6R9H

Crystal structure of the PDZ tandem of syntenin in complex with fragment C58

  • Classification: SIGNALING PROTEIN
  • Organism(s): Homo sapiens
  • Expression System: Escherichia coli K-12
  • Mutation(s): No 

  • Deposited: 2019-04-03 Released: 2021-02-03 
  • Deposition Author(s): Feracci, M., Barral, K.
  • Funding Organization(s): KU Leuven, French National Research Agency, Belgian Foundation against Cancer, Fondation ARC, Research Foundation - Flanders, Other private

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.208 
  • R-Value Observed: 0.212 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Pharmacological inhibition of syntenin PDZ2 domain impairs breast cancer cell activities and exosome loadifing with syndecan and EpCAM cargo.

Leblanc, R.Kashyap, R.Barral, K.Egea-Jimenez, A.L.Kovalskyy, D.Feracci, M.Garcia, M.Derviaux, C.Betzi, S.Ghossoub, R.Platonov, M.Roche, P.Morelli, X.Hoffer, L.Zimmermann, P.

(2020) J Extracell Vesicles 10: e12039-e12039

  • DOI: https://doi.org/10.1002/jev2.12039
  • Primary Citation of Related Structures:  
    6R9H, 6RLC

  • PubMed Abstract: 

    Exosomes support cell-to-cell communication in physiology and disease, including cancer. We currently lack tools, such as small chemicals, capable of modifying exosome composition and activity in a specific manner. Building on our previous understanding of how syntenin, and its PDZ partner syndecan (SDC), impact on exosome composition we optimized a small chemical compound targeting the PDZ2 domain of syntenin. In vitro , in tests on MCF-7 breast carcinoma cells, this compound is non-toxic and impairs cell proliferation, migration and primary sphere formation. It does not affect the size or the number of secreted particles, yet it decreases the amounts of exosomal syntenin, ALIX and SDC4 while leaving other exosomal markers unaffected. Interestingly, it also blocks the sorting of EpCAM, a bona fide target used for carcinoma exosome immunocapture. Our study highlights the first characterization of a small pharmacological inhibitor of the syntenin-exosomal pathway, of potential interest for exosome research and oncology.


  • Organizational Affiliation

    Equipe labellisée Ligue 2018 Centre de Recherche en Cancérologie de Marseille (CRCM) Aix-Marseille Université, Inserm, CNRS, Institut Paoli-Calmettes Marseille France.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Syntenin-1
A, B, C, D
166Homo sapiensMutation(s): 0 
Gene Names: SDCBPMDA9SYCL
UniProt & NIH Common Fund Data Resources
Find proteins for O00560 (Homo sapiens)
Explore O00560 
Go to UniProtKB:  O00560
PHAROS:  O00560
GTEx:  ENSG00000137575 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO00560
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
JVK
Query on JVK

Download Ideal Coordinates CCD File 
G [auth A],
K [auth C]
(2~{S})-2-[2-(4-chlorophenyl)sulfanylethanoylamino]-3-methyl-butanoic acid
C13 H16 Cl N O3 S
IKYARSKDJJAPDW-LBPRGKRZSA-N
PO4
Query on PO4

Download Ideal Coordinates CCD File 
E [auth A],
F [auth A],
J [auth C],
L [auth D]
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
ACT
Query on ACT

Download Ideal Coordinates CCD File 
H [auth A],
I [auth B],
M [auth D]
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.208 
  • R-Value Observed: 0.212 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 28.937α = 82.59
b = 56.185β = 84.21
c = 100.874γ = 78.59
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
KU LeuvenBelgiumGOA/12/016
French National Research AgencyFranceAMIDEX project ANR-11-IDEX-0001-02
Belgian Foundation against CancerBelgiumSTK-FAF-FA/2016/828
Fondation ARCFranceARC PDF20151203700
Fondation ARCFrancePJA 2016204584
Research Foundation - FlandersBelgiumFWO, G.0C57.18N
Other privateFranceNational League Against Cancer

Revision History  (Full details and data files)

  • Version 1.0: 2021-02-03
    Type: Initial release
  • Version 1.1: 2024-01-24
    Changes: Data collection, Database references, Refinement description