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PDBsum entry 2a5s
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Metal transport,membrane protein
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PDB id
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2a5s
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Contents |
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* Residue conservation analysis
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DOI no:
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Nature
438:185-192
(2005)
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PubMed id:
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Subunit arrangement and function in NMDA receptors.
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H.Furukawa,
S.K.Singh,
R.Mancusso,
E.Gouaux.
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ABSTRACT
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Excitatory neurotransmission mediated by NMDA (N-methyl-D-aspartate) receptors
is fundamental to the physiology of the mammalian central nervous system. These
receptors are heteromeric ion channels that for activation require binding of
glycine and glutamate to the NR1 and NR2 subunits, respectively. NMDA receptor
function is characterized by slow channel opening and deactivation, and the
resulting influx of cations initiates signal transduction cascades that are
crucial to higher functions including learning and memory. Here we report
crystal structures of the ligand-binding core of NR2A with glutamate and that of
the NR1-NR2A heterodimer with glutamate and glycine. The NR2A-glutamate complex
defines the determinants of glutamate and NMDA recognition, and the NR1-NR2A
heterodimer suggests a mechanism for ligand-induced ion channel opening.
Analysis of the heterodimer interface, together with biochemical and
electrophysiological experiments, confirms that the NR1-NR2A heterodimer is the
functional unit in tetrameric NMDA receptors and that tyrosine 535 of NR1,
located in the subunit interface, modulates the rate of ion channel deactivation.
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Selected figure(s)
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Figure 2.
Figure 2: Structure of NR1-NR2A S1S2. a, Side view of the
NR1-NR2A S1S2 heterodimer in complex with glycine and glutamate.
NR1 and NR2A are coloured green and blue, respectively. Glycine,
glutamate and the C  atom
of the glycine residue in the Gly-Thr dipeptide linker are shown
as spheres. The arrow indicates the pseudo two-fold axis between
the protomers. b, View of the structure from the 'top'. The
interface between NR1 and NR2A is sliced into three sections
denoted sites I-III. c-e, Magnified view of the interactions at
sites I, II and III. Dashed lines indicate hydrogen bonds or
salt bridges. The interacting residues from NR1 and NR2A are
coloured white and orange, respectively. f, g, Structural
comparison between the NR1-NR2A (green-blue) S1S2 heterodimer
and the glutamate-bound GluR2 S1S2 (pink) homodimer (PDB code
1FTJ). Superimposed structures are viewed from the side and
'top' of the molecules in f and g, respectively. Superposition
was carried out on 256 residues from domain 1 with the program
LSQKAB^50. The C atoms
of the glycine residues in the Gly-Thr dipeptide linkers are
shown as spheres.
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Figure 5.
Figure 5: Superposition of NR1-NR2A S1S2 and the GluR2
S1S2-aniracetam complex. a, Overlay of the GluR2 S1S2 dimer
bound to glutamate and aniracetam (Ani, pink) onto the NR1-NR2A
S1S2 dimer (green and blue) viewed from the same angle as in
Fig. 1b. b, Magnification of the NR1 Y535 site and the
aniracetam-binding site viewed from the same angle as in a. Two
water molecules, W1 and W2 (cyan spheres), participate in
stabilizing the NR1-NR2A interaction. c, Side view of the NR1
Y535 site. Note that the position of the aniracetam molecule
(pink) overlaps with that of the aromatic side chain of NR1 Y535.
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The above figures are
reprinted
by permission from Macmillan Publishers Ltd:
Nature
(2005,
438,
185-192)
copyright 2005.
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Figures were
selected
by an automated process.
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Literature references that cite this PDB file's key reference
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PubMed id
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Reference
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A.Spalloni,
N.Origlia,
C.Sgobio,
A.Trabalza,
M.Nutini,
N.Berretta,
G.Bernardi,
L.Domenici,
M.Ammassari-Teule,
and
P.Longone
(2011).
