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PDBsum entry 1p1w

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protein ligands Protein-protein interface(s) links
Membrane protein PDB id
1p1w
Jmol
Contents
Protein chains
258 a.a. *
Ligands
SO4 ×2
AMQ ×2
Waters ×235
* Residue conservation analysis
PDB id:
1p1w
Name: Membrane protein
Title: Crystal structure of the glur2 ligand-binding core (s1s2j) with the l483y and l650t mutations and in complex with ampa
Structure: Glutamate receptor 2 precursor. Chain: a, b. Fragment: ligand binding core (s1s2j). 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: gria2 or glur2. Expressed in: escherichia coli bl21. Expression_system_taxid: 511693.
Biol. unit: Dimer (from PQS)
Resolution:
1.80Å     R-factor:   0.234     R-free:   0.264
Authors: N.Armstrong,M.L.Mayer,E.Gouaux
Key ref:
N.Armstrong et al. (2003). Tuning activation of the AMPA-sensitive GluR2 ion channel by genetic adjustment of agonist-induced conformational changes. Proc Natl Acad Sci U S A, 100, 5736-5741. PubMed id: 12730367 DOI: 10.1073/pnas.1037393100
Date:
14-Apr-03     Release date:   10-Jun-03    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
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 4 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: 10.1073/pnas.1037393100 Proc Natl Acad Sci U S A 100:5736-5741 (2003)
PubMed id: 12730367  
 
 
Tuning activation of the AMPA-sensitive GluR2 ion channel by genetic adjustment of agonist-induced conformational changes.
N.Armstrong, M.Mayer, E.Gouaux.
 
  ABSTRACT  
 
The (S)-2-amino-3-(3-hydroxy-5-methyl-4-isoxazole) propionic acid (AMPA) receptor discriminates between agonists in terms of binding and channel gating; AMPA is a high-affinity full agonist, whereas kainate is a low-affinity partial agonist. Although there is extensive literature on the functional characterization of partial agonist activity in ion channels, structure-based mechanisms are scarce. Here we investigate the role of Leu-650, a binding cleft residue conserved among AMPA receptors, in maintaining agonist specificity and regulating agonist binding and channel gating by using physiological, x-ray crystallographic, and biochemical techniques. Changing Leu-650 to Thr yields a receptor that responds more potently and efficaciously to kainate and less potently and efficaciously to AMPA relative to the WT receptor. Crystal structures of the Leu-650 to Thr mutant reveal an increase in domain closure in the kainate-bound state and a partially closed and a fully closed conformation in the AMPA-bound form. Our results indicate that agonists can induce a range of conformations in the GluR2 ligand-binding core and that domain closure is directly correlated to channel activation. The partially closed, AMPA-bound conformation of the L650T mutant likely captures the structure of an agonist-bound, inactive state of the receptor. Together with previously solved structures, we have determined a mechanism of agonist binding and subsequent conformational rearrangements.
 
  Selected figure(s)  
 
Figure 4.
Fig. 4. Comparison of WT and S1S2J L650T/AMPA(AS) conformations. (A) Superposition of WT S1S2J/AMPA (gray) with S1S2J L650T/AMPA (AS form) protomer A (blue). (B) Superposition of WT S1S2J/AMPA (gray) with S1S2J L650T/AMPA(AS) protomer B (green). The black arrows in A and B indicate the axis of rotation relating the conformational difference between the WT and L650T structures. (C) Superimposed WT and mutant AMPA dimers.
Figure 6.
Fig. 6. Mechanism of agonist binding and domain closure. (A) The binding site of the open-cleft, closed-channel state (Apo S1S2J, protomer A). (B) The possible first step in agonist binding as observed in molecule B of the L650T/AMPA(AS) structure. We suggest that this semiclosed cleft conformation represents the agonist-bound, closed-channel state. (C) The closed-cleft, open-channel conformation as observed in the WT S1S2J/AMPA binding cleft (protomer A). In B and C, water molecules are shown as green spheres, AMPA is drawn in magenta, and hydrogen bonds are depicted by black dashed lines. The degrees of domain closure relative to the Apo conformation are indicated below each structure.
 
