Biological Assembly 1  

 3D View: Structure

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 8.70 kDa 
• Atom Count: 612 
• Modelled Residue Count: 76 
• Deposited Residue Count: 76 
• Unique protein chains: 2

2ROL

Structural Basis of PxxDY motif recognition in SH3 binding

• DOI: 10.2210/pdb2ROL/pdb
• BMRB: 11040

• Classification: SPLICING/SIGNALING PROTEIN
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2008-04-02 Released: 2009-03-03 
• Deposition Author(s): Aitio, O., Hellman, M., Kesti, T., Kleino, I., Samuilova, O., Tossavainen, H., Paakkonen, K., Saksela, K., Permi, P.

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Experimental Data Snapshot

• Method: SOLUTION NMR
• Conformers Calculated: 100 
• Conformers Submitted: 20 
• Selection Criteria: structures with the least restraint violations 

Literature

Structural basis of PxxDY motif recognition in SH3 binding

Aitio, O., Hellman, M., Kesti, T., Kleino, I., Samuilova, O., Paakkonen, K., Tossavainen, H., Saksela, K., Permi, P.

(2008) J Mol Biol 382: 167-178

• PubMed: 18644376 
• DOI: 10.1016/j.jmb.2008.07.008
• Primary Citation of Related Structures:  
  2ROL, 2K2M


• PubMed Abstract: 
  

We have determined the solution structure of epidermal growth factor receptor pathway substrate 8 (Eps8) L1 Src homology 3 (SH3) domain in complex with the PPVPNPDYEPIR peptide from the CD3epsilon cytoplasmic tail. Our structure reveals the distinct structural features that account for the unusual specificity of the Eps8 family SH3 domains for ligands containing a PxxDY motif instead of canonical PxxP ligands. The CD3epsilon peptide binds Eps8L1 SH3 in a class II orientation, but neither adopts a polyproline II helical conformation nor engages the first proline-binding pocket of the SH3 ligand binding interface. Ile531 of Eps8L1 SH3, instead of Tyr or Phe residues typically found in this position in SH3 domains, renders this hydrophobic pocket smaller and nonoptimal for binding to conventional PxxP peptides. A positively charged arginine at position 512 in the n-Src loop of Eps8L1 SH3 plays a key role in PxxDY motif recognition by forming a salt bridge to D7 of the CD3epsilon peptide. In addition, our structural model suggests a hydrogen bond between the hydroxyl group of the aromatic ring of Y8 and the carboxyl group of E496, thus explaining the critical role of the PxxDY motif tyrosine residue in binding to Eps8 family SH3. These finding have direct implications also for understanding the atypical binding specificity of the amino-terminal SH3 of the Nck family proteins.

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Organizational Affiliation: 

Program in Structural Biology and Biophysics, Institute of Biotechnology/NMR Laboratory, University of Helsinki, FI-00014 Helsinki, Finland.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Epidermal growth factor receptor kinase substrate 8-like protein 1	A	64	Homo sapiens	Mutation(s): 0  Gene Names: EPS8L1, DRC3, EPS8R1, PP10566
Find proteins for Q8TE68 (Homo sapiens) Explore Q8TE68  Go to UniProtKB:  Q8TE68
NIH Common Fund Data Resources
PHAROS:  Q8TE68 GTEx:  ENSG00000131037

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
12-meric peptide from T-cell surface glycoprotein CD3 epsilon chain	B	12	N/A	Mutation(s): 0
Find proteins for P07766 (Homo sapiens) Explore P07766  Go to UniProtKB:  P07766
NIH Common Fund Data Resources
PHAROS:  P07766 GTEx:  ENSG00000198851

Experimental Data & Validation

Experimental Data

• Method: SOLUTION NMR
• Conformers Calculated: 100 
• Conformers Submitted: 20 
• Selection Criteria: structures with the least restraint violations 
• OLDERADO: 2ROL Olderado

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2008-04-02 
• Released Date: 2009-03-03 
Deposition Author(s): Aitio, O., Hellman, M., Kesti, T., Kleino, I., Samuilova, O., Tossavainen, H., Paakkonen, K., Saksela, K., Permi, P.

Revision History  

• Version 1.0: 2009-03-03
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2020-02-26
  Changes: Data collection, Database references, Derived calculations, Other