2LCS

Yeast Nbp2p SH3 domain in complex with a peptide from Ste20p


Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 20 
  • Conformers Submitted: 20 
  • Selection Criteria: target function 

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This is version 1.1 of the entry. See complete history


Literature

Distinct Peptide Binding Specificities of Src Homology 3 (SH3) Protein Domains Can Be Determined by Modulation of Local Energetics across the Binding Interface.

Gorelik, M.Davidson, A.R.

(2012) J Biol Chem 287: 9168-9177

  • DOI: 10.1074/jbc.M111.330753
  • Primary Citation of Related Structures:  
    2LCS

  • PubMed Abstract: 
  • The yeast Nbp2p SH3 and Bem1p SH3b domains bind certain target peptides with similar high affinities, yet display vastly different affinities for other targets. To investigate this unusual behavior, we have solved the structure of the Nbp2p SH3-Ste20 ...

    The yeast Nbp2p SH3 and Bem1p SH3b domains bind certain target peptides with similar high affinities, yet display vastly different affinities for other targets. To investigate this unusual behavior, we have solved the structure of the Nbp2p SH3-Ste20 peptide complex and compared it with the previously determined structure of the Bem1p SH3b bound to the same peptide. Although the Ste20 peptide interacts with both domains in a structurally similar manner, extensive in vitro studies with domain and peptide mutants revealed large variations in interaction strength across the binding interface of the two complexes. Whereas the Nbp2p SH3 made stronger contacts with the peptide core RXXPXXP motif, the Bem1p SH3b domain made stronger contacts with residues flanking the core motif. Remarkably, this modulation of local binding energetics can explain the distinct and highly nuanced binding specificities of these two domains.


    Organizational Affiliation

    Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
NAP1-binding protein 2A73Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: NBP2YDR162C
Find proteins for Q12163 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore Q12163 
Go to UniProtKB:  Q12163
Protein Feature View
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  • Reference Sequence
  • Find similar proteins by:  Sequence   |   Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Serine/threonine-protein kinase STE20B16Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: STE20YHL007C
EC: 2.7.11.1
Find proteins for Q03497 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore Q03497 
Go to UniProtKB:  Q03497
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 20 
  • Conformers Submitted: 20 
  • Selection Criteria: target function 
  • OLDERADO: 2LCS Olderado

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-02-01
    Type: Initial release
  • Version 1.1: 2012-04-11
    Changes: Database references