9QCD | pdb_00009qcd

Micro-ED structure of the NSH2-CSH2 tandem domain of SHP2 in complex with the bis-phosphorylated pY627-pY659-Gab1 (613-694) peptide

• PDB DOI: https://doi.org/10.2210/pdb9QCD/pdb

• Classification: SIGNALING PROTEIN
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2025-03-04 Released: 2025-12-31 
• Deposition Author(s): Machner, L., Shaikhqasem, A., Hamdi, F., Breithaupt, C., Parthier, C., Kyrilis, F.L., Kastritis, P.L., Feller, S.M., Stubbs, M.T.
• Funding Organization(s): German Research Foundation (DFG), European Regional Development Fund

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Experimental Data Snapshot

• Method: ELECTRON CRYSTALLOGRAPHY
• Resolution: 3.20 Å
• R-Value Free: 
  0.353 (Depositor), 0.353 (DCC) 
• R-Value Work: 
  0.300 (Depositor), 0.308 (DCC) 
• R-Value Observed: 
  0.303 (Depositor) 

Literature

Mechanism of SHP2 activation by bis-Tyr-phosphorylated Gab1.

Machner, L., Shaikhqasem, A., Gruber, T., Hamdi, F., Breithaupt, C., Kniest, J., Wiebe, F., Lewitzky, M., Parthier, C., Kyrilis, F.L., Balbach, J., Kastritis, P.L., Feller, S.M., Stubbs, M.T.

(2025) Structure 

• PubMed: 41435833 
• DOI: https://doi.org/10.1016/j.str.2025.11.018
• Primary Citation of Related Structures:  
  9QA5, 9QCD


• PubMed Abstract: 
  

  The non-receptor tyrosine phosphatase SHP2 (SH2 domain-containing protein tyrosine phosphatase 2) (PTPN11) is a regulator of diverse cellular functions including mitogenic activation and cell migration. It comprises two tandem Src-homology 2 (SH2) domains followed by the catalytic domain and is autoinhibited by the N-terminal SH2 domain blocking access to the active site. Mutations influencing auto-inhibition have been implicated in cancer and other diseases, and allosteric inhibitors have been developed that stabilize the inactive state. Here, we show that the intrinsically disordered bis-phosphorylated SHP2-activating peptide pY ⁶²⁷ pY ⁶⁵⁹ -Gab1 binds to both SH2 domains, undergoing partial ordering in the process. In addition to eliciting changes in SH2 domain dynamics, the peptide reorganizes their relative orientations to generate a new SH2-SH2 interface. Our data suggest an active conformation for SHP2 that is also applicable to the hematopoietic cell-specific SHP1 (PTPN6), shedding light on the activation mechanism of both enzymes and paving the way for the development of novel compounds to modulate SHP2 activity.

