Research Article

Structure of the MDM2 Oncoprotein Bound to the p53 Tumor Suppressor Transactivation Domain

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Science  08 Nov 1996:
Vol. 274, Issue 5289, pp. 948-953
DOI: 10.1126/science.274.5289.948

Figures

  • Fig. 1.

    MIR electron density map of the X. laevis MDM2-p53 interface at 3.0 Å resolution, contoured at 1.0 σ, with the refined 2.3 Å resolution atomic model in a stick representation. Stereo view focuses on the interactions of Phe19, Trp23, and Leu26 of p53 (labeled) with the α2 helix of MDM2.

  • Fig. 2.

    The MDM2 NH2-terminal domain (in cyan) forms a structure reminiscent of a twisted trough. It has a hydrophobic cleft where the p53 peptide (in yellow) binds as an amphipathic α helix. Three approximately orthogonal views of the complex are shown. (A) The MDM2-p53 complex in an orientation where the floor of the MDM2 cleft is in the plane of the figure. MDM2, p53 and the NH2- and COOH-termini are labeled C and N. (B) The complex rotated approximately 90° about the horizontal axis of (A). (C) The complex rotated approximately 90° about the vertical axis of (B), looking down the helix axis of p53. Also shown are Phe19, Trp23, and Leu26 of p53, which insert deep into the MDM2 cleft [prepared with the programs MOLSCRIPT (50) and RASTER3D (51)]. Abbreviations for the amino acid residues are: A, Ala; C, Cys; D, Asp; E, Glu; F, Phe; G, Gly; H, His; I, Ile; K, Lys; L, Leu; M, Met; N, Asn; P, Pro; Q, Gln; R, Arg; S, Ser; T, Thr; V, Val; W, Trp; Y, Tyr.

  • Fig. 3.

    The MDM2 NH2-terminal domain contains two structurally similar portions related by an approximate dyad axis of pseudosymmetry. In this topological diagram of the secondary structure elements of MDM2, the residues at the start and the end of each secondary structure element are indicated. The structural elements of the second repeat are distinguished from those of the first repeat by the ‘prime’ symbol.

  • Fig. 4.

    The p53 peptide (in yellow) forms an amphipathic helix whose hydrophobic face binds the MDM2 cleft (in blue). The cleft is formed by the α2 helix, on one side, and the middle β sheet, on the other side, and is lined with hydrophobic and aromatic amino acids (or both). (A) The helical p53 amino acids show and emphasize the amphipathic nature of the α helix, where blue and red spheres indicate nitrogen and oxygen atoms, respectively, and the carbon atoms are in yellow. View is looking down the helix axis, as in Fig. 2C. For simplicity, only the p53 amino acids are labeled, although the MDM2 amino acids at the interface are also shown. The backbone regions of p53 and MDM2 are colored in a darker tone, and the two intermolecular hydrogen bonds at the interface are shown as red dotted lines. (B) The interface in an orientation rotated 90° about the vertical axis of (A). The MDM2 α2 helix is below the plane of the figure, its β sheet is above the plane, and p53 is between the two. Only the interacting amino acids at the interface are shown, and they are labeled.

  • Fig. 5.

    The MDM2 cleft contains, in its p53 binding portion, a deep pocket where a triad of hydrophobic and aromatic p53 amino acids—Phe19, Trp23, and Leu26—insert into. (A) Surface representation of the MDM2 cleft with gray concave regions highlighting its pocket-like characteristics. The p53 amino acids that interact with this surface are shown in yellow, and are labeled. Orientation is similar to Fig. 2A and the regions corresponding to the α2 helix and β sheet of MDM2 are labeled. (B) Phe19, Trp23, and Leu26 of p53 form a structure that is highly complementary to the MDM2 pocket, and fit tightly in it. A cross section of the interface showing the complementarity of p53 with the MDM2 pocket. The MDM2 surface is represented as a blue wire mesh and p53 residues 18 to 27 are in space filling representation. The orientation is similar to that of Fig. 4B [prepared with the program GRASP (52)].

Tables

  • Table 1.

    Statistics from the crystallographic analysis.

    Data setResolution (Å)ReflectionsData coverage (%)Rsym*MFIDPhasing power
    MeasuredUnique
    Native (X. laevis)2.315953625797.00.055
    Native (human)2.616069355990.00.052
    Thimerosal3.06707288694.80.0560.251.9
    UO2(OAc)23.16039254593.20.0780.121.4
    UO2(OAc)2 + K2Pt(CN)43.214350218186.90.0880.161.8
    K2Au(CN)43.04316259286.40.0240.080.8
    Refinement statistics
    Resolution (Å)Reflections§Protein atomsWater atomsRRfreermsd#
    Bonds (Å)Angles (°)B factors (Å2)
    X. laevis7.0-2.35423801400.1880.2530.0101.393.1
    Human8.0-2.632938070.2000.2760.0131.552.7
    • * Rsym = ΣhΣi|Ih,i − Ih|/ΣhΣiIh,i for the intensity (I) of i observations of reflection h.

    • † MFID, mean isomorphous difference = Σ|FPHFP |/ΣFPH, where FPH and FP are the derivative and native structure factors, respectively.

    • ‡ Phasing power = {[FH(c)2/(FPH(o)FPH(c)]2}1/2.

    • § Reflections with |F|>2σ and |F|>1σ for the data sets from X. laevis and humans, respectively.

    • R factor = Σ|FoFc|/Σ|Fo|, where Fo and Fc are the observed and calculated structure factors, respectively.

    • ¶ Free R factor calculated from 10 percent of the data chosen randomly and omitted from simulated annealing refinement from 3000 K.

    • # Root-mean-square deviations from ideal geometry and root-mean-square variation in the B factors of bonded atoms.