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* Residue conservation analysis
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References listed in PDB file
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Key reference
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Title
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Glur2 ligand-Binding core complexes: importance of the isoxazolol moiety and 5-Substituent for the binding mode of ampa-Type agonists.
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Authors
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C.Kasper,
M.L.Lunn,
T.Liljefors,
E.Gouaux,
J.Egebjerg,
J.S.Kastrup.
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Ref.
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FEBS Lett, 2002,
531,
173-178.
[DOI no: ]
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PubMed id
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Abstract
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X-ray structures of the GluR2 ligand-binding core in complex with
(S)-Des-Me-AMPA and in the presence and absence of zinc ions have been
determined. (S)-Des-Me-AMPA, which is devoid of a substituent in the 5-position
of the isoxazolol ring, only has limited interactions with the partly
hydrophobic pocket of the ligand-binding site, and adopts an AMPA-like binding
mode. The structures, in comparison with other agonist complex structures,
disclose the relative importance of the isoxazolol ring and of the substituent
in the 5-position for the mode of binding. A relationship appears to exist
between the extent of interaction of the ligand with the hydrophobic pocket and
the affinity of the ligand.
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Figure 1.
Fig. 1. A: The GluR2-S1S2J construct, comprising the
ligand-binding core of the AMPA-receptor subunit GluR2, is
composed of segments S1 and S2, joined by a linker (dashed
line). The two domains D1 and D2 are shown in yellow and green,
respectively. The amino-terminal domain is outlined as a red
sphere, and integral membrane parts are blue. B: The chemical
structures of (S)-Des-Me-AMPA, (S)-AMPA and (S)-2-Me-Tet-AMPA.
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Figure 3.
Fig. 3. The ligand-binding site of GluR2-S1S2J. A:
Interactions between GluR2-S1S2J and (S)-Des-Me-AMPA. Dashed
lines indicate potential hydrogen bonds/ionic interactions (up
to 3.3 Å). Water molecules are displayed as red spheres.
Nitrogen atoms are shown in blue, oxygen atoms in red, and
sulfur atoms in dark green. B: Superimposition of the
(S)-Des-Me-AMPA (cyan), (S)-AMPA (green), (S)-2-Me-Tet-AMPA
(magenta) and (S)-glutamate (yellow) complexes (shown in
stereo). For all structures MolA is used as a representative.
The conformation of Met708 in the glutamate complex is unique
for MolA, as the other two molecules have extended Met708 chains.
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The above figures are
reprinted
by permission from the Federation of European Biochemical Societies:
FEBS Lett
(2002,
531,
173-178)
copyright 2002.
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Secondary reference #1
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Title
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Structural basis for ampa receptor activation and ligand selectivity: crystal structures of five agonist complexes with the glur2 ligand-Binding core.
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Authors
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A.Hogner,
J.S.Kastrup,
R.Jin,
T.Liljefors,
M.L.Mayer,
J.Egebjerg,
I.K.Larsen,
E.Gouaux.
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Ref.
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J Mol Biol, 2002,
322,
93.
[DOI no: ]
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PubMed id
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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.]
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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.).
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The above figures are
reproduced from the cited reference
with permission from Elsevier
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Secondary reference #2
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Title
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Mechanisms for activation and antagonism of an ampa-Sensitive glutamate receptor: crystal structures of the glur2 ligand binding core.
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Authors
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N.Armstrong,
E.Gouaux.
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Ref.
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Neuron, 2000,
28,
165-181.
[DOI no: ]
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PubMed id
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Figure 1.
Figure 1. Ligand Binding Constants for S1S2J(A) Domain
structure of iGluRs showing the S1 and S2 segments in turquoise
and pink, respectively. “Cut” and “link” denote the
edges of the S1S2 construct.(B) K[D] for ^3H-AMPA binding was
24.8 ± 1.8 nM.(C) IC[50] for displacement of ^3H-AMPA by
glutamate, kainate, and DNQX were 821 nM, 14.5 μM, and 998 nM,
respectively.
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Figure 2.
Figure 2. Superposition of the Expanded Cleft Structures and
Stereo View of the DNQX Binding Site(A) The two apo molecules
(ApoA and ApoB) and two DNQX molecules (DNQXA and DNQXB) in each
asymmetric unit were superimposed using only Cα atoms from
domain 1. Apo protomers are shaded red and pink while DNQX
protomers are colored light green and dark green. DNQX is
depicted in black, and selected side chains from DNQXB are shown
in dark green. The conformational change undergone by Glu-705 is
illustrated by comparing its orientation in ApoB and DNQXB. In
the apo state, Glu-705 accepts hydrogen bonds from the side
chains of Lys-730 and Thr-655.(B) The chemical structure of DNQX
and F[o]-F[c] omit electron density for DNQX and sulfate
contoured at 2.5 σ.(C) Stereo image of the interactions between
DNQX, sulfate, and S1S2J. DNQXB side chains are colored gray.
Water molecules are shown as green balls. DNQX is colored black.
Hydrogen bonds between DNQX, sulfate, and S1S2J are indicated by
black dashed lines.
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The above figures are
reproduced from the cited reference
with permission from Cell Press
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Secondary reference #3
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Title
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Mechanism of glutamate receptor desensitization.
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Authors
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Y.Sun,
R.Olson,
M.Horning,
N.Armstrong,
M.Mayer,
E.Gouaux.
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Ref.
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Nature, 2002,
417,
245-253.
[DOI no: ]
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PubMed id
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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.
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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
in the DNQX structure and 36.3 in the AMPA structure. In
addition, Ile 633 rotates around the 2-fold axis by 1.25 and
moves 2.5 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.
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The above figures are
reproduced from the cited reference
with permission from Macmillan Publishers Ltd
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Secondary reference #4
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Title
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Probing the ligand binding domain of the glur2 receptor by proteolysis and deletion mutagenesis defines domain boundaries and yields a crystallizable construct.
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Authors
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G.Q.Chen,
Y.Sun,
R.Jin,
E.Gouaux.
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Ref.
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Protein Sci, 1998,
7,
2623-2630.
[DOI no: ]
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PubMed id
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