PDBsum entry 1i2h

Signaling protein

PDB id: 1i2h

Contents

Protein chain

138 a.a. *

Waters ×114

* Residue conservation analysis

PDB id:

1i2h

Name:

Signaling protein

Title:

Crystal structure analysis of psd-zip45(homer1c/vesl-1l)conserved homer 1 domain

Structure:

Psd-zip45(homer-1c/vesl-1l). Chain: a. Fragment: n-terminal conserved homer 1 region (ch1 domain). Engineered: yes

Source:

Rattus norvegicus. Norway rat. Organism_taxid: 10116. Organ: brain. Gene: psd-zip45. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.

Biol. unit:

Dimer (from PQS)

Resolution:

1.80Å R-factor: 0.223 R-free: 0.218

Authors:

K.Irie,T.Nakatsu,K.Mitsuoka,Y.Fujiyoshi,H.Kato

Key ref:

K.Irie et al. (2002). Crystal structure of the Homer 1 family conserved region reveals the interaction between the EVH1 domain and own proline-rich motif. J Mol Biol, 318, 1117-1126. PubMed id: 12054806 DOI: 10.1016/S0022-2836(02)00170-5

Date:

09-Feb-01 Release date: 29-May-02

Protein chain

Q9Z214  (HOME1_RAT) -  Homer protein homolog 1 from Rattus norvegicus

Seq: 366 a.a.

Struc: 138 a.a.

DOI no: 10.1016/S0022-2836(02)00170-5

J Mol Biol 318:1117-1126 (2002)

PubMed id: 12054806

Crystal structure of the Homer 1 family conserved region reveals the interaction between the EVH1 domain and own proline-rich motif.

K.Irie, T.Nakatsu, K.Mitsuoka, A.Miyazawa, K.Sobue, Y.Hiroaki, T.Doi, Y.Fujiyoshi, H.Kato.

ABSTRACT

PSD-Zip45 (also named Homer 1c/Vesl-1L) is a synaptic scaffolding protein, which interacts with neurotransmitter receptors and other scaffolding proteins to target them into post-synaptic density (PSD), a specialized protein complex at the synaptic junction. Binding of the PSD-Zip45 to the receptors and scaffolding proteins results in colocalization and clustering of its binding partners in PSD. It has an Ena/VASP homology 1 (EVH1) domain in the N terminus for receptor binding, two leucine zipper motifs in the C terminus for clustering, and a linking region whose function is unclear despite the high level of conservation within the Homer 1 family. The X-ray crystallographic analysis of the largest fragment of residues 1-163, including an EVH1 domain reported here, demonstrates that the EVH1 domain contains an alpha-helix longer than that of the previous models, and that the linking part included in the conserved region of Homer 1 (CRH1) of the PSD-Zip45 interacts with the EVH1 domain of the neighbour CRH1 molecule in the crystal. The results suggest that the EVH1 domain recognizes the PPXXF motif found in the binding partners, and the SPLTP sequence (P-motif) in the linking region of the CRH1. The two types of binding are partly overlapped in the EVH1 domain, implying a mechanism to regulate multimerization of Homer 1 family proteins.

Selected figure(s)

Figure 3.
Figure 3. Stereo pair of electron density at the interaction interface between the P-motif and the EVH1 domain. The 2F[o] -F[c] electron density map was refined by REFMAC[33.] and is contoured at 1.0s. The residues of the P-motif and the EVH1 domain are represented by yellow-green and sky-blue, respectively. This Figure was generated with TURBO-FRODO. [32.]

Figure 4.
Figure 4. Comparison of binding modes of the EVH1 domains. A ribbon representation of the complex of the binding peptide and the EVH1 domain, and ball-and-stick models of the binding regions are shown. (a) and (b) The complex of the P-motif (138-SPLTP-142) of PSD-Zip45 and the EVH1 domain analysed in this study. (c) and (d) The complex of the proline-rich part (1151-TPPSPF-1156) of mGluR and the EVH1 domain of Homer 1a.[16.] (e) and (f) The complex of the ActA peptide (1-FPPPP-5) and the EVH1 domain of Mena. [14.] In (a), (c) and (e), all binding peptides are indicated in red, and the EVH1 domains are viewed from the same orientation. In the stereo pairs shown in (b), (d) and (f), all binding peptides are indicated in red, especially residues interacting with the EVH1 domain, which are indicated in vivid red. Residues forming the EVH1 domain are indicated in green, especially residues interacting with binding peptides, which are indicated in vivid green. Residue labels indicate the numbers for the binding peptide in Helvetica font, and the numbers for the EVH1 domain in Times font. The Figure was generated with MOLSCRIPT [36.] and Raster3D. [37.]

The above figures are reprinted by permission from Elsevier: J Mol Biol (2002, 318, 1117-1126) copyright 2002.

Figures were selected by an automated process.