Structures of a platelet-derived growth factor/propeptide complex and a platelet-derived growth factor/receptor complex

Abstract

Platelet-derived growth factors (PDGFs) and their receptors (PDGFRs) are prototypic growth factors and receptor tyrosine kinases which have critical functions in development. We show that PDGFs share a conserved region in their prodomain sequences which can remain noncovalently associated with the mature cystine-knot growth factor domain after processing. The structure of the PDGF-A/propeptide complex reveals this conserved, hydrophobic association mode. We also present the structure of the complex between PDGF-B and the first three Ig domains of PDGFRbeta, showing that two PDGF-B protomers clamp PDGFRbeta at their dimerization seam. The PDGF-B:PDGFRbeta interface is predominantly hydrophobic, and PDGFRs and the PDGF propeptides occupy overlapping positions on mature PDGFs, rationalizing the need of propeptides by PDGFs to cover functionally important hydrophobic surfaces during secretion. A large-scale structural organization and rearrangement is observed for PDGF-B upon receptor binding, in which the PDGF-B L1 loop, disordered in the structure of the free form, adopts a highly specific conformation to form hydrophobic interactions with the third Ig domain of PDGFRbeta. Calorimetric data also shows that the membrane-proximal homotypic PDGFRalpha interaction, albeit required for activation, contributes negatively to ligand binding. The structural and biochemical data together offer insights into PDGF-PDGFR signaling, as well as strategies for PDGF-antagonism.

Fig. 1.

Structure of the PDGF-A/propeptide complex. (A) Ribbons model of the complex, with the mature PDGF-A protomers in green and blue, and the propeptides in pink and magenta. (B) The hydrophobic PDGF-A/propeptide interface. The side chains involved in the PDGF-A/propeptide interaction are depicted as sticks.

Fig. 2.

Structure of the PDGF-B:PDGFRβ complex. (A) Side view of the ribbon model of the complex, with the PDGF-B protomers in green and blue, and the PDGFRβ protomers in pink and orange. The N-linked glycans attached to PDGFRβ are depicted as sticks. (B) Top view of the PDGF-B:PDGFRβ complex in surface representation.

Fig. 3.

The PDGF-B:PDGFRβ interface. (A) An overview of the composite interface. The structural segments involved in binding are shown as thicker coils than the nonbinding segments, with the protruding PDGF-B protomer in cyan, the receding PDGF-B protomer in green, and PDGFRβ in pink. (B) Stereo view of the receptor-ligand interface in the same orientation, with main chains shown as coils and side chains shown as sticks. Note that upper patch and the lower patch of the interface are related by ∼110°. (C) The role of PDGF-B residues Arg27 and Ile30 (highlighted in green) in maintaining the receptor-binding conformation of the L1 loop. The view is rotated ∼70° from B.

Fig. 4.

The PDGF-B conformational change upon PDGFRβ binding. (A) Comparison between the free PDGF-B (PDB code 1PDG) dimer (red) and the PDGFRβ-bound PDGF-B dimer (cyan for the protruding protomer and green for the receding protomer) shows that PDGFRβ-binding induces the structural organization of the previously disordered large L1 loop, and a rotation of the protruding L3 loop. (B) and (C) Comparison of PDGF-B Trp40 and its neighboring residues in the free form and receptor-bound form shows a 180° flipping of Trp40, as induced by its interactions with PDGFRβ Tyr205, Tyr207 and Phe136 (pink).

Fig. 5.

Comparison of thermodynamic profiles of (A) PDGF-C:PDGFRα-D1-D3 binding and (B) PDGF-C:PDGFRα-D1-D5 binding, showing a negative contribution from PDGFRα-D4-D5.