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)

Macromolecule Content

• Total Structure Weight: 11.07 kDa 
• Atom Count: 815 
• Residue Count: 90 
• Unique protein chains: 1

4Q2Q

ZO1 PDZ3 in Complex with a Phage-Derived Peptide

• DOI: 10.2210/pdb4Q2Q/pdb

• Classification: PROTEIN BINDING
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2014-04-09 Released: 2014-09-10 
• Deposition Author(s): Appleton, B.A., Wiesmann, C.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.45 Å
• R-Value Free: 0.210 
• R-Value Work: 0.160 
• R-Value Observed: 0.163 

Literature

A structural portrait of the PDZ domain family.

Ernst, A., Appleton, B.A., Ivarsson, Y., Zhang, Y., Gfeller, D., Wiesmann, C., Sidhu, S.S.

(2014) J Mol Biol 426: 3509-3519

• PubMed: 25158098 
• DOI: 10.1016/j.jmb.2014.08.012
• Primary Citation of Related Structures:  
  4Q2N, 4Q2O, 4Q2P, 4Q2Q


• PubMed Abstract: 
  

PDZ (PSD-95/Discs-large/ZO1) domains are interaction modules that typically bind to specific C-terminal sequences of partner proteins and assemble signaling complexes in multicellular organisms. We have analyzed the existing database of PDZ domain structures in the context of a specificity tree based on binding specificities defined by peptide-phage binding selections. We have identified 16 structures of PDZ domains in complex with high-affinity ligands and have elucidated four additional structures to assemble a structural database that covers most of the branches of the PDZ specificity tree. A detailed comparison of the structures reveals features that are responsible for the diverse specificities across the PDZ domain family. Specificity differences can be explained by differences in PDZ residues that are in contact with the peptide ligands, but these contacts involve both side-chain and main-chain interactions. Most PDZ domains bind peptides in a canonical conformation in which the ligand main chain adopts an extended β-strand conformation by interacting in an antiparallel fashion with a PDZ β-strand. However, a subset of PDZ domains bind peptides with a bent main-chain conformation and the specificities of these non-canonical domains could not be explained based on canonical structures. Our analysis provides a structural portrait of the PDZ domain family, which serves as a guide in understanding the structural basis for the diverse specificities across the family.

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Organizational Affiliation: 

Banting and Best Department of Medical Research and Department of Molecular Genetics, University of Toronto, The Donnelly Centre, 160 College Street, Toronto, ON M5S 3E1, Canada. Electronic address: [e-mail].

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Tight junction protein ZO-1	A	102	Homo sapiens	Mutation(s): 0  Gene Names: TJP1, ZO1
Find proteins for Q07157 (Homo sapiens) Explore Q07157  Go to UniProtKB:  Q07157
NIH Common Fund Data Resources
PHAROS:  Q07157 GTEx:  ENSG00000104067

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.45 Å
• R-Value Free: 0.210 
• R-Value Work: 0.160 
• R-Value Observed: 0.163 
• Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 50.607	α = 90
b = 50.607	β = 90
c = 78.678	γ = 90

Software Package:

Software Name	Purpose
SCALEPACK	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data collection
HKL-2000	data reduction

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2014-04-09 
• Released Date: 2014-09-10 
Deposition Author(s): Appleton, B.A., Wiesmann, C.

Revision History 

• Version 1.0: 2014-09-10
  Type: Initial release
  
• Version 1.1: 2014-11-26
  Changes: Database references