2ZMV

Crystal structure of Synbindin


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.290 
  • R-Value Work: 0.243 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

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: 10.1016/j.bbrc.2008.04.143

  • 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/s ...

    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.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Trafficking protein particle complex subunit 4
A, B
227Homo sapiensMutation(s): 0 
Gene Names: TRAPPC4 (SBDN)
Find proteins for Q9Y296 (Homo sapiens)
Go to Gene View: TRAPPC4
Go to UniProtKB:  Q9Y296
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.290 
  • R-Value Work: 0.243 
  • Space Group: P 21 3
Unit Cell:
Length (Å)Angle (°)
a = 124.391α = 90.00
b = 124.391β = 90.00
c = 124.391γ = 90.00
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
PDB_EXTRACTdata extraction
HKL-2000data collection
REFMACrefinement
SOLVEphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2008-04-21 
  • Released Date: 2008-07-01 
  • Deposition Author(s): Fan, F.

Revision History 

  • Version 1.0: 2008-07-01
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Advisory, Refinement description, Version format compliance
  • Version 1.2: 2017-10-11
    Type: Advisory, Refinement description