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

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)

wwPDB Validation 3D Report Full Report

This is version 1.0 of the entry. See complete history.

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

DOI: https://doi.org/10.1016/j.str.2025.11.018

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

Find similar proteins by:

(by identity cutoff) | 3D Structure

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 Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q06124
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q13480
Sequence Annotations Expand
Reference Sequence

Small Molecules

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
PTR Query on 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

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2025-12-31

Deposition Author(s):

Shaikhqasem, A.

Kastritis, P.L.

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

Revision History (Full details and data files)

Version 1.0: 2025-12-31
Type: Initial release

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.