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PDBsum entry 3dp6

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protein ligands metals Protein-protein interface(s) links
Signaling protein PDB id
3dp6
Jmol
Contents
Protein chains
258 a.a. *
Ligands
GLU ×3
Metals
_ZN ×6
Waters ×673
* Residue conservation analysis
PDB id:
3dp6
Name: Signaling protein
Title: Crystal structure of the binding domain of the ampa subunit glur2 bound to glutamate
Structure: Glutamate receptor 2. Chain: a, b, c. Fragment: s1s2 binding domain. Synonym: glur-2, glur-b, glur-k2, glutamate receptor ionotropic, ampa 2, ampa-selective glutamate receptor 2. Engineered: yes
Source: Rattus norvegicus. Organism_taxid: 10116. Gene: gria2, glur2. Expressed in: escherichia coli. Expression_system_taxid: 562.
Resolution:
1.55Å     R-factor:   0.222     R-free:   0.244
Authors: A.H.Ahmed,Q.Wang,H.Sondermann,R.E.Oswald
Key ref:
A.H.Ahmed et al. (2008). Structure of the S1S2 glutamate binding domain of GLuR3. Proteins, 75, 628-637. PubMed id: 19003990 DOI: 10.1002/prot.22274
Date:
07-Jul-08     Release date:   25-Nov-08    
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 2 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: 10.1002/prot.22274 Proteins 75:628-637 (2008)
PubMed id: 19003990  
 
 
Structure of the S1S2 glutamate binding domain of GLuR3.
A.H.Ahmed, Q.Wang, H.Sondermann, R.E.Oswald.
 
  ABSTRACT  
 
Glutamate receptors are the most prevalent excitatory neurotransmitter receptors in the vertebrate central nervous system. Determining the structural differences between the binding sites of different subtypes is crucial to our understanding of neuronal circuits and to the development of subtype specific drugs. The structures of the binding domain (S1S2) of the GluR3 (flip) AMPA receptor subunit bound to glutamate and AMPA and the GluR2 (flop) subunit bound to glutamate were determined by X-ray crystallography to 1.9, 2.1, and 1.55 A, respectively. Overall, the structure of GluR3 (flip) S1S2 is very similar to GluR2 (flop) S1S2 (backbone RMSD of 0.30 +/- 0.05 for glutamate-bound and 0.26 +/- 0.01 for AMPA-bound). The differences in the flip and flop isoforms are subtle and largely arise from one hydrogen bond across the dimer interface and associated water molecules. Comparison of the binding affinity for various agonists and partial agonists suggest that the S1S2 domains of GluR2 and GluR3 show only small differences in affinity, unlike what is found for the intact receptors (with the exception of one ligand, Cl-HIBO, which has a 10-fold difference in affinity for GluR2 vs. GluR3). Proteins 2009. (c) 2008 Wiley-Liss, Inc.
 
  Selected figure(s)  
 
Figure 3.
Figure 3. (A) The dimeric structure of GluR3 bound to glutamate. The helices are labeled as in Armstrong et al.[6] Residues participating in contacts across the dimer interface are labeled. P632 (yellow) flanks the artificial linker region of the construct and is the point that connects to the linkers to the ion channel. The four residues that differ in flip and flop are shown in shades of red. (B) The dimer interface at the S754 (flip)/N754 (flop) interaction with S729. Both can form hydrogen bonds, but the structure of the water surrounding the hydrogen bond differs.
Figure 4.
Figure 4. (A) Binding of [^3H]AMPA to the S1S2 domains of GluR2[o] and GluR3[i]. The K[D] of binding differed by less than twofold: 19 ± 2 nM for GluR2 and 43 ± 5 nM for GluR3. Armstrong and Gouaux[5] reported a K[D] of 24.8 ± 1.8 nM for [^3H]AMPA binding to GluR2. (B) Structures of the ligands used in the binding studies, (C) The inhibition of [^3H]AMPA binding by agonists, partial agonists, and antagonist to the S1S2 domains of GluR2[o] and GluR3[i]. Except for willardiine, the IC[50] values were within twofold for the two subtypes: (ligand, GluR2 IC[50]/GluR3 IC[50]; IC[50] expressed in M) fluorowillardiine, 0.0040 ± 0009/0.0062 ± 0.0014; iodowillardiine, 0.46 ± 0.05/0.79 ± 0.14; Cl-HIBO, 5.0 ± 0.3/55 ± 4; willardiine, 3.1 ± 0.2/0.99 ± 0.18; UBP277, 135 ± 12/69 ± 10. In all cases, GluR2[o] is shown with filled symbols, and GluR3[i] is shown with open symbols.
 
  The above figures are reprinted by permission from John Wiley & Sons, Inc.: Proteins (2008, 75, 628-637) copyright 2008.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
22948927 S.S.Cha, Y.J.An, C.S.Jeong, M.K.Kim, S.G.Lee, K.H.Lee, and B.H.Oh (2012).
Experimental phasing using zinc anomalous scattering.
  Acta Crystallogr D Biol Crystallogr, 68, 1253-1258.
PDB codes: 4dt3 4dwz 4fc5
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.  
21349697 M.L.Mayer (2011).
Structure and mechanism of glutamate receptor ion channel assembly, activation and modulation.
  Curr Opin Neurobiol, 21, 283-290.  
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.  
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.