2JSN

Solution structure of the atypical PDZ-like domain of synbindin


Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 100 
  • Conformers Submitted: 20 
  • Selection Criteria: structures with the lowest energy 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Solution structure of synbindin atypical PDZ domain and interaction with syndecan-2

Fan, S.Feng, Y.Wei, Z.Xia, B.Gong, W.

(2009) Protein Pept Lett 16: 189-195

  • DOI: https://doi.org/10.2174/092986609787316342
  • Primary Citation of Related Structures:  
    2JSN

  • PubMed Abstract: 

    Synbindin is one component of Transport protein particle (TRAPP) complexes. In the hippocampal neurons, synbindin binds syndecan-2 by its atypical PDZ domain (APD) and may regulate the formation of dendritic spines. To investigate the interaction of synbindin and syndecan-2, we determined the solution structure of the synbindin APD by NMR. The structure of APD is different from the classical canonical PDZ domains by lacking the typical alphaA helix and the signature sequence Gly-Psi-Gly-Psi. These differences indicate that APD may not bind syndecan-2 with the typical binding mode of other PDZ domain proteins. In NMR titration experiments, APD do not bind with the C-terminal TKEFYA peptide of syndecan-2, but can interact with the 32-residue cytoplasmic domain of syndecan-2 very weakly.


  • Organizational Affiliation

    School of Life Sciences, University of Science and Technology of China, Hefei, Anhui, 230026, China.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Trafficking protein particle complex subunit 496Homo sapiensMutation(s): 0 
Gene Names: TRAPPC4SBDN
UniProt & NIH Common Fund Data Resources
Find proteins for Q9Y296 (Homo sapiens)
Explore Q9Y296 
Go to UniProtKB:  Q9Y296
GTEx:  ENSG00000196655 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9Y296
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 100 
  • Conformers Submitted: 20 
  • Selection Criteria: structures with the lowest energy 

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2008-07-15
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2020-02-19
    Changes: Data collection, Database references, Derived calculations, Other
  • Version 1.3: 2023-06-14
    Changes: Database references, Other