5G1D

The complex structure of syntenin-1 PDZ domain with c-terminal extension


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.81 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.194 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

New Structural Insight of C-Terminal Region of Syntenin-1, Enhancing the Molecular Dimerization and Inhibitory Function Related on Syndecan-4 Signaling.

Choi, Y.Yun, J.H.Yoo, J.Kim, H.Lee, I.Son, H.N.Kim, I.S.Yoon, H.S.Zimmermann, P.Couchman, J.R.Cho, H.S.Oh, E.S.Lee, W.

(2016) Sci.Rep. 6: 36818

  • DOI: 10.1038/srep36818
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The PDZ domain-containing scaffold protein, syntenin-1, binds to the transmembrane proteoglycan, syndecan-4, but the molecular mechanism/function of this interaction are unknown. Crystal structure analysis of syntenin-1/syndecan-4 cytoplasmic domains ...

    The PDZ domain-containing scaffold protein, syntenin-1, binds to the transmembrane proteoglycan, syndecan-4, but the molecular mechanism/function of this interaction are unknown. Crystal structure analysis of syntenin-1/syndecan-4 cytoplasmic domains revealed that syntenin-1 forms a symmetrical pair of dimers anchored by a syndecan-4 dimer. The syndecan-4 cytoplasmic domain is a compact intertwined dimer with a symmetrical clamp shape and two antiparallel strands forming a cavity within the dimeric twist. The PDZ2 domain of syntenin-1 forms a direct antiparallel interaction with the syndecan-4 cytoplasmic domain, inhibiting the functions of syndecan-4 such as focal adhesion formation. Moreover, C-terminal region of syntenin-1 reveals an essential role for enhancing the molecular homodimerization. Mutation of key syntenin-1 residues involved in the syndecan-4 interaction or homodimer formation abolishes the inhibitory function of syntenin-1, as does deletion of the homodimerization-related syntenin-1 C-terminal domain. Syntenin-1, but not dimer-formation-incompetent mutants, rescued the syndecan-4-mediated inhibition of migration and pulmonary metastasis by B16F10 cells. Therefore, we conclude that syntenin-1 negatively regulates syndecan-4 function via oligomerization and/or syndecan-4 interaction, impacting cytoskeletal organization and cell migration.


    Organizational Affiliation

    Biomedical Research Institute, Korea Institute of Science and Technology, Seoul 136-791, Republic of Korea.,Department of Biochemistry, College of Life Science &Biotechnology, Yonsei University, Seoul 120-749, Korea.,Department of Biomedical Sciences, University of Copenhagen, Biocenter, 2200 Copenhagen, Denmark.,Department of Biology, College of Life Science &Biotechnology, Yonsei University, Seoul 136-791, Republic of Korea.,Department of Life Sciences, Division of Life and Pharmaceutical Sciences and the Research Center for Cellular Homeostasis, Ewha Womans University, Seoul 120-750, Korea.,Department of Genetic Engineering, College of Life Sciences, Kyung Hee University,Yongin-si Gyeonggi-do, 446-701, Republic of Korea.,Laboratory for Glycobiology, University of Leuven &Flanders Interuniversity Institute for Biotechnology, Leuven, Belgium.,Division of Structural and Computational Biology, School of Biological Sciences, Nanyang Technological University, Singapore.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
SYNTENIN-1
A, B
201Rattus norvegicusMutation(s): 0 
Gene Names: Sdcbp
Find proteins for Q9JI92 (Rattus norvegicus)
Go to UniProtKB:  Q9JI92
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
SYNDECAN-4
C, D
8Rattus norvegicusMutation(s): 0 
Gene Names: Sdc4 (Synd4)
Find proteins for P34901 (Rattus norvegicus)
Go to UniProtKB:  P34901
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.81 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.194 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 67.525α = 90.00
b = 88.529β = 90.00
c = 90.368γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data reduction
REFMACrefinement
PHENIXphasing
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2016-11-23
    Type: Initial release
  • Version 1.1: 2017-03-29
    Type: Other
  • Version 1.2: 2017-07-12
    Type: Refinement description