3U23

Atomic resolution crystal structure of the 2nd SH3 domain from human CD2AP (CMS) in complex with a proline-rich peptide from human RIN3

Summary for 3U23

• Entry DOI: 10.2210/pdb3u23/pdb
• Related: 2FEI 2KRN 4WCI
• Descriptor: CD2-associated protein, Ras and Rab interactor 3, 1,2-ETHANEDIOL, ... (4 entities in total)
• Functional Keywords: structural genomics, structural genomics consortium, sgc, beta-barrel, adaptor protein, protein binding
• Biological source: Homo sapiens (human); More
• Cellular location: Cytoplasm, cytoskeleton : Q9Y5K6; Cytoplasm : Q8TB24
• Total number of polymer chains: 2
• Total formula weight: 9309.63

Authors

Simister, P.C.,Rouka, E.,Janning, M.,Muniz, J.R.C.,Kirsch, K.H.,Knapp, S.,von Delft, F.,Filippakopoulos, P.,Arrowsmith, C.H.,Krojer, T.,Edwards, A.M.,Weigelt, J.,Bountra, C.,Feller, S.M.,Structural Genomics Consortium (SGC) (deposition date: 2011-09-30, release date: 2011-12-28, Last modification date: 2024-11-06)

Primary citation

Rouka, E.,Simister, P.C.,Janning, M.,Kumbrink, J.,Konstantinou, T.,Muniz, J.R.,Joshi, D.,O'Reilly, N.,Volkmer, R.,Ritter, B.,Knapp, S.,von Delft, F.,Kirsch, K.H.,Feller, S.M.
Differential Recognition Preferences of the Three Src Homology 3 (SH3) Domains from the Adaptor CD2-associated Protein (CD2AP) and Direct Association with Ras and Rab Interactor 3 (RIN3).
J.Biol.Chem., 290:25275-25292, 2015

PubMed Abstract: CD2AP is an adaptor protein involved in membrane trafficking, with essential roles in maintaining podocyte function within the kidney glomerulus. CD2AP contains three Src homology 3 (SH3) domains that mediate multiple protein-protein interactions. However, a detailed comparison of the molecular binding preferences of each SH3 remained unexplored, as well as the discovery of novel interactors. Thus, we studied the binding properties of each SH3 domain to the known interactor Casitas B-lineage lymphoma protein (c-CBL), conducted a peptide array screen based on the recognition motif PxPxPR and identified 40 known or novel candidate binding proteins, such as RIN3, a RAB5-activating guanine nucleotide exchange factor. CD2AP SH3 domains 1 and 2 generally bound with similar characteristics and specificities, whereas the SH3-3 domain bound more weakly to most peptide ligands tested yet recognized an unusually extended sequence in ALG-2-interacting protein X (ALIX). RIN3 peptide scanning arrays revealed two CD2AP binding sites, recognized by all three SH3 domains, but SH3-3 appeared non-functional in precipitation experiments. RIN3 recruited CD2AP to RAB5a-positive early endosomes via these interaction sites. Permutation arrays and isothermal titration calorimetry data showed that the preferred binding motif is Px(P/A)xPR. Two high-resolution crystal structures (1.65 and 1.11 Å) of CD2AP SH3-1 and SH3-2 solved in complex with RIN3 epitopes 1 and 2, respectively, indicated that another extended motif is relevant in epitope 2. In conclusion, we have discovered novel interaction candidates for CD2AP and characterized subtle yet significant differences in the recognition preferences of its three SH3 domains for c-CBL, ALIX, and RIN3.

PubMed: 26296892
DOI: 10.1074/jbc.M115.637207

Experimental method

X-RAY DIFFRACTION (1.11 Å)