3VQG

Crystal Structure Analysis of the PDZ Domain Derived from the Tight Junction Regulating Protein

• PDB DOI: https://doi.org/10.2210/pdb3VQG/pdb

• Classification: PEPTIDE BINDING PROTEIN
• Organism(s): Mus musculus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2012-03-23 Released: 2013-03-27 
• Deposition Author(s): Akiyoshi, Y., Hamada, D., Goda, N., Tenno, T., Narita, H., Nakagawa, A., Furuse, M., Suzuki, M., Hiroaki, H.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.35 Å
• R-Value Free: 
  0.207 (Depositor), 0.200 (DCC) 
• R-Value Work: 
  0.170 (Depositor), 0.160 (DCC) 
• R-Value Observed: 
  0.172 (Depositor) 

Starting Model: experimental

Literature

Structural basis for down regulation of tight junction by PDZ-domain containing E3-Ubiquitin ligase

Akiyoshi, Y., Nakakura, Y., Hamada, D., Goda, N., Tenno, T., Narita, H., Nakagawa, A., Furuse, M., Suzuki, M., Hiroaki, H.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

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

Macromolecule Content

• Total Structure Weight: 11.58 kDa 
• Atom Count: 850 
• Modelled Residue Count: 89 
• Deposited Residue Count: 103 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
E3 ubiquitin-protein ligase LNX	A	94	Mus musculus	Mutation(s): 0  Gene Names: Lnx1 EC: 2.3.2.27
UniProt
Find proteins for O70263 (Mus musculus) Explore O70263  Go to UniProtKB:  O70263

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
C-terminal peptide from Immunoglobulin superfamily member 5	B	9	Mus musculus	Mutation(s): 0
UniProt
Find proteins for Q7TSN7 (Mus musculus) Explore Q7TSN7  Go to UniProtKB:  Q7TSN7

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	C [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.35 Å
• R-Value Free:  0.207 (Depositor), 0.200 (DCC) 
• R-Value Work:  0.170 (Depositor), 0.160 (DCC) 
• R-Value Observed: 0.172 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 60.852	α = 90
b = 50.768	β = 120.08
c = 33.136	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
MOLREP	phasing
PHENIX	refinement
HKL-2000	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-03-27 
Deposition Author(s): Akiyoshi, Y., Hamada, D., Goda, N., Tenno, T., Narita, H., Nakagawa, A., Furuse, M., Suzuki, M., Hiroaki, H.

Revision History  

• Version 1.0: 2013-03-27
  Type: Initial release
  
• Version 1.1: 2023-11-08
  Changes: Data collection, Database references, Derived calculations, Refinement description