Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

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

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

Macromolecule Content

• Total Structure Weight: 11.78 kDa 
• Atom Count: 937 
• Modelled Residue Count: 107 
• Deposited Residue Count: 107 
• Unique protein chains: 1

2H2B

Crystal Structure of ZO-1 PDZ1 Bound to a Phage-Derived Ligand (WRRTTYL)

• PDB DOI: 10.2210/pdb2H2B/pdb

• Classification: CELL ADHESION
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2006-05-18 Released: 2006-06-13 
• Deposition Author(s): Appleton, B.A., Zhang, Y., Wu, P., Yin, J.P., Hunziker, W., Skelton, N.J., Sidhu, S.S., Wiesmann, C.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 0.232 
• R-Value Work: 0.203 
• R-Value Observed: 0.205 

Literature

Comparative structural analysis of the Erbin PDZ domain and the first PDZ domain of ZO-1. Insights into determinants of PDZ domain specificity.

Appleton, B.A., Zhang, Y., Wu, P., Yin, J.P., Hunziker, W., Skelton, N.J., Sidhu, S.S., Wiesmann, C.

(2006) J Biol Chem 281: 22312-22320

• PubMed: 16737969 
• DOI: 10.1074/jbc.M602901200
• Primary Citation of Related Structures:  
  2H2B, 2H2C, 2H3L, 2H3M


• PubMed Abstract: 
  

We report a structural comparison of the first PDZ domain of ZO-1 (ZO1-PDZ1) and the PDZ domain of Erbin (Erbin-PDZ). Although the binding profile of Erbin-PDZ is extremely specific ([D/E][T/S]WV(COOH)), that of ZO1-PDZ1 is similar ([R/K/S/T][T/S][W/Y][V/I/L](COOH)) but broadened by increased promiscuity for three of the last four ligand residues. Consequently, the biological function of ZO-1 is also broadened, as it interacts with both tight and adherens junction proteins, whereas Erbin is restricted to adherens junctions. Structural analyses reveal that the differences in specificity can be accounted for by two key differences in primary sequence. A reduction in the size of the hydrophobic residue at the base of the site(0) pocket enables ZO1-PDZ1 to accommodate larger C-terminal residues. A single additional difference alters the specificity of both site(-1) and site(-3). In ZO1-PDZ1, an Asp residue makes favorable interactions with both Tyr(-1) and Lys/Arg(-3). In contrast, Erbin-PDZ contains an Arg at the equivalent position, and this side chain cannot accommodate either Tyr(-1) or Lys/Arg(-3) but, instead, interacts favorably with Glu/Asp(-3). We propose a model for ligand recognition that accounts for interactions extending across the entire binding site but that highlights several key specificity switches within the PDZ domain fold.

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Related Citations: 

• Convergent and Divergent Ligand Specificity Amongst the PDZ Domains of the LAP and ZO Families
  Zhang, Y., Yeh, S., Appleton, B.A., Held, H.A., Kausalya, J.P., Phua, D.C.Y., Wong, W.L., Lasky, L.A., Wiesmann, C., Hunziker, W., Sidhu, S.S.
  (2006) J Biol Chem 281: 22299

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Organizational Affiliation: 

Department of Protein Engineering, Genentech, Inc., South San Francisco, California 94080, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Tight junction protein ZO-1	A	107	Homo sapiens	Mutation(s): 0  Gene Names: ZO1 (TJP1), TJP1, ZO1
UniProt & NIH Common Fund Data Resources
Find proteins for Q07157 (Homo sapiens) Explore Q07157  Go to UniProtKB:  Q07157
PHAROS:  Q07157 GTEx:  ENSG00000104067

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ACY	B [auth A]	ACETIC ACID C2 H4 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 0.232 
• R-Value Work: 0.203 
• R-Value Observed: 0.205 
• Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 52.425	α = 90
b = 52.425	β = 90
c = 92.932	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2006-05-18 
• Released Date: 2006-06-13 
Deposition Author(s): Appleton, B.A., Zhang, Y., Wu, P., Yin, J.P., Hunziker, W., Skelton, N.J., Sidhu, S.S., Wiesmann, C.

Revision History  

• Version 1.0: 2006-06-13
  Type: Initial release
  
• Version 1.1: 2008-05-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Advisory, Derived calculations, Version format compliance
• Version 1.3: 2017-10-18
  Changes: Refinement description
• Version 1.4: 2018-01-24
  Changes: Database references