Crystal structure of Synbindin

Experimental Data Snapshot

  • Resolution: 2.80 Å
  • R-Value Free: 0.290 
  • R-Value Work: 0.243 
  • R-Value Observed: 0.245 

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Crystal structure of human synbindin reveals two conformations of longin domain

Fan, S.Wei, Z.Xu, H.Gong, W.

(2009) Biochem Biophys Res Commun 378: 338-343

  • DOI: https://doi.org/10.1016/j.bbrc.2008.04.143
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    Transport protein particle (TRAPP) is a large multiprotein complex that involves in ER-to-Golgi and intra-Golgi traffic. Synbindin, the human ortholog of yeast Trs23, is one component of the TRAPP complexes. In the hippocampal neurons the synbindin/syndecan complex is involved in synaptic membrane trafficking and thereby regulates the formation of dendritic spines. Here we present the three-dimensional structure of human synbindin, which contains a longin domain (LD) and an atypical PDZ domain (APD). In the crystal, synbindin forms a hexamer, in which the LD forms two different conformations and the APD is quite disordered. These conformational changes of synbindin suggest a possible interaction mode of the LD.

  • Organizational Affiliation

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

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Trafficking protein particle complex subunit 4
A, B
227Homo sapiensMutation(s): 0 
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
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 2.80 Å
  • R-Value Free: 0.290 
  • R-Value Work: 0.243 
  • R-Value Observed: 0.245 
  • Space Group: P 21 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 124.391α = 90
b = 124.391β = 90
c = 124.391γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
PDB_EXTRACTdata extraction
HKL-2000data collection

Structure Validation

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Entry History 

Deposition Data

  • Released Date: 2008-07-01 
  • Deposition Author(s): Fan, F.

Revision History  (Full details and data files)

  • Version 1.0: 2008-07-01
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Advisory, Refinement description, Version format compliance
  • Version 1.2: 2017-10-11
    Changes: Advisory, Refinement description
  • Version 1.3: 2024-03-13
    Changes: Advisory, Data collection, Database references