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 
  • R-Value Observed: 0.196 

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:  
    5G1D, 5G1E

  • 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 revealed that syntenin-1 forms a symmetrical pair of dimers anchored by a syndecan-4 dimer ...

    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

    Department of Biochemistry, College of Life Science &Biotechnology, Yonsei University, Seoul 120-749, Korea.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
SYNTENIN-1A, B201Rattus norvegicusMutation(s): 0 
Gene Names: Sdcbp
UniProt
Find proteins for Q9JI92 (Rattus norvegicus)
Explore Q9JI92 
Go to UniProtKB:  Q9JI92
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
SYNDECAN-4C, D8Rattus norvegicusMutation(s): 0 
Gene Names: Sdc4Synd4
UniProt
Find proteins for P34901 (Rattus norvegicus)
Explore P34901 
Go to UniProtKB:  P34901
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.81 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.194 
  • R-Value Observed: 0.196 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 67.525α = 90
b = 88.529β = 90
c = 90.368γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
SCALEPACKdata scaling
PHENIXphasing

Structure Validation

View Full Validation Report




Entry History 

Deposition Data

Revision History  (Full details and data files)

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