PDBsum entry 3l4f

Signaling protein/protein binding

PDB id: 3l4f

Contents

Protein chains

61 a.a. *

53 a.a. *

107 a.a. *

Waters ×20

* Residue conservation analysis

PDB id:

3l4f

Name:

Signaling protein/protein binding

Title:

Crystal structure of betapix coiled-coil domain and shank pdz complex

Structure:

Rho guanine nucleotide exchange factor 7. Chain: a, b, c. Fragment: thE C-terminal coiled-coil domain. Synonym: pak-interacting exchange factor beta, beta-pix. Engineered: yes. Sh3 and multiple ankyrin repeat domains protein 1. Chain: d. Fragment: pdz domain. Synonym: shank1, gkap/sapap-interacting protein, spank-1, synamon,

Source:

Rattus norvegicus. Rat. Organism_taxid: 10116. Gene: beta1pix. Expressed in: escherichia coli. Expression_system_taxid: 562. Gene: shank1.

Resolution:

2.80Å R-factor: 0.272 R-free: 0.307

Authors:

Y.J.Im,G.B.Kang,J.H.Lee,H.E.Song,K.R.Park,E.Kim,W.K.Song,D.Park, S.H.Eom

Key ref:

Y.J.Im et al. (2010). Structural basis for asymmetric association of the betaPIX coiled coil and shank PDZ. J Mol Biol, 397, 457-466. PubMed id: 20117114

Date:

19-Dec-09 Release date: 16-Feb-10

Protein chains

O55043  (ARHG7_RAT) -  Rho guanine nucleotide exchange factor 7 from Rattus norvegicus

Seq: 646 a.a.

Struc: 61 a.a.*

Protein chain

O55043  (ARHG7_RAT) -  Rho guanine nucleotide exchange factor 7 from Rattus norvegicus

Seq: 646 a.a.

Struc: 53 a.a.*

Protein chain

Q9WV48  (SHAN1_RAT) -  SH3 and multiple ankyrin repeat domains protein 1 from Rattus norvegicus

Seq: 2167 a.a.

Struc: 107 a.a.*

* PDB and UniProt seqs differ at 3 residue positions (black crosses)

Enzyme reactions

• Enzyme class: Chains A, B, C, D: E.C.?

J Mol Biol 397:457-466 (2010)

PubMed id: 20117114

Structural basis for asymmetric association of the betaPIX coiled coil and shank PDZ.

Y.J.Im, G.B.Kang, J.H.Lee, K.R.Park, H.E.Song, E.Kim, W.K.Song, D.Park, S.H.Eom.

ABSTRACT

betaPIX (p21-activated kinase interacting exchange factor) and Shank/ProSAP protein form a complex acting as a protein scaffold that integrates signaling pathways and regulates postsynaptic structure. Complex formation is mediated by the C-terminal PDZ binding motif of betaPIX and the Shank PDZ domain. The coiled-coil (CC) domain upstream of the PDZ binding motif allows multimerization of betaPIX, which is important for its physiological functions. We have solved the crystal structure of the betaPIX CC-Shank PDZ complex and determined the stoichiometry of complex formation. The betaPIX CC forms a 76-A-long parallel CC trimer. Despite the fact that the betaPIX CC exposes three PDZ binding motifs in the C-termini, the betaPIX trimer associates with a single Shank PDZ. One of the C-terminal ends of the CC forms an extensive beta-sheet interaction with the Shank PDZ, while the other two ends are not involved in ligand binding and form random coils. The two C-terminal ends of betaPIX have significantly lower affinity than the first PDZ binding motif due to the steric hindrance in the C-terminal tails, which results in binding of a single PDZ domain to the betaPIX trimer. The structure shows canonical class I PDZ binding with a beta-sheet interaction extending to position -6 of betaPIX. The betaB-betaC loop of Shank PDZ undergoes a conformational change upon ligand binding to form the beta-sheet interaction and to accommodate the bulky side chain of Trp -5. This structural study provides a clear picture of the molecular recognition of the PDZ ligand and the asymmetric association of betaPIX CC and Shank PDZ.