PDBsum entry 1zub

Endocytosis/exocytosis

PDB id: 1zub

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 protein 2, cast2, rab6 interacting protein 2, c-terminal peptide.

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

Protein chain

Q9JIR4  (RIMS1_RAT) -  Regulating synaptic membrane exocytosis protein 1 from Rattus norvegicus

Seq: 1615 a.a.

Struc: 109 a.a.

Enzyme reactions

• Enzyme class: E.C.?

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.