6ROY: PDB entry 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. Determined by X-ray diffraction at 2.1 Å resolution. Released 19 Feb 2020.

Method: X-ray diffraction
Resolution: 2.1 Å
Organisms: Homo sapiens, synthetic construct
Chains: 4
Atoms: 1,822
Mol. weight: 26.38 kDa
Released: 19 Feb 2020

Explore 6ROY in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6ROY contains 7 α-helices and 28 β-strands across 4 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.

Chains A and B: 3 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	7	1	1
α-helix	13-23	11
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
α-helix	85-87	3
β-strand	89-90	2	4
β-strand	95	1	4
β-strand	100-101	2	1

Chain C: 1 helix, 2 β-strands

Element	Residues	Length	Sheet
β-strand	1	1	5
α-helix	2-3	2
β-strand	4-5	2	8

Chain D: 0 helices, 2 β-strands

Element	Residues	Length	Sheet
β-strand	1	1	1
β-strand	4-5	2	4

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Tyrosine-protein phosphatase non-receptor type 11	A, B	protein	104	Homo sapiens	Q06124 (AlphaFold model)
immune receptor tyrosine-based inhibitory motif (ITIM)	C, D	protein	11	synthetic construct	Q15116 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>6ROY_1 Tyrosine-protein phosphatase non-receptor type 11 (chains A, B)
MASRRWFHPNITGVEAENLLLTRGVDGSFLARPSKSNPGDFTLSVRRNGAVTHIKIQNTG
DYYDLYGGEKFATLAELVQYYMEHHGQLKEKNGDVIELKYPLNC

Sequence of entity 2 (C, D), FASTA

>6ROY_2 immune receptor tyrosine-based inhibitory motif (ITIM) (chains C, D)
FSVDYGELDFQ

Primary citation

Molecular mechanism of SHP2 activation by PD-1 stimulation. Marasco, M., Berteotti, A., Weyershaeuser, J. et al. Sci Adv (2020) 6:eaay4458-eaay4458. DOI 10.1126/sciadv.aay4458 · 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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