Postsynaptic alteration of NR2A subunit and defective autophosphorylation of alphaCaMKII at threonine-286 contribute to abnormal plasticity and morphology of upper motor neurons in presymptomatic SOD1G93A mice, a murine model for amyotrophic lateral sclerosis.
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Cereb Cortex,
21,
796-805.
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D.Stroebel,
S.Carvalho,
and
P.Paoletti
(2011).
Functional evidence for a twisted conformation of the NMDA receptor GluN2A subunit N-terminal domain.
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Neuropharmacology,
60,
151-158.
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E.Karakas,
N.Simorowski,
and
H.Furukawa
(2011).
Subunit arrangement and phenylethanolamine binding in GluN1/GluN2B NMDA receptors.
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Nature,
475,
249-253.
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PDB codes:
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G.M.Alushin,
D.Jane,
and
M.L.Mayer
(2011).
Binding site and ligand flexibility revealed by high resolution crystal structures of GluK1 competitive antagonists.
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Neuropharmacology,
60,
126-134.
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PDB codes:
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H.J.Otton,
A.Lawson McLean,
M.A.Pannozzo,
C.H.Davies,
and
D.J.Wyllie
(2011).
Quantification of the Mg(2+)-induced potency shift of amantadine and memantine voltage-dependent block in human recombinant GluN1/GluN2A NMDARs.
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Neuropharmacology,
60,
388-396.
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I.Ali,
M.R.Salzberg,
C.French,
and
N.C.Jones
(2011).
Electrophysiological insights into the enduring effects of early life stress on the brain.
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Psychopharmacology (Berl),
214,
155-173.
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K.M.Vance,
N.Simorowski,
S.F.Traynelis,
and
H.Furukawa
(2011).
Ligand-specific deactivation time course of GluN1/GluN2D NMDA receptors.
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Nat Commun,
2,
294.
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PDB codes:
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M.Ghafari,
S.S.Patil,
H.Höger,
A.Pollak,
and
G.Lubec
(2011).
NMDA-complexes linked to spatial memory performance in the Barnes maze in CD1 mice.
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Behav Brain Res,
221,
142-148.
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P.Paoletti
(2011).
Molecular basis of NMDA receptor functional diversity.
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Eur J Neurosci,
33,
1351-1365.
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S.A.Amico-Ruvio,
S.E.Murthy,
T.P.Smith,
and
G.K.Popescu
(2011).
Zinc effects on NMDA receptor gating kinetics.
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Biophys J,
100,
1910-1918.
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S.R.Das,
and
K.R.Magnusson
(2011).
Changes in expression of splice cassettes of NMDA receptor GluN1 subunits within the frontal lobe and memory in mice during aging.
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Behav Brain Res,
222,
122-133.
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Z.Zhang,
and
Q.Q.Sun
(2011).
Development of NMDA NR2 subunits and their roles in critical period maturation of neocortical GABAergic interneurons.
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Dev Neurobiol,
71,
221-245.
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A.H.Ahmed,
and
R.E.Oswald
(2010).
Piracetam defines a new binding site for allosteric modulators of alpha-amino-3-hydroxy-5-methyl-4-isoxazole-propionic acid (AMPA) receptors.
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J Med Chem,
53,
2197-2203.
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PDB codes:
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J.Herrou,
C.Bompard,
R.Wintjens,
E.Dupré,
E.Willery,
V.Villeret,
C.Locht,
R.Antoine,
and
F.Jacob-Dubuisson
(2010).
Periplasmic domain of the sensor-kinase BvgS reveals a new paradigm for the Venus flytrap mechanism.
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Proc Natl Acad Sci U S A,
107,
17351-17355.
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PDB codes:
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J.Z.Ma,
T.J.Payne,
and
M.D.Li
(2010).
Significant association of glutamate receptor, ionotropic N-methyl-D-aspartate 3A (GRIN3A), with nicotine dependence in European- and African-American smokers.
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Hum Genet,
127,
503-512.
