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PDBsum entry 1zub

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Endocytosis/exocytosis PDB id
1zub
Jmol
Contents
Protein chain
109 a.a. *
Ligands
GLU-GLU-GLY-ILE-
TRP-ALA
* Residue conservation analysis
PDB id:
1zub
Name: Endocytosis/exocytosis
Title: Solution structure of the rim1alpha pdz domain in complex with an elks1b c-terminal peptide
Structure: Regulating synaptic membrane exocytosis protein 1. Chain: a. Fragment: pdz domain. Synonym: rab3-interacting molecule 1, rim 1. Engineered: yes. Elks1b. Chain: b. Synonym: erc protein 1, erc1, caz-associated structural
Source: Rattus norvegicus. Norway rat. Organism_taxid: 10116. Gene: rims1, rim1. Expressed in: escherichia coli. Expression_system_taxid: 562. Gene: rab6ip2, cast2, elks, erc1. Expressed in: escherichia coli bl21. Expression_system_taxid: 511693.
NMR struc: 20 models
Authors: J.Lu,H.Li,Y.Wang,T.C.Sudhof,J.Rizo
Key ref:
J.Lu et al. (2005). Solution structure of the RIM1alpha PDZ domain in complex with an ELKS1b C-terminal peptide. J Mol Biol, 352, 455-466. PubMed id: 16095618 DOI: 10.1016/j.jmb.2005.07.047
Date:
30-May-05     Release date:   30-Aug-05    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
Q9JIR4  (RIMS1_RAT) -  Regulating synaptic membrane exocytosis protein 1
Seq:
Struc:
 
Seq:
Struc:
 
Seq:
Struc:
 
Seq:
Struc:
1615 a.a.
109 a.a.
Key:    PfamA domain  PfamB domain  Secondary structure  CATH domain

 

 
DOI no: 10.1016/j.jmb.2005.07.047 J Mol Biol 352:455-466 (2005)
PubMed id: 16095618  
 
 
Solution structure of the RIM1alpha PDZ domain in complex with an ELKS1b C-terminal peptide.
J.Lu, H.Li, Y.Wang, T.C.Südhof, J.Rizo.
 
  ABSTRACT  
 
PDZ domains are widespread protein modules that commonly recognize C-terminal sequences of target proteins and help to organize macromolecular signaling complexes. These sequences usually bind in an extended conformation to relatively shallow grooves formed between a beta-strand and an alpha-helix in the corresponding PDZ domains. Because of this binding mode, many PDZ domains recognize primarily the C-terminal and the antepenultimate side-chains of the target protein, which commonly conform to motifs that have been categorized into different classes. However, an increasing number of PDZ domains have been found to exhibit unusual specificities. These include the PDZ domain of RIMs, which are large multidomain proteins that regulate neurotransmitter release and help to organize presynaptic active zones. The RIM PDZ domain binds to the C-terminal sequence of ELKS with a unique specificity that involves each of the four ELKS C-terminal residues. To elucidate the structural basis for this specificity, we have determined the 3D structure in solution of an RIM/ELKS C-terminal peptide complex using NMR spectroscopy. The structure shows that the RIM PDZ domain contains an unusually deep and narrow peptide-binding groove with an exquisite shape complementarity to the four ELKS C-terminal residues in their bound conformation. This groove is formed, in part, by a set of side-chains that is conserved selectively in RIM PDZ domains and that hence determines, at least in part, their unique specificity.
 
