3E17 | pdb_00003e17

Crystal structure of the second PDZ domain from human Zona Occludens-2


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 
    0.237 (Depositor), 0.236 (DCC) 
  • R-Value Work: 
    0.206 (Depositor), 0.203 (DCC) 
  • R-Value Observed: 
    0.208 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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This is version 1.3 of the entry. See complete history

Literature

Structure of the second PDZ domain from human zonula occludens 2

Chen, H.Tong, S.Li, X.Wu, J.Zhu, Z.Niu, L.Teng, M.

(2009) Acta Crystallogr Sect F Struct Biol Cryst Commun 65: 327-330

  • DOI: https://doi.org/10.1107/S1744309109002334
  • Primary Citation Related Structures: 
    3E17

  • PubMed Abstract: 

    Human zonula occludens 2 (ZO-2) protein is a multi-domain protein that consists of an SH3 domain, a GK domain and three copies of a PDZ domain with slight divergence. The three PDZ domains act as protein-recognition modules that may mediate protein assembly and subunit localization. The crystal structure of the second PDZ domain of ZO-2 (ZO-2 PDZ2) was determined by molecular replacement at 1.75 A resolution, revealing a dimer in the asymmetric unit. The dimer is stabilized by extensive symmetrical domain-swapping of the beta1 and beta2 strands. Structural comparison shows that the ZO-2 PDZ2 homodimer may have a similar ligand-binding pattern to the ZO-1 PDZ2-connexin 43 complex.


  • Organizational Affiliation
    • Hefei National Laboratory for Physical Sciences at Microscale, School of Life Sciences, University of Science and Technology of China, Hefei, Anhui, People's Republic of China.

Macromolecule Content 

  • Total Structure Weight: 20.03 kDa 
  • Atom Count: 1,427 
  • Modeled Residue Count: 159 
  • Deposited Residue Count: 176 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Tight junction protein ZO-2
A, B
88Homo sapiensMutation(s): 0 
Gene Names: TJP2X104ZO2
UniProt & NIH Common Fund Data Resources
Find proteins for Q9UDY2 (Homo sapiens)
Explore Q9UDY2 
Go to UniProtKB:  Q9UDY2
PHAROS:  Q9UDY2
GTEx:  ENSG00000119139 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9UDY2
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free:  0.237 (Depositor), 0.236 (DCC) 
  • R-Value Work:  0.206 (Depositor), 0.203 (DCC) 
  • R-Value Observed: 0.208 (Depositor) 
Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 30.177α = 80.05
b = 41.325β = 68.63
c = 41.292γ = 68.52
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACTdata extraction
MAR345dtbdata collection
AUTOMARdata reduction

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2009-07-21
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2017-10-25
    Changes: Refinement description
  • Version 1.3: 2023-11-01
    Changes: Data collection, Database references, Refinement description