9QCD image
Deposition Date 2025-03-04
Release Date 2025-12-31
Last Version Date 2026-01-07
Entry Detail
PDB ID:
9QCD
Title:
Micro-ED structure of the NSH2-CSH2 tandem domain of SHP2 in complex with the bis-phosphorylated pY627-pY659-Gab1 (613-694) peptide
Biological Source:
Source Organism(s):
Homo sapiens (Taxon ID: 9606)
Expression System(s):
Method Details:
Experimental Method:
Resolution:
3.20 Å
R-Value Free:
0.35
R-Value Work:
0.30
R-Value Observed:
0.30
Space Group:
P 21 21 21
Macromolecular Entities
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Tyrosine-protein phosphatase non-receptor type 11
Gene (Uniprot):PTPN11
Chain IDs:A (auth: B)
Chain Length:223
Number of Molecules:1
Biological Source:Homo sapiens
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:GRB2-associated-binding protein 1
Gene (Uniprot):GAB1
Chain IDs:B (auth: C)
Chain Length:69
Number of Molecules:1
Biological Source:Homo sapiens
Modified Residue
Compound ID Chain ID Parent Comp ID Details 2D Image
PTR B TYR modified residue
Ligand Molecules
Primary Citation

Abstact

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 pY627pY659-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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Chemical

Disease

Primary Citation of related structures
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