Table 1.
Statistics for data collection and structure refinement.
Figure 1.
The structure of the Grb2 SH2 domain in complex with a CD28-derived peptide.
(A) The overall structure. Grb2 SH2 is shown as a cartoon model, whereas the peptide is shown as a stick model. (B) The interactions between the phosphotyrosine, pTyr191pep, and the SH2 domain. The main-chain trace of the SH2 domain is shown as blue tubes with the side-chains of some key residues in thin sticks. The phosphopeptides are shown as thick stick models. The green dashed lines indicate hydrogen bonds. (C) The interactions between the conserved asparagine, Asn193pep, of the peptide (thick sticks) and the SH2 domain (thin sticks).
Figure 2.
Comparison of the structures of phosphopeptides bound to Grb2 SH2.
(A) CD28 (present work, D-pY-M-N-M-T). (B) BCR-Abl (a typical type-I β-turn, PDB ID: 1BMB, F-pY-V-N-V-E) (C) AICD (with a Pro residue at the pY+3 position, PDB ID: 3MXC, G-pY-E-N-P-T-Y). The SH2 domains are shown as surface models, whereas the phosphopeptides are shown as stick models. The thin green lines indicate the distance between the main-chain O of pY and the main-chain N of pY+3, which form a hydrogen bond in the type-I β-turn. The side-chains of some flanking residues are missing due to their weak electron density. (D) Superposition of the 3 peptides. The tubes represent the main-chain traces of CD28 (green), BCR-Abl (red), and AICD (blue). (E) Superposition of CD28, BCR-Abl, and AICD as in (D) but vertically rotated by approximately 90°.
Table 2.
Main-chain torsion angles (φ/ψ) of the phosphopeptide bound to the Grb2 SH2 domain and their amino acid sequencesa.
Figure 3.
(A) The cadmium binding site located between 2 neighboring molecules in the crystal. The cadmium ion is shown as a green sphere. The Grb2 SH2 molecule is shown in thick lines, whereas a symmetrically-related molecule is shown in thin lines. Green dashed lines indicated the coordinate and hydrogen bonds. (B) The corresponding site in Grb2 SH2/AICD (PDB ID: 3MXC). The red sphere represents a water molecule.
Figure 4.
The 2Fo–Fc map around the phosphate group of the phosphotyrosine residue, pTyr191pep.
The contour level is set to 1.2 σ, where σ is the root-mean-square deviation of the electron density.
Table 3.
Selected bond angles and torsion angles of the phosphate group of the phosphotyrosine (degrees).
Figure 5.
A model structure of the CD28-derived peptide bound to PI3K N.
(A) The crystal structure of the amino-terminal SH2 domain of PI3K (PI3K N SH2) with a phosphopeptide derived from c-Kit (T-N-E-pY-M-D-M-K) and (B) a molecular model of PI3K N SH2 with the CD28-derived peptide (S-D-pY-M-N-M-T). The SH2 domains are shown as surface models, whereas the phosphopeptides are shown as stick models.