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21297640 C.F.Landes, A.Rambhadran, J.N.Taylor, F.Salatan, and V.Jayaraman (2011).
Structural landscape of isolated agonist-binding domains from single AMPA receptors.
  Nat Chem Biol, 7, 168-173.  
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
20110361 M.K.Fenwick, and R.E.Oswald (2010).
On the mechanisms of alpha-amino-3-hydroxy-5-methylisoxazole-4-propionic acid (AMPA) receptor binding to glutamate and kainate.
  J Biol Chem, 285, 12334-12343.  
19737573 P.A.Postila, G.T.Swanson, and O.T.Pentikäinen (2010).
Exploring kainate receptor pharmacology using molecular dynamics simulations.
  Neuropharmacology, 58, 515-527.  
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.  
21080238 T.Nakagawa (2010).
The biochemistry, ultrastructure, and subunit assembly mechanism of AMPA receptors.
  Mol Neurobiol, 42, 161-184.  
20404149 U.Das, J.Kumar, M.L.Mayer, and A.J.Plested (2010).
Domain organization and function in GluK2 subtype kainate receptors.
  Proc Natl Acad Sci U S A, 107, 8463-8468.  
19284741 A.H.Ahmed, M.D.Thompson, M.K.Fenwick, B.Romero, A.P.Loh, D.E.Jane, H.Sondermann, and R.E.Oswald (2009).
Mechanisms of antagonism of the GluR2 AMPA receptor: structure and dynamics of the complex of two willardiine antagonists with the glutamate binding domain.
  Biochemistry, 48, 3894-3903.
PDB codes: 3h03 3h06
19776277 A.J.Plested, and M.L.Mayer (2009).
AMPA receptor ligand binding domain mobility revealed by functional cross linking.
  J Neurosci, 29, 11912-11923.  
19297335 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.
  J Biol Chem, 284, 14219-14229.
PDB codes: 3gba 3gbb
19544581 M.Du, A.Rambhadran, and V.Jayaraman (2009).
Vibrational spectroscopic investigation of the ligand binding domain of kainate receptors.
  Protein Sci, 18, 1585-1591.  
19102704 A.Gill, A.Birdsey-Benson, B.L.Jones, L.P.Henderson, and D.R.Madden (2008).
Correlating AMPA receptor activation and cleft closure across subunits: crystal structures of the GluR4 ligand-binding domain in complex with full and partial agonists.
  Biochemistry, 47, 13831-13841.
PDB codes: 3en3 3epe
18795801 A.S.Maltsev, A.H.Ahmed, M.K.Fenwick, D.E.Jane, and R.E.Oswald (2008).
Mechanism of partial agonism at the GluR2 AMPA receptor: Measurements of lobe orientation in solution.
  Biochemistry, 47, 10600-10610.  
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.  
18759455 J.Gonzalez, A.Rambhadran, M.Du, and V.Jayaraman (2008).
LRET investigations of conformational changes in the ligand binding domain of a functional AMPA receptor.
  Biochemistry, 47, 10027-10032.  
18081322 K.A.Mankiewicz, A.Rambhadran, L.Wathen, and V.Jayaraman (2008).
Chemical interplay in the mechanism of partial agonist activation in alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid receptors.
  Biochemistry, 47, 398-404.  
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.  
18450751 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.  
18636091 Y.Yao, C.B.Harrison, P.L.Freddolino, K.Schulten, and M.L.Mayer (2008).
Molecular mechanism of ligand recognition by NR3 subtype glutamate receptors.
  EMBO J, 27, 2158-2170.
PDB codes: 2rc7 2rc8 2rc9 2rca 2rcb
17937910 A.Y.Lau, and B.Roux (2007).
The free energy landscapes governing conformational changes in a glutamate receptor ligand-binding domain.
  Structure, 15, 1203-1214.  
17260963 K.A.Mankiewicz, A.Rambhadran, M.Du, G.Ramanoudjame, and V.Jayaraman (2007).