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Organizational Affiliation: 
• Institut für Biochemie und Biotechnologie, Martin-Luther-Universität Halle-Wittenberg, 06120 Halle (Saale), Germany; Institut für Molekulare Medizin, Martin-Luther-Universität Halle-Wittenberg, 06120 Halle (Saale), Germany; Charles-Tanford-Proteinzentrum, Martin-Luther-Universität Halle-Wittenberg, 06120 Halle (Saale), Germany.
Institut für Biochemie und Biotechnologie, Martin-Luther-Universität Halle-Wittenberg, 06120 Halle (Saale), Germany; Charles-Tanford-Proteinzentrum, Martin-Luther-Universität Halle-Wittenberg, 06120 Halle (Saale), Germany.
Institut für Molekulare Medizin, Martin-Luther-Universität Halle-Wittenberg, 06120 Halle (Saale), Germany; Institut für Physik, Martin-Luther-Universität Halle-Wittenberg, 06120 Halle (Saale), Germany; Charles-Tanford-Proteinzentrum, Martin-Luther-Universität Halle-Wittenberg, 06120 Halle (Saale), Germany.
Institut für Biochemie und Biotechnologie, Martin-Luther-Universität Halle-Wittenberg, 06120 Halle (Saale), Germany; ZIK HALOmem, Biozentrum, Martin-Luther-Universität Halle-Wittenberg, 06120 Halle (Saale), Germany.
Institut für Molekulare Medizin, Martin-Luther-Universität Halle-Wittenberg, 06120 Halle (Saale), Germany; Charles-Tanford-Proteinzentrum, Martin-Luther-Universität Halle-Wittenberg, 06120 Halle (Saale), Germany.
Institut für Biochemie und Biotechnologie, Martin-Luther-Universität Halle-Wittenberg, 06120 Halle (Saale), Germany; ZIK HALOmem, Biozentrum, Martin-Luther-Universität Halle-Wittenberg, 06120 Halle (Saale), Germany; Institute of Chemical Biology, National Hellenic Research Foundation, 11635 Athens, Greece.
Institut für Physik, Martin-Luther-Universität Halle-Wittenberg, 06120 Halle (Saale), Germany; ZIK HALOmem, Biozentrum, Martin-Luther-Universität Halle-Wittenberg, 06120 Halle (Saale), Germany; Mitteldeutsches Zentrum für Struktur und Dynamik der Proteine, Martin-Luther-Universität Halle-Wittenberg, 06120 Halle (Saale), Germany.
Institut für Biochemie und Biotechnologie, Martin-Luther-Universität Halle-Wittenberg, 06120 Halle (Saale), Germany; ZIK HALOmem, Biozentrum, Martin-Luther-Universität Halle-Wittenberg, 06120 Halle (Saale), Germany; Institute of Chemical Biology, National Hellenic Research Foundation, 11635 Athens, Greece; Mitteldeutsches Zentrum für Struktur und Dynamik der Proteine, Martin-Luther-Universität Halle-Wittenberg, 06120 Halle (Saale), Germany.
Institut für Molekulare Medizin, Martin-Luther-Universität Halle-Wittenberg, 06120 Halle (Saale), Germany; Charles-Tanford-Proteinzentrum, Martin-Luther-Universität Halle-Wittenberg, 06120 Halle (Saale), Germany. Electronic address: [e-mail].
Institut für Biochemie und Biotechnologie, Martin-Luther-Universität Halle-Wittenberg, 06120 Halle (Saale), Germany; ZIK HALOmem, Biozentrum, Martin-Luther-Universität Halle-Wittenberg, 06120 Halle (Saale), Germany; Charles-Tanford-Proteinzentrum, Martin-Luther-Universität Halle-Wittenberg, 06120 Halle (Saale), Germany; Mitteldeutsches Zentrum für Struktur und Dynamik der Proteine, Martin-Luther-Universität Halle-Wittenberg, 06120 Halle (Saale), Germany. Electronic address: [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

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

Biological Assembly Evidence: isothermal titration calorimetry

Macromolecule Content 

• Total Structure Weight: 32.84 kDa 
• Atom Count: 1,932 
• Modeled Residue Count: 241 
• Deposited Residue Count: 292 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Tyrosine-protein phosphatase non-receptor type 11	A [auth B]	223	Homo sapiens	Mutation(s): 0  Gene Names: PTPN11, PTP2C, SHPTP2 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 GTEx:  ENSG00000179295

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
GRB2-associated-binding protein 1	B [auth C]	69	Homo sapiens	Mutation(s): 0  Gene Names: GAB1
UniProt & NIH Common Fund Data Resources
Find proteins for Q13480 (Homo sapiens) Explore Q13480  Go to UniProtKB:  Q13480
PHAROS:  Q13480 GTEx:  ENSG00000109458

Small Molecules

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
PTR	B [auth C]	L-PEPTIDE LINKING	C9 H12 N O6 P		TYR

Experimental Data & Validation

Experimental Data

• Method: ELECTRON CRYSTALLOGRAPHY
• Resolution: 3.20 Å
• R-Value Free:  0.353 (Depositor), 0.353 (DCC) 
• R-Value Work:  0.300 (Depositor), 0.308 (DCC) 
• R-Value Observed: 0.303 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 30.595	α = 90
b = 82.253	β = 90
c = 117.764	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-12-31 
Deposition Author(s): Machner, L., Shaikhqasem, A., Hamdi, F., Breithaupt, C., Parthier, C., Kyrilis, F.L., Kastritis, P.L., Feller, S.M., Stubbs, M.T.

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Funding Organization	Location	Grant Number
German Research Foundation (DFG)	Germany	--
European Regional Development Fund	European Union	--

Revision History  

• Version 1.0: 2025-12-31
  Type: Initial release
  
• Version 1.1: 2026-01-07
  Changes: Database references