ion channel. Our analysis defines the dimer interface in the resting and activated state, indicates how ligand binding is coupled to gating, and suggests modes of dimer dimer interaction in the assembled tetramer. Desensitization occurs through rearrangement of the dimer interface, which disengages the agonist-induced conformational change in the ligand-binding core from the ion channel gate.

Figure 2.
Figure 2: The L483Y mutation and CTZ stabilize the GluR2 S1S2J dimer. a, Side view of the S1S2J -L483Y dimer in complex with AMPA. Subunit A is grey (domain 1) and blue (domain 2). Subunit B is pink (domain 1) and purple (domain 2). Residues from A are cyan; residues from B are yellow. Lys 505 and Ile 633 flank transmembrane segments 1 and 2, respectively. b, Top view of the L483Y dimer looking down the 2-fold axis. c, CTZ stabilizes the GluR2 S1S2J -N754S dimer by binding in the dimer interface. Side view of the S1S2J dimer in a complex with glutamate and CTZ. The two CTZ molecules are green and are shown in CPK representation. d, Top view of the S1S2J-Glu -CTZ dimer, looking down the 2-fold axis. e, Interactions between Tyr 483 from one subunit and Leu 748 and Lys 752 from another subunit. Similar interactions also occur in the dimer of S1S2J -L483Y in complex with DNQX. Note the intersubunit hydrogen bond between Asn 754 and the carbonyl oxygen of Ser 729. f, Interactions between CTZ and residues from subunits A (cyan) and B (yellow). The black dashed lines are hydrogen bonds and the light blue spheres are water molecules. Stereoviews of e and f are provided in Supplementary Information.

Figure 5.
Figure 5: Agonist-induced conformational changes in the dimer and gating model. a, Overlap of the S1S2J -L483Y dimers bound with either an agonist (AMPA, green) or an antagonist (DNQX, red). The relative movement of the linker region, which connects the ligand-binding core to the channel-forming segments, is represented by the difference in position of Ile 633 in the two structures. Distances between Ile 633 on two protomers are 28.3 Å in the DNQX structure and 36.3 Å in the AMPA structure. In addition, Ile 633 rotates around the 2-fold axis by 1.25° and moves 2.5 Å along the 2-fold axis, away from the membrane. b, A model for glutamate receptor activation and desensitization. Domain 1 and domain 2 of the ligand-binding core are labelled D1 and D2, respectively. Transmembrane segments of each subunit are indicated by a single green cylinder and the N-terminal domain (ATD) has not been included in the model. Each subunit binds a single agonist (A, red circle) and exists in three distinct conformations: closed (C), open (O) and desensitized (D). The closed and open states share the same S1S2 dimer interface. After the binding of agonist, closure of domain 2 towards domain 1 opens the channel gate, whereas closure of domain 1 towards domain 2 disrupts the dimer interface and desensitizes the receptor. The states are connected by using a simplified model for activation and desensitization, more complex versions of which quantitatively describe AMPA receptor responses10,25. A hypothetical plot of the free-energy change occurring during activation and desensitization is shown in the lower left panel for the wild-type (black line), L483Y (green line) and S754D (red line) species.

The above figures are reprinted by permission from Macmillan Publishers Ltd: Nature (2002, 417, 245-253) copyright 2002.