4XGZ

Crystal structure of human paxillin LD2 motif in complex with Fab fragment


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.245 
  • R-Value Work: 0.228 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Engineering Synthetic Antibody Inhibitors Specific for LD2 or LD4 Motifs of Paxillin.

Nocula-Lugowska, M.Lugowski, M.Salgia, R.Kossiakoff, A.A.

(2015) J.Mol.Biol. 427: 2532-2547

  • DOI: 10.1016/j.jmb.2015.06.004
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Focal adhesion protein paxillin links integrin and growth factor signaling to actin cytoskeleton. Most of paxillin signaling activity is regulated via leucine-rich LD motifs (LD1-LD5) located at the N-terminus. Here, we demonstrate a method to engine ...

    Focal adhesion protein paxillin links integrin and growth factor signaling to actin cytoskeleton. Most of paxillin signaling activity is regulated via leucine-rich LD motifs (LD1-LD5) located at the N-terminus. Here, we demonstrate a method to engineer highly selective synthetic antibodies (sABs) against LD2 and LD4 that are binding sites for focal adhesion kinase (FAK) and other proteins. Phage display selections against peptides were used to generate sABs recognizing each LD motif. In the obtained X-ray crystal structures of the LD-sAB complexes, the LD motifs are helical and bind sABs through a hydrophobic side, similarly as in the structures with natural paxillin partners. The sABs are capable of pulling down endogenous paxillin in complex with FAK and can visualize paxillin in focal adhesions in cells. They were also used as selective inhibitors to effectively compete with focal adhesion targeting domain of FAK for the binding to LD2 and LD4. The sABs are tools for investigation of paxillin LD binding "platforms" and are capable of inhibiting paxillin interactions, thereby useful as potential therapeutics in the future.


    Organizational Affiliation

    Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL 60607, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
FAB HEAVY CHAIN
A, C, E, G, H, J, M, O, Q, S, U, W
229N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
FAB LIGHT CHAIN
B, D, F, I, K, L, N, P, R, T, V, X
215N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
PAXILLIN LD2
a, c, e, g, h, j, m, o, q, s, u, w
19Homo sapiensMutation(s): 0 
Gene Names: PXN
Find proteins for P49023 (Homo sapiens)
Go to Gene View: PXN
Go to UniProtKB:  P49023
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
EDO
Query on EDO

Download SDF File 
Download CCD File 
N, Q, W
1,2-ETHANEDIOL
ETHYLENE GLYCOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
NO3
Query on NO3

Download SDF File 
Download CCD File 
B, D, F, I, K, L, N, P, R, T, V, X
NITRATE ION
N O3
NHNBFGGVMKEFGY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.245 
  • R-Value Work: 0.228 
  • Space Group: P 1
Unit Cell:
Length (Å)Angle (°)
a = 108.189α = 94.65
b = 111.004β = 95.28
c = 143.865γ = 114.53
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
XSCALEdata scaling
PHASERphasing
REFMACrefinement
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of HealthUnited States--

Revision History 

  • Version 1.0: 2015-07-01
    Type: Initial release
  • Version 1.1: 2015-08-05
    Type: Database references
  • Version 1.2: 2017-05-31
    Type: Other