9UA8 | pdb_00009ua8

structure of PTP-MEG2 and IFG1R-pY1165/pY1166 peptide complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 
    0.254 (Depositor), 0.248 (DCC) 
  • R-Value Work: 
    0.217 (Depositor), 0.210 (DCC) 
  • R-Value Observed: 
    0.219 (Depositor) 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


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Literature

PTPN9 dephosphorylates IGF1R Y1165/1166 and alleviates IGF1R-mediated resistance to tyrosine kinase inhibitor in cholangiocarcinoma.

Hu, J.M.Liu, H.Q.Zhang, M.H.Chen, T.L.Shi, A.D.Gao, Q.Liu, Y.J.Wang, X.Sun, K.Y.Deng, J.Xu, Y.F.Pan, C.Li, K.S.Zhang, Z.L.

(2025) J Exp Clin Cancer Res 44: 332-332

  • DOI: https://doi.org/10.1186/s13046-025-03594-2
  • Primary Citation Related Structures: 
    9UA8

  • PubMed Abstract: 

    Cholangiocarcinoma (CCA) is an aggressive malignancy with limited therapeutic options. Increasing evidence suggests that a subset of CCA patients can benefit from multiple tyrosine kinase inhibitors (mTKIs) such as surufatinib. Biomarker studies that can identify potential responders to mTKI therapy are crucial for improving treatment outcomes. In this study, we examined the expression of protein tyrosine phosphatase non-receptor type 9 (PTPN9) in CCA patients treated with surufatinib and analyzed its association with treatment response. Immunoprecipitation coupled with mass spectrometry (IP-MS) was performed to identify novel PTPN9 substrates. Orthotopic mouse models, biochemical assays, structural analyses, and functional experiments were conducted to validate these novel findings. Single-cell RNA sequencing, ELISA, and immunohistochemistry were utilized to investigate microenvironmental tumor-promoting factors.CCA patients with surufatinib non-response exhibited significantly decreased PTPN9 expression compared to that response to surufatinib. PTPN9 knockdown in orthotopic models led to reduced sensitivity to surufatinib. IGF1R was identified as a new substrate of PTPN9, which preferably to dephosphorylate IGF1R at Y1166. In clinical tissues, PTPN9 expression was inversely correlated with IGF1R Y1165/1166 phosphorylation. Establishment of a surufatinib-resistant CCA cell line further confirmed decreased PTPN9 expression and elevated IGF1R signaling. In vivo blockade of IGF1R signaling significantly enhanced surufatinib sensitivity. Mechanistically, crystal structure analysis revealed Tyr333 and Asp335 as key PTPN9 residues interacting with IGF1R; mutation of these residues restored IGF1R signaling and abolished the tumor-suppressive effect of PTPN9. Furthermore, cancer-associated fibroblasts (CAFs) were identified as the major source of IGF1 in CCA microenvironment, essential for IGF1R-driven tumor progression.In summary, the PTPN9-IGF1R axis plays a pivotal role in modulating mTKI sensitivity and tumor progression in CCA. This axis serves as a promising biomarker for identifying potential mTKI beneficiaries and represents a potential therapeutic target to enhance mTKI efficacy and overcome resistance.


  • Organizational Affiliation
    • Department of General Surgery, Qilu Hospital, Cheeloo College of Medicine, Shandong University, 107 Wenhua Xi Road, Jinan, Shandong, 250012, P.R. China.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Tyrosine-protein phosphatase non-receptor type 9A,
C [auth B],
E [auth D],
G
305Homo sapiensMutation(s): 0 
Gene Names: PTPN9
EC: 3.1.3.48
UniProt
Find proteins for Q6IQ43 (Homo sapiens)
Explore Q6IQ43 
Go to UniProtKB:  Q6IQ43
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ6IQ43
Sequence Annotations
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  • Reference Sequence

Find similar proteins by:  Sequence   |   3D Structure  

Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
THR-ASP-PTR-PTR-ARGB [auth F],
D [auth C],
F [auth E],
H
6Homo sapiensMutation(s): 0 
Sequence Annotations
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  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
PTR
Query on PTR
B [auth F],
D [auth C],
F [auth E],
H
L-PEPTIDE LINKINGC9 H12 N O6 PTYR
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free:  0.254 (Depositor), 0.248 (DCC) 
  • R-Value Work:  0.217 (Depositor), 0.210 (DCC) 
  • R-Value Observed: 0.219 (Depositor) 
Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 74.294α = 86.03
b = 84.707β = 94.16
c = 52.675γ = 90.05
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)ChinaT2422013

Revision History  (Full details and data files)

  • Version 1.0: 2026-04-08
    Type: Initial release