6ROY

Structure of the N-SH2 domain of the human tyrosine-protein phosphatase non-receptor type 11 in complex with the phosphorylated immune receptor tyrosine-based inhibitory motif


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.279 
  • R-Value Work: 0.225 
  • R-Value Observed: 0.228 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Molecular mechanism of SHP2 activation by PD-1 stimulation.

Marasco, M.Berteotti, A.Weyershaeuser, J.Thorausch, N.Sikorska, J.Krausze, J.Brandt, H.J.Kirkpatrick, J.Rios, P.Schamel, W.W.Kohn, M.Carlomagno, T.

(2020) Sci Adv 6: eaay4458-eaay4458

  • DOI: 10.1126/sciadv.aay4458
  • Primary Citation of Related Structures:  
    6R5G, 6ROZ, 6ROY

  • PubMed Abstract: 
  • In cancer, the programmed death-1 (PD-1) pathway suppresses T cell stimulation and mediates immune escape. Upon stimulation, PD-1 becomes phosphorylated at its immune receptor tyrosine-based inhibitory motif (ITIM) and immune receptor tyrosine-based switch motif (ITSM), which then bind the Src homology 2 (SH2) domains of SH2-containing phosphatase 2 (SHP2), initiating T cell inactivation ...

    In cancer, the programmed death-1 (PD-1) pathway suppresses T cell stimulation and mediates immune escape. Upon stimulation, PD-1 becomes phosphorylated at its immune receptor tyrosine-based inhibitory motif (ITIM) and immune receptor tyrosine-based switch motif (ITSM), which then bind the Src homology 2 (SH2) domains of SH2-containing phosphatase 2 (SHP2), initiating T cell inactivation. The SHP2-PD-1 complex structure and the exact functions of the two SH2 domains and phosphorylated motifs remain unknown. Here, we explain the structural basis and provide functional evidence for the mechanism of PD-1-mediated SHP2 activation. We demonstrate that full activation is obtained only upon phosphorylation of both ITIM and ITSM: ITSM binds C-SH2 with strong affinity, recruiting SHP2 to PD-1, while ITIM binds N-SH2, displacing it from the catalytic pocket and activating SHP2. This binding event requires the formation of a new inter-domain interface, offering opportunities for the development of novel immunotherapeutic approaches.


    Organizational Affiliation

    Helmholtz Centre for Infection Research, Group of Structural Chemistry, Inhoffenstrasse 7, 38124 Braunschweig, Germany.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Tyrosine-protein phosphatase non-receptor type 11A, C [auth B]104Homo sapiensMutation(s): 0 
Gene Names: PTPN11PTP2CSHPTP2
EC: 3.1.3.48
UniProt & NIH Common Fund Data Resources
Find proteins for Q06124 (Homo sapiens)
Explore Q06124 
Go to UniProtKB:  Q06124
PHAROS:  Q06124
Protein Feature View
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  • Reference Sequence
  • Find similar proteins by:  Sequence   |   Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
immune receptor tyrosine-based inhibitory motif (ITIM)D [auth C], B [auth D]11synthetic constructMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for Q15116 (Homo sapiens)
Explore Q15116 
Go to UniProtKB:  Q15116
PHAROS:  Q15116
Protein Feature View
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  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
PTR
Query on PTR
B [auth D], D [auth C]L-PEPTIDE LINKINGC9 H12 N O6 PTYR
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.279 
  • R-Value Work: 0.225 
  • R-Value Observed: 0.228 
  • Space Group: P 43
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 29.856α = 90
b = 29.856β = 90
c = 208.227γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2020-02-19
    Type: Initial release
  • Version 1.1: 2020-02-26
    Changes: Database references