Biological Assembly 1  

 3D View: Structure | Electron Density

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

 3D View: Structure | Electron Density

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 2 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 25.58 kDa 
• Atom Count: 1711 
• Residue Count: 213 
• Unique protein chains: 2

1Q3P

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

• DOI: 10.2210/pdb1Q3P/pdb

• Classification: PEPTIDE BINDING PROTEIN
• Organism(s): Rattus norvegicus
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2003-07-31 Released: 2004-01-27 
• Deposition Author(s): Im, Y.J., Lee, J.H., Park, S.H., Park, S.J., Rho, S.-H., Kang, G.B., Kim, E., Eom, S.H.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.25 Å
• R-Value Free: 0.280 
• R-Value Work: 0.251 
• R-Value Observed: 0.251 

Literature

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

Im, Y.J., Lee, J.H., Park, S.H., Park, S.J., Rho, S.-H., Kang, G.B., Kim, E., Eom, S.H.

(2003) J Biol Chem 278: 48099-48104

• PubMed: 12954649 
• DOI: 10.1074/jbc.M306919200
• Primary Citation of Related Structures:  
  1Q3P, 1Q3O


• 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.

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Organizational Affiliation: 

Department of Life Science, Kwangju Institute of Science and Technology, Gwangju 500-712, South Korea.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Shank1	A, B	109	Rattus norvegicus	Mutation(s): 0  Gene Names: Shank1
Find proteins for Q9WV48 (Rattus norvegicus) Explore Q9WV48  Go to UniProtKB:  Q9WV48

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
C-terminal hexapeptide from Guanylate kinase-associated protein	C, D	6	N/A	Mutation(s): 0

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.25 Å
• R-Value Free: 0.280 
• R-Value Work: 0.251 
• R-Value Observed: 0.251 
• Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 60.763	α = 90
b = 60.763	β = 90
c = 157.902	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
DENZO	data reduction
SCALEPACK	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2003-07-31 
• Released Date: 2004-01-27 
Deposition Author(s): Im, Y.J., Lee, J.H., Park, S.H., Park, S.J., Rho, S.-H., Kang, G.B., Kim, E., Eom, S.H.

Revision History 

• Version 1.0: 2004-01-27
  Type: Initial release
  
• Version 1.1: 2008-04-29
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance