4XEF

Pyk2-FAT complexed with Leupaxin LD motif LD1

• PDB DOI:  https://doi.org/10.2210/pdb4XEF/pdb

• Classification: CELL ADHESION
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2014-12-23 Released: 2015-12-23 
• Deposition Author(s): Miller, D.J.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 0.266 
• R-Value Work: 0.224 
• R-Value Observed: 0.227 

Literature

Structural Basis for the Interaction between Pyk2-FAT Domain and Leupaxin LD Repeats.

Vanarotti, M.S., Finkelstein, D.B., Guibao, C.D., Nourse, A., Miller, D.J., Zheng, J.J.

(2016) Biochemistry 55: 1332-1345

• PubMed: 26866573 
• DOI: https://doi.org/10.1021/acs.biochem.5b01274
• Primary Citation of Related Structures:  
  4XEF, 4XEK, 4XEV


• PubMed Abstract: 
  

Proline-rich tyrosine kinase 2 (Pyk2) is a nonreceptor tyrosine kinase and belongs to the focal adhesion kinase (FAK) family. Like FAK, the C-terminal focal adhesion-targeting (FAT) domain of Pyk2 binds to paxillin, a scaffold protein in focal adhesions; however, the interaction between the FAT domain of Pyk2 and paxillin is dynamic and unstable. Leupaxin is another member in the paxillin family and was suggested to be the native binding partner of Pyk2; Pyk2 gene expression is strongly correlated with that of leupaxin in many tissues including primary breast cancer. Here, we report that leupaxin interacts with Pyk2-FAT. Leupaxin has four leucine-aspartate (LD) motifs. The first and third LD motifs of leupaxin preferably target the two LD-binding sites on the Pyk2-FAT domain, respectively. Moreover, the full-length leupaxin binds to Pyk2-FAT as a stable one-to-one complex. Together, we propose that there is an underlying selectivity between leupaxin and paxillin for Pyk2, which may influence the differing behavior of the two proteins at focal adhesion sites.

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Organizational Affiliation: 

Stein Eye Institute, Department of Ophthalmology, David Geffen School of Medicine at UCLA , Los Angeles, California 90095, United States.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A2B1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 3-mer - A1B1C1 Local Symmetry: Cyclic - C2  (3D View)
Local Stoichiometry: Homo 2-mer - A2 

Local Symmetry: Cyclic - C2  (3D View)
Local Stoichiometry: Homo 2-mer - A2 

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

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A2B1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 3-mer - A1B1C1 Local Symmetry: Cyclic - C2  (3D View)
Local Stoichiometry: Homo 2-mer - A2 

Local Symmetry: Cyclic - C2  (3D View)
Local Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 39.81 kDa 
• Atom Count: 2,442 
• Modelled Residue Count: 325 
• Deposited Residue Count: 358 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Protein-tyrosine kinase 2-beta	A, D	139	Homo sapiens	Mutation(s): 2  Gene Names: PTK2B, FAK2, PYK2, RAFTK EC: 2.7.10.2
UniProt & NIH Common Fund Data Resources
Find proteins for Q14289 (Homo sapiens) Explore Q14289  Go to UniProtKB:  Q14289
PHAROS:  Q14289

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
20-mer peptide containing LD1 motif of leupaxin	B, C, E, F	20	Homo sapiens	Mutation(s): 0  Gene Names: LPXN, LDLP
UniProt & NIH Common Fund Data Resources
Find proteins for O60711 (Homo sapiens) Explore O60711  Go to UniProtKB:  O60711
PHAROS:  O60711

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 0.266 
• R-Value Work: 0.224 
• R-Value Observed: 0.227 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 27.482	α = 90
b = 78.094	β = 90
c = 165.418	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2015-12-23 
Deposition Author(s): Miller, D.J.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	R01GM100909-03

Revision History  

• Version 1.0: 2015-12-23
  Type: Initial release
  
• Version 1.1: 2016-02-24
  Changes: Database references
• Version 1.2: 2016-03-16
  Changes: Database references
• Version 1.3: 2017-09-27
  Changes: Author supporting evidence, Database references, Derived calculations
• Version 1.4: 2019-12-25
  Changes: Author supporting evidence