PDBsum entry 3u23

Protein binding

PDB id: 3u23

Contents

Protein chains

56 a.a.

14 a.a.

Ligands

EDO

Waters ×86

PDB id:

3u23

Name:

Protein binding

Title:

Atomic resolution crystal structure of the 2nd sh3 domain from human cd2ap (cms) in complex with a proline-rich peptide from human rin3

Structure:

Cd2-associated protein. Chain: a. Fragment: unp residues 109-168. Synonym: adapter protein cms, cas ligand with multiple sh3 domains. Engineered: yes. Ras and rab interactor 3. Chain: b. Fragment: unp residues 452-467. Synonym: ras interaction/interference protein 3.

Source:

Homo sapiens. Human. Organism_taxid: 9606. Gene: cd2ap. Expressed in: escherichia coli. Expression_system_taxid: 562. Synthetic: yes. Other_details: synthesised peptide

Resolution:

1.11Å R-factor: 0.152 R-free: 0.167

Authors:

P.C.Simister,E.Rouka,M.Janning,J.R.C.Muniz,K.H.Kirsch,S.Knapp,F.Von Delft,P.Filippakopoulos,C.H.Arrowsmith,T.Krojer,A.M.Edwards, J.Weigelt,C.Bountra,S.M.Feller,Structural Genomics Consortium (Sgc)

Key ref:

E.Rouka et al. (2015). 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. PubMed id: 26296892 DOI: 10.1074/jbc.M115.637207

Date:

30-Sep-11 Release date: 28-Dec-11

Protein chain

Q9Y5K6  (CD2AP_HUMAN) -  CD2-associated protein from Homo sapiens

Seq: 639 a.a.

Struc: 56 a.a.

Protein chain

Q8TB24  (RIN3_HUMAN) -  Ras and Rab interactor 3 from Homo sapiens

Seq: 985 a.a.

Struc: 14 a.a.*

* PDB and UniProt seqs differ at 1 residue position (black cross)

DOI no: 10.1074/jbc.M115.637207

J Biol Chem 290:25275-25292 (2015)

PubMed id: 26296892

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).

E.Rouka, P.C.Simister, M.Janning, J.Kumbrink, T.Konstantinou, J.R.Muniz, D.Joshi, N.O'Reilly, R.Volkmer, B.Ritter, S.Knapp, F.von Delft, K.H.Kirsch, S.M.Feller.

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.