9QCD: PDB entry 9QCD

Micro-ED structure of the NSH2-CSH2 tandem domain of SHP2 in complex with the bis-phosphorylated pY627-pY659-Gab1 (613-694) peptide. Determined by electron crystallography at 3.2 Å resolution. Released 31 Dec 2025.

Method: Electron crystallography
Resolution: 3.2 Å
Organism: Homo sapiens
Chains: 2
Atoms: 1,932
Mol. weight: 32.84 kDa
Released: 31 Dec 2025

Explore 9QCD in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9QCD contains 6 α-helices and 25 β-strands across 2 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain B: 5 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	7	1	1
α-helix	13-22	10
β-strand	28-33	6	1
β-strand	38	1	2
β-strand	40	1	2
β-strand	41-47	7	1
β-strand	50-56	7	1
β-strand	57-58	2	3
β-strand	63-64	2	3
β-strand	71	1	3
α-helix	74-83	10
β-strand	89-90	2	4
β-strand	95	1	4
β-strand	100-101	2	1
α-helix	102-103	2
β-strand	113	1	5
α-helix	119-129	11
β-strand	134-139	6	5
β-strand	147-152	6	5
β-strand	167-172	6	5
β-strand	173-175	3	6
β-strand	178-180	3	6
β-strand	187	1	6
α-helix	190-199	10
β-strand	202-203	2	7
β-strand	209-210	2	7
β-strand	214-215	2	5

Chain C: 1 helix, 3 β-strands

Element	Residues	Length	Sheet
β-strand	627	1	1
β-strand	630-631	2	4
β-strand	659-660	2	5
α-helix	664-675	12

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Tyrosine-protein phosphatase non-receptor type 11	B	protein	223	Homo sapiens	Q06124 (AlphaFold model)
GRB2-associated-binding protein 1	C	protein	69	Homo sapiens	Q13480 (AlphaFold model)

Sequence of entity 1 (B), FASTA

>9QCD_1 Tyrosine-protein phosphatase non-receptor type 11 (chains B)
SMTSRRWFHPNITGVEAENLLLTRGVDGSFLARPSKSNPGDFTLSVRRNGAVTHIKIQNT
GDYYDLYGGEKFATLAELVQYYMEHHGQLKEKNGDVIELKYPLNCADPTSERWFHGHLSG
KEAEKLLTEKGKHGSFLVRESQSHPGDFVLSVRTGDDKGESNDGKSKVTHVMIRCQELKY
DVGGGERFDSLTDLVEHYKKNPMVETLGTVLQLKQPLNTTRIN

Sequence of entity 2 (C), FASTA

>9QCD_2 GRB2-associated-binding protein 1 (chains C)
GPIKPKGDKQVEYLDLDLDSGKSTPPRKQKSSGSGSSVADERVDYVVVDQQKTLALKSTR
EAWTDGRQS

Primary citation

Mechanism of SHP2 activation by bis-Tyr-phosphorylated Gab1. Machner, L., Shaikhqasem, A., Gruber, T. et al. Structure (2026) 34:441-453.e7. DOI 10.1016/j.str.2025.11.018 · PubMed

Other PDB entries of the same protein (UniProt Q06124 (AlphaFold model), which also has an AlphaFold model), best resolution first:

9EIK 1.25 Å, Crystal structure of N-SH2 domain of SHP2 with T42A mutation bound to GAB1 tyrosine…
3ZM1 1.4 Å, Catalytic domain of human SHP2
4JMG 1.4 Å, Crystal structure of the synthetic protein in complex with pY peptide
7PPM 1.48 Å, SHP2 catalytic domain in complex with IRS1 (889-901) phosphopeptide (pSer-892, pTyr-896)
3ZM0 1.5 Å, Catalytic domain of human SHP2
3ZM2 1.5 Å, Catalytic domain of human SHP2
3ZM3 1.5 Å, Catalytic domain of human SHP2
7PPL 1.53 Å, SHP2 catalytic domain in complex with IRS1 (625-639) phosphopeptide (pTyr-632, pSer-636)
9EIC 1.58 Å, Crystal structure of unbound N-SH2 domain of SHP2 with T42A mutation
9EHD 1.59 Å, Crystal structure of N-SH2 domain of SHP2 bound to GAB1 tyrosine phosphorylated peptide…
3B7O 1.6 Å, Crystal structure of the human tyrosine phosphatase SHP2 (PTPN11) with an accessible…
4RDD 1.6 Å, Co-crystal structure of SHP2 in complex with a Cefsulodin derivative

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