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M.A.Henson,
A.C.Roberts,
I.Pérez-Otaño,
and
B.D.Philpot
(2010).
Influence of the NR3A subunit on NMDA receptor functions.
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Prog Neurobiol,
91,
23-37.
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R.Risgaard,
K.B.Hansen,
and
R.P.Clausen
(2010).
Partial agonists and subunit selectivity at NMDA receptors.
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Chemistry,
16,
13910-13918.
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R.Vijayan,
M.A.Sahai,
T.Czajkowski,
and
P.C.Biggin
(2010).
A comparative analysis of the role of water in the binding pockets of ionotropic glutamate receptors.
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Phys Chem Chem Phys,
12,
14057-14066.
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S.Endele,
G.Rosenberger,
K.Geider,
B.Popp,
C.Tamer,
I.Stefanova,
M.Milh,
F.Kortüm,
A.Fritsch,
F.K.Pientka,
Y.Hellenbroich,
V.M.Kalscheuer,
J.Kohlhase,
U.Moog,
G.Rappold,
A.Rauch,
H.H.Ropers,
S.von Spiczak,
H.Tönnies,
N.Villeneuve,
L.Villard,
B.Zabel,
M.Zenker,
B.Laube,
A.Reis,
D.Wieczorek,
L.Van Maldergem,
and
K.Kutsche
(2010).
Mutations in GRIN2A and GRIN2B encoding regulatory subunits of NMDA receptors cause variable neurodevelopmental phenotypes.
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Nat Genet,
42,
1021-1026.
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S.M.Dravid,
P.B.Burger,
A.Prakash,
M.T.Geballe,
R.Yadav,
P.Le,
K.Vellano,
J.P.Snyder,
and
S.F.Traynelis
(2010).
Structural determinants of D-cycloserine efficacy at the NR1/NR2C NMDA receptors.
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J Neurosci,
30,
2741-2754.
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T.Nakagawa
(2010).
The biochemistry, ultrastructure, and subunit assembly mechanism of AMPA receptors.
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Mol Neurobiol,
42,
161-184.
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X.Zhou,
Z.Nie,
A.Roberts,
D.Zhang,
J.Sebat,
D.Malhotra,
J.R.Kelsoe,
and
M.A.Geyer
(2010).
Reduced NMDAR1 expression in the Sp4 hypomorphic mouse may contribute to endophenotypes of human psychiatric disorders.
|
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Hum Mol Genet,
19,
3797-3805.
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A.H.Ahmed,
Q.Wang,
H.Sondermann,
and
R.E.Oswald
(2009).
Structure of the S1S2 glutamate binding domain of GLuR3.
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Proteins,
75,
628-637.
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PDB codes:
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A.I.Sobolevsky,
M.P.Rosconi,
and
E.Gouaux
(2009).
X-ray structure, symmetry and mechanism of an AMPA-subtype glutamate receptor.
|
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Nature,
462,
745-756.
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PDB codes:
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B.Gu,
N.Nakamichi,
W.S.Zhang,
Y.Nakamura,
Y.Kambe,
R.Fukumori,
K.Takuma,
K.Yamada,
T.Takarada,
H.Taniura,
and
Y.Yoneda
(2009).
Possible protection by notoginsenoside R1 against glutamate neurotoxicity mediated by N-methyl-D-aspartate receptors composed of an NR1/NR2B subunit assembly.
|
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J Neurosci Res,
87,
2145-2156.
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C.A.Puddifoot,
P.E.Chen,
R.Schoepfer,
and
D.J.Wyllie
(2009).
Pharmacological characterization of recombinant NR1/NR2A NMDA receptors with truncated and deleted carboxy termini expressed in Xenopus laevis oocytes.
|
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Br J Pharmacol,
156,
509-518.
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C.Chaudhry,
A.J.Plested,
P.Schuck,
and
M.L.Mayer
(2009).
Energetics of glutamate receptor ligand binding domain dimer assembly are modulated by allosteric ions.
|
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Proc Natl Acad Sci U S A,
106,
12329-12334.
