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RCSB PDB
234,785 Structures from the PDB
1,068,577 Computed Structure Models (CSM)
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 3TSW|pdb_00003tsw

crystal structure of the PDZ3-SH3-GUK core module of Human ZO-1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.85 Å
  • R-Value Free: 
    0.290 (Depositor), 0.250 (DCC) 
  • R-Value Work: 
    0.211 (Depositor), 0.190 (DCC) 
  • R-Value Observed: 
    0.218 (Depositor) 

Starting Model:experimental
View more details

wwPDB Validation  3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

The Src Homology 3 Domain Is Required for Junctional Adhesion Molecule Binding to the Third PDZ Domain of the Scaffolding Protein ZO-1.

Nomme, J.Fanning, A.S.Caffrey, M.Lye, M.F.Anderson, J.M.Lavie, A.

(2011) J Biological Chem 286: 43352-43360

  • PubMed22030391 Search on PubMedSearch on PubMed Central
  • DOI: https://doi.org/10.1074/jbc.M111.304089
  • Primary Citation of Related Structures:  
    3TSV,3TSW,3TSZ

  • PubMed Abstract: 

    Tight junctions are cell-cell contacts that regulate the paracellular flux of solutes and prevent pathogen entry across cell layers. The assembly and permeability of this barrier are dependent on the zonula occludens (ZO) membrane-associated guanylate kinase (MAGUK) proteins ZO-1, -2, and -3. MAGUK proteins are characterized by a core motif of protein-binding domains that include a PDZ domain, a Src homology 3 (SH3) domain, and a region of homology to guanylate kinase (GUK); the structure of this core motif has never been determined for any MAGUK. To better understand how ZO proteins organize the assembly of protein complexes we have crystallized the entire PDZ3-SH3-GUK core motif of ZO-1. We have also crystallized this core motif in complex with the cytoplasmic tail of the ZO-1 PDZ3 ligand, junctional adhesion molecule A (JAM-A) to determine how the activity of different domains is coordinated. Our study shows a new feature for PDZ class II ligand binding that implicates the two highly conserved Phe(-2) and Ser(-3) residues of JAM. Our x-ray structures and NMR experiments also show for the first time a role for adjacent domains in the binding of ligands to PDZ domains in the MAGUK proteins family.


  • Organizational Affiliation

    Department of Biochemistry and Molecular Genetics, University of Illinois, Chicago, Illinois 60607, USA.

Biological Assembly 1  

 Explore in 3DStructure |Sequence Annotations |Electron Density |Validation Report |Ligand Interaction (SO4)


Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 


Find Similar Assemblies

Biological assembly 1 assigned by authors.

Biological Assembly 2  

 Explore in 3DStructure |Sequence Annotations |Electron Density |Validation Report |Ligand Interaction (SO4)


Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 


Find Similar Assemblies

Biological assembly 2 assigned by authors.

Biological Assembly 3  

 Explore in 3DStructure |Sequence Annotations |Electron Density |Validation Report |Ligand Interaction (SO4)


Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 


Find Similar Assemblies

Biological assembly 3 assigned by authors.

Biological Assembly 4  

 Explore in 3DStructure |Sequence Annotations |Electron Density |Validation Report |Ligand Interaction (SO4)


Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 


Find Similar Assemblies

Biological assembly 4 assigned by authors.

Biological Assembly 5  

 Explore in 3DStructure |Sequence Annotations |Electron Density |Validation Report |Ligand Interaction (SO4)


Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Hetero 4-mer - A2B2 
Pseudo Symmetry: Cyclic - C2  (Explore in 3D)
Pseudo Stoichiometry: Homo 4-mer - A4 


Find Similar Assemblies

Biological assembly 5 generated by PISA (software)

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Macromolecule Content

  • Total Structure Weight: 179.32 kDa 
  • Atom Count: 8,637 
  • Modelled Residue Count: 1,064 
  • Deposited Residue Count: 1,564 
  • Unique protein chains: 1

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Tight junction protein ZO-1
A,B,C,D
391Homo sapiensMutation(s): 0 
Gene Names: TJP1ZO1
UniProt & NIH Common Fund Data Resources
Find proteins for Q07157 (Homo sapiens)
Explore Q07157 
Go to UniProtKB:  Q07157
PHAROS:  Q07157
GTEx:  ENSG00000104067 
Entity Groups 
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ07157
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download Ideal Coordinates CCD File 
E [auth A]
F [auth A]
G [auth B]
H [auth B]
I [auth C]
E [auth A],
F [auth A],
G [auth B],
H [auth B],
I [auth C],
J [auth D],
K [auth D]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.85 Å
  • R-Value Free: 0.290 (Depositor), 0.250 (DCC) 
  • R-Value Work: 0.211 (Depositor), 0.190 (DCC) 
  • R-Value Observed: 0.218 (Depositor) 
Space Group: P 32
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 100.634α = 90
b = 100.634β = 90
c = 182.516γ = 120
Software Package:
Software NamePurpose
SERGUIdata collection
PHASERphasing
REFMACrefinement
XDSdata reduction
XDSdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2011-10-12
    Type: Initial release
  • Version 1.1: 2011-11-16
    Changes: Database references
  • Version 1.2: 2011-12-28
    Changes: Database references
  • Version 1.3: 2023-09-13
    Changes: Data collection, Database references, Derived calculations, Refinement description
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RCSB PDB Core Operations are funded by theU.S. National Science Foundation (DBI-2321666), theUS Department of Energy (DE-SC0019749), and theNational Cancer Institute,National Institute of Allergy and Infectious Diseases, andNational Institute of General Medical Sciences of theNational Institutes of Health under grant R01GM157729.


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