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PDBsum entry 1m5d

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Membrane protein PDB id
1m5d
Jmol
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-y702 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 ionotr 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    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P19491  (GRIA2_RAT) -  Glutamate receptor 2
Seq:
Struc:
 
Seq:
Struc:
883 a.a.
258 a.a.*
Key:    PfamA domain  PfamB domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 3 residue positions (black crosses)

 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     membrane   1 term 
  Biological process     transport   1 term 
  Biochemical function     transporter activity     3 terms  

 

 
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.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21516102 A.S.Kristensen, M.A.Jenkins, T.G.Banke, A.Schousboe, Y.Makino, R.C.Johnson, R.Huganir, and S.F.Traynelis (2011).
Mechanism of Ca(2+)/calmodulin-dependent kinase II regulation of AMPA receptor gating.
  Nat Neurosci, 14, 727-735.  
21317895 A.Y.Lau, and B.Roux (2011).
The hidden energetics of ligand binding and activation in a glutamate receptor.
  Nat Struct Mol Biol, 18, 283-287.  
20558186 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.
  Neuropharmacology, 60, 126-134.
PDB codes: 2qs1 2qs2 2qs4
20713069 J.Pøhlsgaard, K.Frydenvang, U.Madsen, and J.S.Kastrup (2011).
Lessons from more than 80 structures of the GluA2 ligand-binding domain in complex with agonists, antagonists and allosteric modulators.
  Neuropharmacology, 60, 135-150.  
20107073 A.Birdsey-Benson, A.Gill, L.P.Henderson, and D.R.Madden (2010).
Enhanced efficacy without further cleft closure: reevaluating twist as a source of agonist efficacy in AMPA receptors.
  J Neurosci, 30, 1463-1470.
PDB codes: 3kei 3kfm
20155979 A.F.Petrik, M.P.Strub, and J.C.Lee (2010).
Energy transfer ligands of the GluR2 ligand binding core.
  Biochemistry, 49, 2051-2057.  
20163115 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.
  J Med Chem, 53, 2197-2203.
PDB codes: 3lsf 3lsl 3lsw 3lsx
20457909 J.Gonzalez, M.Du, K.Parameshwaran, V.Suppiramaniam, and V.Jayaraman (2010).
Role of dimer interface in activation and desensitization in AMPA receptors.
  Proc Natl Acad Sci U S A, 107, 9891-9896.  
20877838 R.Edwards, J.Madine, L.Fielding, and D.A.Middleton (2010).
Measurement of multiple torsional angles from one-dimensional solid-state NMR spectra: application to the conformational analysis of a ligand in its biological receptor site.
  Phys Chem Chem Phys, 12, 13999-14008.  
19003990 A.H.Ahmed, Q.Wang, H.Sondermann, and R.E.Oswald (2009).
Structure of the S1S2 glutamate binding domain of GLuR3.
  Proteins, 75, 628-637.
PDB codes: 3dln 3dp4 3dp6
19779829 D.B.Tikhonov, and L.G.Magazanik (2009).
Origin and molecular evolution of ionotropic glutamate receptors.
  Neurosci Behav Physiol, 39, 763-773.  
18214958 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.  
18754610 L.A.Cruz, E.Estébanez-Perpiñá, S.Pfaff, S.Borngraeber, N.Bao, J.Blethrow, R.J.Fletterick, and P.M.England (2008).
6-Azido-7-nitro-1,4-dihydroquinoxaline-2,3-dione (ANQX) forms an irreversible bond to the active site of the GluR2 AMPA receptor.
  J Med Chem, 51, 5856-5860.
PDB code: 3bki
18387631 M.K.Fenwick, and R.E.Oswald (2008).
NMR spectroscopy of the ligand-binding core of ionotropic glutamate receptor 2 bound to 5-substituted willardiine partial agonists.
  J Mol Biol, 378, 673-685.  
18491377 T.Mamonova, K.Speranskiy, and M.Kurnikova (2008).
Interplay between structural rigidity and electrostatic interactions in the ligand binding domain of GluR2.
  Proteins, 73, 656-671.  
18823129 T.Mamonova, M.J.Yonkunas, and M.G.Kurnikova (2008).
Energetics of the cleft closing transition and the role of electrostatic interactions in conformational rearrangements of the glutamate receptor ligand binding domain.
  Biochemistry, 47, 11077-11085.  
18022568 B.H.Kaae, K.Harpsøe, J.S.Kastrup, A.C.Sanz, D.S.Pickering, B.Metzler, R.P.Clausen, M.Gajhede, P.Sauerberg, T.Liljefors, and U.Madsen (2007).
Structural proof of a dimeric positive modulator bridging two identical AMPA receptor-binding sites.
  Chem Biol, 14, 1294-1303.
PDB code: 3bbr
16892196 D.Catarzi, V.Colotta, and F.Varano (2007).
Competitive AMPA receptor antagonists.
  Med Res Rev, 27, 239-278.  
16406088 A.S.Kristensen, M.T.Geballe, J.P.Snyder, and S.F.Traynelis (2006).
Glutamate receptors: variation in structure-function coupling.
  Trends Pharmacol Sci, 27, 65-69.  
16793923 G.Ramanoudjame, M.Du, K.A.Mankiewicz, and V.Jayaraman (2006).