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C.Chaudhry,
M.C.Weston,
P.Schuck,
C.Rosenmund,
and
M.L.Mayer
(2009).
Stability of ligand-binding domain dimer assembly controls kainate receptor desensitization.
|
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EMBO J,
28,
1518-1530.
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PDB codes:
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C.H.Lin,
C.C.Chen,
C.M.Chou,
C.Y.Wang,
C.C.Hung,
J.Y.Chen,
H.W.Chang,
Y.C.Chen,
G.C.Yeh,
and
Y.H.Lee
(2009).
Knockdown of the aryl hydrocarbon receptor attenuates excitotoxicity and enhances NMDA-induced BDNF expression in cortical neurons.
|
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J Neurochem,
111,
777-789.
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C.L.Kussius,
and
G.K.Popescu
(2009).
Kinetic basis of partial agonism at NMDA receptors.
|
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Nat Neurosci,
12,
1114-1120.
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E.Karakas,
N.Simorowski,
and
H.Furukawa
(2009).
Structure of the zinc-bound amino-terminal domain of the NMDA receptor NR2B subunit.
|
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EMBO J,
28,
3910-3920.
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PDB codes:
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G.T.Swanson,
and
R.Sakai
(2009).
Ligands for ionotropic glutamate receptors.
|
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Prog Mol Subcell Biol,
46,
123-157.
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H.Yuan,
K.B.Hansen,
K.M.Vance,
K.K.Ogden,
and
S.F.Traynelis
(2009).
Control of NMDA receptor function by the NR2 subunit amino-terminal domain.
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J Neurosci,
29,
12045-12058.
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J.P.Ridge,
A.M.Ho,
and
P.R.Dodd
(2009).
Sex differences in NMDA receptor expression in human alcoholics.
|
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Alcohol Alcohol,
44,
594-601.
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K.Frydenvang,
L.L.Lash,
P.Naur,
P.A.Postila,
D.S.Pickering,
C.M.Smith,
M.Gajhede,
M.Sasaki,
R.Sakai,
O.T.Pentikaïnen,
G.T.Swanson,
and
J.S.Kastrup
(2009).
Full Domain Closure of the Ligand-binding Core of the Ionotropic Glutamate Receptor iGluR5 Induced by the High Affinity Agonist Dysiherbaine and the Functional Antagonist 8,9-Dideoxyneodysiherbaine.
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J Biol Chem,
284,
14219-14229.
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PDB codes:
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M.Baudry
(2009).
Multi-level control of ionotropic glutamate receptor function.
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Cellscience,
6,
79.
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M.Gielen,
B.Siegler Retchless,
L.Mony,
J.W.Johnson,
and
P.Paoletti
(2009).
Mechanism of differential control of NMDA receptor activity by NR2 subunits.
|
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Nature,
459,
703-707.
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M.Sivaprakasam,
K.B.Hansen,
O.David,
B.Nielsen,
S.F.Traynelis,
R.P.Clausen,
F.Couty,
and
L.Bunch
(2009).
Stereocontrolled synthesis and pharmacological evaluation of azetidine-2,3-dicarboxylic acids at NMDA receptors.
|
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ChemMedChem,
4,
110-117.
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Y.Shinohara,
and
H.Hirase
(2009).
Size and Receptor Density of Glutamatergic Synapses: A Viewpoint from Left-Right Asymmetry of CA3-CA1 Connections.
|
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Front Neuroanat,
3,
10.
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Z.Sheng,
Z.Liang,
J.H.Geiger,
M.Prorok,
and
F.J.Castellino
(2009).
The selectivity of conantokin-G for ion channel inhibition of NR2B subunit-containing NMDA receptors is regulated by amino acid residues in the S2 region of NR2B.
|
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Neuropharmacology,
57,
127-136.
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C.Madry,
H.Betz,
J.R.Geiger,
and
B.Laube
(2008).