  Selected figure(s)  
 
Figure 5.
Figure 5. Superpositions of ribbon diagrams of the RIM1α PDZ domain (blue) with the piccolo PDZ domain (a) and the third PDZ domain of PSD-95 (b) (orange). The PDB accession numbers of the piccolo PDZ domain and the third PDZ domain of PSD-95 are 1ujd and 1be9, respectively. The models were prepared with Pymol (DeLano Scientific, San Carlos, CA). Figure 5. Superpositions of ribbon diagrams of the RIM1α PDZ domain (blue) with the piccolo PDZ domain (a) and the third PDZ domain of PSD-95 (b) (orange). The PDB accession numbers of the piccolo PDZ domain and the third PDZ domain of PSD-95 are 1ujd and 1be9, respectively. The models were prepared with Pymol (DeLano Scientific, San Carlos, CA).
Figure 6.
Figure 6. The ELKS1bC peptide binds to a narrow and deep groove of the RIM1α PDZ domain. (a)–(d) Surface representations of (a) the RIM1α PDZ domain, (b) the third PDZ domain of PSD-95, (c) the sixth PDZ of GRIP1 and (d) the PDZ domain of nNOS, complexed with target peptides (the PDB accession numbers are 1be9, 1n7f and 1b8q for (b)–(d), respectively). The surfaces of the PDZ domains are represented in blue, and the bound peptides are shown as stick models with the P[0], P[−1], P-[−2], and P[−3] residues colored pink, red, yellow and orange, respectively. The side-chains that form the top surface of the groove in the RIM1α PDZ domain are labeled in (a). The models were prepared with Pymol (DeLano Scientific, San Carlos, CA; http://pymol.sourceforge.net/). Figure 6. The ELKS1bC peptide binds to a narrow and deep groove of the RIM1α PDZ domain. (a)–(d) Surface representations of (a) the RIM1α PDZ domain, (b) the third PDZ domain of PSD-95, (c) the sixth PDZ of GRIP1 and (d) the PDZ domain of nNOS, complexed with target peptides (the PDB accession numbers are 1be9, 1n7f and 1b8q for (b)–(d), respectively). The surfaces of the PDZ domains are represented in blue, and the bound peptides are shown as stick models with the P[0], P[−1], P-[−2], and P[−3] residues colored pink, red, yellow and orange, respectively. The side-chains that form the top surface of the groove in the RIM1α PDZ domain are labeled in (a). The models were prepared with Pymol (DeLano Scientific, San Carlos, CA; http://pymol.sourceforge.net/).
 
  The above figures are reprinted by permission from Elsevier: J Mol Biol (2005, 352, 455-466) copyright 2005.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21241895 P.S.Kaeser, L.Deng, Y.Wang, I.Dulubova, X.Liu, J.Rizo, and T.C.Südhof (2011).
RIM proteins tether Ca2+ channels to presynaptic active zones via a direct PDZ-domain interaction.
  Cell, 144, 282-295.  
20370319 T.Mittelstaedt, E.Alvaréz-Baron, and S.Schoch (2010).
RIM proteins and their role in synapse function.
  Biol Chem, 391, 599-606.  
19874790 P.S.Kaeser, L.Deng, A.E.Chávez, X.Liu, P.E.Castillo, and T.C.Südhof (2009).
ELKS2alpha/CAST deletion selectively increases neurotransmitter release at inhibitory synapses.
  Neuron, 64, 227-239.  
17630786 R.Guan, H.Dai, D.R.Tomchick, I.Dulubova, M.Machius, T.C.Südhof, and J.Rizo (2007).
Crystal structure of the RIM1alpha C2B domain at 1.7 A resolution.
  Biochemistry, 46, 8988-8998.
PDB code: 2q3x
16737969 B.A.Appleton, Y.Zhang, P.Wu, J.P.Yin, W.Hunziker, N.J.Skelton, S.S.Sidhu, and C.Wiesmann (2006).
Comparative structural analysis of the Erbin PDZ domain and the first PDZ domain of ZO-1. Insights into determinants of PDZ domain specificity.
  J Biol Chem, 281, 22312-22320.
PDB codes: 2h2b 2h2c 2h3l 2h3m
16865347 S.Schoch, and E.D.Gundelfinger (2006).
Molecular organization of the presynaptic active zone.
  Cell Tissue Res, 326, 379-391.  
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 code is shown on the right.