2ZMV | pdb_00002zmv

Crystal structure of Synbindin

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 
    0.290 (Depositor), 0.240 (DCC) 
  • R-Value Work: 
    0.243 (Depositor), 0.240 (DCC) 
  • R-Value Observed: 
    0.245 (Depositor) 

wwPDB Validation   3D Report Full Report


This is version 1.3 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: https://doi.org/10.1016/j.bbrc.2008.04.143
  • Primary Citation of Related Structures:  
    2ZMV

  • 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.


Macromolecules
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 
Gene Names: TRAPPC4, SBDN, CGI-104, HSPC172, PTD009
UniProt & NIH Common Fund Data Resources
Find proteins for Q9Y296 (Homo sapiens)
Explore Q9Y296 
Go to UniProtKB:  Q9Y296
PHAROS:  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: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free:  0.290 (Depositor), 0.240 (DCC) 
  • R-Value Work:  0.243 (Depositor), 0.240 (DCC) 
  • R-Value Observed: 0.245 (Depositor) 
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
SOLVEphasing
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data collection

Structure Validation

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View more in-depth experimental data
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