Supralinear potentiation of NR1/NR3A excitatory glycine receptors by Zn2+ and NR1 antagonist.
|
| |
Proc Natl Acad Sci U S A,
105,
12563-12568.
|
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C.Villmann,
J.Hoffmann,
M.Werner,
S.Kott,
N.Strutz-Seebohm,
T.Nilsson,
and
M.Hollmann
(2008).
Different structural requirements for functional ion pore transplantation suggest different gating mechanisms of NMDA and kainate receptors.
|
| |
J Neurochem,
107,
453-465.
|
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E.J.Bjerrum,
and
P.C.Biggin
(2008).
Rigid body essential X-ray crystallography: distinguishing the bend and twist of glutamate receptor ligand binding domains.
|
| |
Proteins,
72,
434-446.
|
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F.M.Ng,
M.T.Geballe,
J.P.Snyder,
S.F.Traynelis,
and
C.M.Low
(2008).
Structural insights into phenylethanolamines high-affinity binding site in NR2B from binding and molecular modeling studies.
|
| |
Mol Brain,
1,
16.
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J.P.Ridge,
A.M.Ho,
D.J.Innes,
and
P.R.Dodd
(2008).
The expression of NMDA receptor subunit mRNA in human chronic alcoholics.
|
| |
Ann N Y Acad Sci,
1139,
10-19.
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K.Watanabe,
T.Kanno,
T.Oshima,
H.Miwa,
C.Tashiro,
and
T.Nishizaki
(2008).
Vagotomy upregulates expression of the N-methyl-D-aspartate receptor NR2D subunit in the stomach.
|
| |
J Gastroenterol,
43,
322-326.
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M.Du,
A.Rambhadran,
and
V.Jayaraman
(2008).
Luminescence resonance energy transfer investigation of conformational changes in the ligand binding domain of a kainate receptor.
|
| |
J Biol Chem,
283,
27074-27078.
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M.Gielen,
A.Le Goff,
D.Stroebel,
J.W.Johnson,
J.Neyton,
and
P.Paoletti
(2008).
Structural rearrangements of NR1/NR2A NMDA receptors during allosteric inhibition.
|
| |
Neuron,
57,
80-93.
|
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M.H.Ulbrich,
and
E.Y.Isacoff
(2008).
Rules of engagement for NMDA receptor subunits.
|
| |
Proc Natl Acad Sci U S A,
105,
14163-14168.
|
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|
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M.L.Blanke,
and
A.M.VanDongen
(2008).
Constitutive activation of the N-methyl-D-aspartate receptor via cleft-spanning disulfide bonds.
|
| |
J Biol Chem,
283,
21519-21529.
|
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N.P.Barrera,
and
J.M.Edwardson
(2008).
The subunit arrangement and assembly of ionotropic receptors.
|
| |
Trends Neurosci,
31,
569-576.
|
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|
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R.Gómez-Nieto,
J.A.Horta-Junior,
O.Castellano,
M.J.Herrero-Turrión,
M.E.Rubio,
and
D.E.López
(2008).
Neurochemistry of the afferents to the rat cochlear root nucleus: possible synaptic modulation of the acoustic startle.
|
| |
Neuroscience,
154,
51-64.
|
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|
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S.M.Schmid,
and
M.Hollmann
(2008).
To gate or not to gate: are the delta subunits in the glutamate receptor family functional ion channels?
|
| |
Mol Neurobiol,
37,
126-141.
|
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|
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S.S.Ali,
J.I.Hardt,
and
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PDB codes:
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PDB code:
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PDB codes:
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PDB codes:
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PDB codes:
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M.L.Mayer
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The most recent references are shown first.
Citation data come partly from CiteXplore and partly
from an automated harvesting procedure. Note that this is likely to be
only a partial list as not all journals are covered by
either method. However, we are continually building up the citation data
so more and more references will be included with time.
Where a reference describes a PDB structure, the PDB
codes are
shown on the right.
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|
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