8Y8Y

Crystal structure of the PTPN21 FERM domain


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.250 
  • R-Value Work: 0.200 
  • R-Value Observed: 0.205 

wwPDB Validation   3D Report Full Report


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Literature

Structural analysis of the FERM domain of human protein tyrosine phosphatase non-receptor type 21.

Lee, H.S.Ku, B.Shin, H.C.Kim, S.J.

(2024) Acta Crystallogr F Struct Biol Commun 80: 148-153

  • DOI: https://doi.org/10.1107/S2053230X24005260
  • Primary Citation of Related Structures:  
    8Y8Y

  • PubMed Abstract: 

    Protein tyrosine phosphatase non-receptor type 21 (PTPN21) is a cytosolic protein tyrosine phosphatase that regulates cell growth and invasion. Due to its oncogenic properties, PTPN21 has recently emerged as a potential therapeutic target for cancer. In this study, the three-dimensional structure of the PTPN21 FERM domain was determined at 2.1 Å resolution by X-ray crystallography. The crystal structure showed that this domain harbors canonical FERM folding and consists of three subdomains that are tightly packed via highly conserved intramolecular hydrophobic interactions. Consistent with this, the PTPN21 FERM domain shares high structural homology with several other FERM domains. Moreover, structural superimposition demonstrated two putative protein-binding sites of the PTPN21 FERM domain, which are presumed to be associated with interaction with its binding partner, kinesin family member 1C. Thus, these data suggest that the FERM domain of PTPN21 serves as a module that mediates protein-protein interaction, like other FERM domains.


  • Organizational Affiliation

    Disease Target Structure Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon 34141, Republic of Korea.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Tyrosine-protein phosphatase non-receptor type 21293Homo sapiensMutation(s): 0 
Gene Names: PTPN21PTPD1
EC: 3.1.3.48
UniProt & NIH Common Fund Data Resources
Find proteins for Q16825 (Homo sapiens)
Explore Q16825 
Go to UniProtKB:  Q16825
PHAROS:  Q16825
GTEx:  ENSG00000070778 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ16825
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CL
Query on CL

Download Ideal Coordinates CCD File 
B [auth A]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.250 
  • R-Value Work: 0.200 
  • R-Value Observed: 0.205 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 60.789α = 90
b = 113.843β = 90
c = 47.904γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Research Foundation (NRF, Korea)Korea, Republic Of2019M3E5D6063955
National Research Foundation (NRF, Korea)Korea, Republic OfKGM9952314
National Research Foundation (NRF, Korea)Korea, Republic OfCRC22021-700

Revision History  (Full details and data files)

  • Version 1.0: 2024-07-10
    Type: Initial release