Loading
PDBj
MenuPDBj@FacebookPDBj@X(formerly Twitter)PDBj@BlueSkyPDBj@YouTubewwPDB FoundationwwPDBDonate
RCSB PDBPDBeBMRBAdv. SearchSearch help

1Q3O

Crystal structure of the Shank PDZ-ligand complex reveals a class I PDZ interaction and a novel PDZ-PDZ dimerization

Summary for 1Q3O
Entry DOI10.2210/pdb1q3o/pdb
Related1Q3P
DescriptorShank1, BROMIDE ION (3 entities in total)
Functional Keywordsshank, pdz, gkap, peptide binding protein
Biological sourceRattus norvegicus (Norway rat)
Cellular locationCytoplasm: Q9WV48
Total number of polymer chains2
Total formula weight24547.44
Authors
Im, Y.J.,Lee, J.H.,Park, S.H.,Park, S.J.,Rho, S.-H.,Kang, G.B.,Kim, E.,Eom, S.H. (deposition date: 2003-07-31, release date: 2004-01-27, Last modification date: 2024-03-13)
Primary citationIm, Y.J.,Lee, J.H.,Park, S.H.,Park, S.J.,Rho, S.-H.,Kang, G.B.,Kim, E.,Eom, S.H.
Crystal structure of the Shank PDZ-ligand complex reveals a class I PDZ interaction and a novel PDZ-PDZ dimerization
J.Biol.Chem., 278:48099-48104, 2003
Cited by
PubMed Abstract: The Shank/proline-rich synapse-associated protein family of multidomain proteins is known to play an important role in the organization of synaptic multiprotein complexes. For instance, the Shank PDZ domain binds to the C termini of guanylate kinase-associated proteins, which in turn interact with the guanylate kinase domain of postsynaptic density-95 scaffolding proteins. Here we describe the crystal structures of Shank1 PDZ in its peptide free form and in complex with the C-terminal hexapeptide (EAQTRL) of guanylate kinase-associated protein (GKAP1a) determined at 1.8- and 2.25-A resolutions, respectively. The structure shows the typical class I PDZ interaction of PDZ-peptide complex with the consensus sequence -X-(Thr/Ser)-X-Leu. In addition, Asp-634 within the Shank1 PDZ domain recognizes the positively charged Arg at -1 position and hydrogen bonds, and salt bridges between Arg-607 and the side chains of the ligand at -3 and -5 positions contribute further to the recognition of the peptide ligand. Remarkably, whether free or complexed, Shank1 PDZ domains form dimers with a conserved beta B/beta C loop and N-terminal beta A strands, suggesting a novel model of PDZ-PDZ homodimerization. This implies that antiparallel dimerization through the N-terminal beta A strands could be a common configuration among PDZ dimers. Within the dimeric structure, the two-peptide binding sites are arranged so that the N termini of the bound peptide ligands are in close proximity and oriented toward the 2-fold axis of the dimer. This configuration may provide a means of facilitating dimeric organization of PDZ-target assemblies.
PubMed: 12954649
DOI: 10.1074/jbc.M306919200
PDB entries with the same primary citation
Experimental method
X-RAY DIFFRACTION (1.8 Å)
Structure validation

238582

PDB entries from 2025-07-09

PDB statisticsPDBj update infoContact PDBjnumon