› 6rlc

X-ray diffraction
2.2Å resolution

Crystal structure of the PDZ tandem of syntenin in complex with fragment F13

Released:
DOI: 10.2210/pdb6rlc/pdb
PDB entry 6rlc coloured by chain, front view.
PDB entry 6rlc coloured by chain, side view.
PDB entry 6rlc coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Pharmacological inhibition of syntenin PDZ2 domain impairs breast cancer cell activities and exosome loading with syndecan and EpCAM cargo.
Leblanc R, Kashyap R, