Biological Assembly 1  

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

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

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

Macromolecule Content

• Total Structure Weight: 9.93 kDa 
• Atom Count: 835 
• Modelled Residue Count: 88 
• Deposited Residue Count: 88 
• Unique protein chains: 1

4P0C

Crystal Structure of NHERF2 PDZ1 Domain in Complex with LPA2

• PDB DOI: 10.2210/pdb4P0C/pdb

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


• Deposited: 2014-02-20 Released: 2014-05-21 
• Deposition Author(s): Holcomb, J., Jiang, Y., Lu, G., Trescott, L., Brunzelle, J., Sirinupong, N., Li, C., Naren, A., Yang, Z.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.34 Å
• R-Value Free: 0.177 
• R-Value Work: 0.145 
• R-Value Observed: 0.147 

Literature

Structural insights into PDZ-mediated interaction of NHERF2 and LPA2, a cellular event implicated in CFTR channel regulation.

Holcomb, J., Jiang, Y., Lu, G., Trescott, L., Brunzelle, J., Sirinupong, N., Li, C., Naren, A.P., Yang, Z.

(2014) Biochem Biophys Res Commun 446: 399-403

• PubMed: 24613836 
• DOI: 10.1016/j.bbrc.2014.02.128
• Primary Citation of Related Structures:  
  4P0C


• PubMed Abstract: 
  

The formation of CFTR-NHERF2-LPA2 macromolecular complex in airway epithelia regulates CFTR channel function and plays an important role in compartmentalized cAMP signaling. We previously have shown that disruption of the PDZ-mediated NHERF2-LPA2 interaction abolishes the LPA inhibitory effect and augments CFTR Cl(-) channel activity in vitro and in vivo. Here we report the first crystal structure of the NHERF2 PDZ1 domain in complex with the C-terminal LPA2 sequence. The structure reveals that the PDZ1-LPA2 binding specificity is achieved by numerous hydrogen bonds and hydrophobic contacts with the last four LPA2 residues contributing to specific interactions. Comparison of the PDZ1-LPA2 structure to the structure of PDZ1 in complex with a different peptide provides insights into the diverse nature of PDZ1 substrate recognition and suggests that the conformational flexibility in the ligand binding pocket is involved in determining the broad substrate specificity of PDZ1. In addition, the structure reveals a small surface pocket adjacent to the ligand-binding site, which may have therapeutic implications. This study provides an understanding of the structural basis for the PDZ-mediated NHERF2-LPA2 interaction that could prove valuable in selective drug design against CFTR-related human diseases.

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Organizational Affiliation: 

Department of Biochemistry and Molecular Biology, Wayne State University School of Medicine, Detroit, MI, USA. Electronic address: [e-mail].

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Na(+)/H(+) exchange regulatory cofactor NHE-RF2/Lysophosphatidic acid receptor 2 chimeric protein	A	88	Homo sapiens	Mutation(s): 0  Gene Names: SLC9A3R2
UniProt & NIH Common Fund Data Resources
Find proteins for Q15599 (Homo sapiens) Explore Q15599  Go to UniProtKB:  Q15599
PHAROS:  Q15599

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SCN	B [auth A]	THIOCYANATE ION C N S ZMZDMBWJUHKJPS-UHFFFAOYSA-M
CL	C [auth A], D [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.34 Å
• R-Value Free: 0.177 
• R-Value Work: 0.145 
• R-Value Observed: 0.147 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 26.36	α = 90
b = 40.25	β = 107.42
c = 37.1	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2014-02-20 
• Released Date: 2014-05-21 
Deposition Author(s): Holcomb, J., Jiang, Y., Lu, G., Trescott, L., Brunzelle, J., Sirinupong, N., Li, C., Naren, A., Yang, Z.

Revision History  

• Version 1.0: 2014-05-21
  Type: Initial release
  
• Version 1.1: 2015-02-04
  Changes: Derived calculations