4XH2

Crystal structure of human paxillin LD4 motif in complex with Fab fragment


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.258 
  • R-Value Work: 0.224 
  • R-Value Observed: 0.226 

wwPDB Validation   3D Report Full Report


This is version 1.3 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:  
    4XGZ, 4XH2

  • 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 engineer highly selective synthetic antibodies (sABs) against LD2 and LD4 that are binding sites for focal adhesion kinase (FAK) and other proteins ...

    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. Electronic address: koss@bsd.uchicago.edu.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Fab Heavy ChainA, C, E, G, H, J228Homo sapiensMutation(s): 0 
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Fab Light ChainB, D, F, I, K, L217Homo sapiensMutation(s): 0 
Protein Feature View
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  • Reference Sequence
  • Find similar proteins by:  Sequence   |   Structure
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
paxillin LD4M [auth a], N [auth c], O [auth e], P [auth g], Q [auth h], R [auth j]18synthetic constructMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for P49023 (Homo sapiens)
Explore P49023 
Go to UniProtKB:  P49023
PHAROS:  P49023
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
LDA
Query on LDA

Download Ideal Coordinates CCD File 
DA [auth F]LAURYL DIMETHYLAMINE-N-OXIDE
C14 H31 N O
SYELZBGXAIXKHU-UHFFFAOYSA-N
 Ligand Interaction
PO4
Query on PO4

Download Ideal Coordinates CCD File 
BA [auth F], X [auth D]PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
GOL
Query on GOL

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AA [auth F] , EA [auth F] , FA [auth G] , GA [auth H] , HA [auth H] , IA [auth I] , JA [auth I] , KA [auth I] , 
AA [auth F],  EA [auth F],  FA [auth G],  GA [auth H],  HA [auth H],  IA [auth I],  JA [auth I],  KA [auth I],  MA [auth K],  NA [auth K],  OA [auth K],  PA [auth L],  QA [auth L],  S [auth B],  T [auth B],  U [auth C],  V [auth C],  W [auth D],  Y [auth F],  Z [auth F]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
ACT
Query on ACT

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CA [auth F]ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
 Ligand Interaction
ACE
Query on ACE

Download Ideal Coordinates CCD File 
LA [auth J], RA [auth L]ACETYL GROUP
C2 H4 O
IKHGUXGNUITLKF-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.258 
  • R-Value Work: 0.224 
  • R-Value Observed: 0.226 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 117.58α = 90
b = 138.12β = 90
c = 223.51γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
PDB_EXTRACTdata extraction
XSCALEdata scaling
PHASERphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United States--

Revision History  (Full details and data files)

  • Version 1.0: 2015-07-01
    Type: Initial release
  • Version 1.1: 2015-08-05
    Changes: Database references
  • Version 1.2: 2017-05-31
    Changes: Other
  • Version 1.3: 2019-11-27
    Changes: Author supporting evidence