Role of the chemical interactions of the agonist in controlling alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid receptor activation.
  Biochemistry, 46, 1343-1349.  
17934637 K.A.Mankiewicz, and V.Jayaraman (2007).
Glutamate receptors as seen by light: spectroscopic studies of structure-function relationships.
  Braz J Med Biol Res, 40, 1419-1427.  
17975069 K.Menuz, R.M.Stroud, R.A.Nicoll, and F.A.Hays (2007).
TARP auxiliary subunits switch AMPA receptor antagonists into partial agonists.
  Science, 318, 815-817.
PDB code: 3b7d
17588619 M.Du, H.Ulrich, X.Zhao, J.Aronowski, and V.Jayaraman (2007).
Water soluble RNA based antagonist of AMPA receptors.
  Neuropharmacology, 53, 242-251.  
16818875 C.S.Walker, M.M.Francis, P.J.Brockie, D.M.Madsen, Y.Zheng, and A.V.Maricq (2006).
Conserved SOL-1 proteins regulate ionotropic glutamate receptor desensitization.
  Proc Natl Acad Sci U S A, 103, 10787-10792.  
16818877 C.S.Walker, P.J.Brockie, D.M.Madsen, M.M.Francis, Y.Zheng, S.Koduri, J.E.Mellem, N.Strutz-Seebohm, and A.V.Maricq (2006).
Reconstitution of invertebrate glutamate receptor function depends on stargazin-like proteins.
  Proc Natl Acad Sci U S A, 103, 10781-10786.  
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.  
16967334 K.Cohen-Kashi Malina, Y.Ganor, M.Levite, and V.I.Teichberg (2006).
Autoantibodies against an extracellular peptide of the GluR3 subtype of AMPA receptors activate both homomeric and heteromeric AMPA receptor channels.
  Neurochem Res, 31, 1181-1190.  
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.  
16525550 U.Pentikäinen, L.Settimo, M.S.Johnson, and O.T.Pentikäinen (2006).
Subtype selectivity and flexibility of ionotropic glutamate receptors upon antagonist ligand binding.
  Org Biomol Chem, 4, 1058-1070.  
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.  
16418277 Y.Zheng, P.J.Brockie, J.E.Mellem, D.M.Madsen, C.S.Walker, M.M.Francis, and A.V.Maricq (2006).
SOL-1 is an auxiliary subunit that modulates the gating of GLR-1 glutamate receptors in Caenorhabditis elegans.
  Proc Natl Acad Sci U S A, 103, 1100-1105.  
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
16408066 D.R.Madden (2005).
New light on an open-and-shut case.
  Nat Chem Biol, 1, 317-319.  
15476293 J.Rodriguez, L.Carcache, and K.S.Rein (2005).
Low-mode docking search in iGluR homology models implicates three residues in the control of ligand selectivity.
  J Mol Recognit, 18, 183-189.  
15721240 M.L.Mayer (2005).
Crystal structures of the GluR5 and GluR6 ligand binding cores: molecular mechanisms underlying kainate receptor selectivity.
  Neuron, 45, 539-552.
PDB codes: 1s50 1s7y 1s9t 1sd3 1tt1 1txf
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.  
16408071 Q.Cheng, M.Du, G.Ramanoudjame, and V.Jayaraman (2005).
Evolution of glutamate interactions during binding to a glutamate receptor.
  Nat Chem Biol, 1, 329-332.  
16242408 V.Balannik, F.S.Menniti, A.V.Paternain, J.Lerma, and Y.Stern-Bach (2005).
Molecular mechanism of AMPA receptor noncompetitive antagonism.
  Neuron, 48, 279-288.  
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.  
15229875 M.Kubo, and E.Ito (2004).
Structural dynamics of an ionotropic glutamate receptor.
  Proteins, 56, 411-419.  
14766177 M.S.Horning, and M.L.Mayer (2004).
Regulation of AMPA receptor gating by ligand binding core dimers.
  Neuron, 41, 379-388.  
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.