Allosteric mechanism in AMPA receptors: a FRET-based investigation of conformational changes.
  Proc Natl Acad Sci U S A, 103, 10473-10478.  
17115050 M.C.Weston, P.Schuck, A.Ghosal, C.Rosenmund, and M.L.Mayer (2006).
Conformational restriction blocks glutamate receptor desensitization.
  Nat Struct Mol Biol, 13, 1120-1127.
PDB codes: 2i0b 2i0c
16554805 M.L.Mayer (2006).
Glutamate receptors at atomic resolution.
  Nature, 440, 456-462.  
16474411 P.E.Chen, and D.J.Wyllie (2006).
Pharmacological insights obtained from structure-function studies of ionotropic glutamate receptors.
  Br J Pharmacol, 147, 839-853.  
16731549 W.Zhang, A.Robert, S.B.Vogensen, and J.R.Howe (2006).
The relationship between agonist potency and AMPA receptor kinetics.
  Biophys J, 91, 1336-1346.  
15996549 A.Inanobe, H.Furukawa, and E.Gouaux (2005).
Mechanism of partial agonist action at the NR1 subunit of NMDA receptors.
  Neuron, 47, 71-84.
PDB codes: 1y1m 1y1z 1y20
15794751 B.B.Nielsen, D.S.Pickering, J.R.Greenwood, L.Brehm, M.Gajhede, A.Schousboe, and J.S.Kastrup (2005).
Exploring the GluR2 ligand-binding core in complex with the bicyclical AMPA analogue (S)-4-AHCP.
  FEBS J, 272, 1639-1648.
PDB code: 1wvj
16043357 B.Frølund, J.R.Greenwood, M.M.Holm, J.Egebjerg, U.Madsen, B.Nielsen, H.Bräuner-Osborne, T.B.Stensbøl, and P.Krogsgaard-Larsen (2005).
Tetrazolyl isoxazole amino acids as ionotropic glutamate receptor antagonists: synthesis, modelling and molecular pharmacology.
  Bioorg Med Chem, 13, 5391-5398.  
15755731 D.R.Madden, N.Armstrong, D.Svergun, J.Pérez, and P.Vachette (2005).
Solution X-ray scattering evidence for agonist- and antagonist-induced modulation of cleft closure in a glutamate receptor ligand-binding domain.
  J Biol Chem, 280, 23637-23642.  
16240010 H.Bräuner-Osborne, L.Bunch, N.Chopin, F.Couty, G.Evano, A.A.Jensen, M.Kusk, B.Nielsen, and N.Rabasso (2005).
Azetidinic amino acids: stereocontrolled synthesis and pharmacological characterization as ligands for glutamate receptors and transporters.
  Org Biomol Chem, 3, 3926-3936.  
15632199 M.Du, S.A.Reid, and V.Jayaraman (2005).
Conformational changes in the ligand-binding domain of a functional ionotropic glutamate receptor.
  J Biol Chem, 280, 8633-8636.  
15677325 M.H.Nanao, T.Green, Y.Stern-Bach, S.F.Heinemann, and S.Choe (2005).
Structure of the kainate receptor subunit GluR6 agonist-binding domain complexed with domoic acid.
  Proc Natl Acad Sci U S A, 102, 1708-1713.
PDB code: 1yae
15919192 M.L.Mayer (2005).
Glutamate receptor ion channels.
  Curr Opin Neurobiol, 15, 282-288.  
16099829 M.M.Holm, M.L.Lunn, S.F.Traynelis, J.S.Kastrup, and J.Egebjerg (2005).
Structural determinants of agonist-specific kinetics at the ionotropic glutamate receptor 2.
  Proc Natl Acad Sci U S A, 102, 12053-12058.  
16103115 M.M.Holm, P.Naur, B.Vestergaard, M.T.Geballe, M.Gajhede, J.S.Kastrup, S.F.Traynelis, and J.Egebjerg (2005).
A binding site tyrosine shapes desensitization kinetics and agonist potency at GluR2. A mutagenic, kinetic, and crystallographic study.
  J Biol Chem, 280, 35469-35476.
PDB code: 2anj
16280619 T.Mamonova, B.Hespenheide, R.Straub, M.F.Thorpe, and M.Kurnikova (2005).
Protein flexibility using constraints from molecular dynamics simulations.
  Phys Biol, 2, S137-S147.  
15224382 K.Strømgaard, and I.Mellor (2004).
AMPA receptor ligands: synthetic and pharmacological studies of polyamines and polyamine toxins.
  Med Res Rev, 24, 589-620.  
15236343 L.Brehm, J.R.Greenwood, F.A.Sløk, M.M.Holm, B.Nielsen, U.Geneser, T.B.Stensbøl, H.Bräuner-Osborne, M.Begtrup, J.Egebjerg, and P.Krogsgaard-Larsen (2004).
Synthesis, theoretical and structural analyses, and enantiopharmacology of 3-carboxy homologs of AMPA.
  Chirality, 16, 452-466.  
15229875 M.Kubo, and E.Ito (2004).
Structural dynamics of an ionotropic glutamate receptor.
  Proteins, 56, 411-419.  
14977400 M.L.Mayer, and N.Armstrong (2004).
Structure and function of glutamate receptor ion channels.
  Annu Rev Physiol, 66, 161-181.  
15100219 Q.Cheng, and V.Jayaraman (2004).
Chemistry and conformation of the ligand-binding domain of GluR2 subtype of glutamate receptors.
  J Biol Chem, 279, 26346-26350.  
14573861 A.Datta, and M.J.Stone (2003).
Soluble mimics of a chemokine receptor: chemokine binding by receptor elements juxtaposed on a soluble scaffold.
  Protein Sci, 12, 2482-2491.  
12520509 T.N.Johansen, J.R.Greenwood, K.Frydenvang, U.Madsen, and P.Krogsgaard-Larsen (2003).
Stereostructure-activity studies on agonists at the AMPA and kainate subtypes of ionotropic glutamate receptors.
  Chirality, 15, 167-179.  
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.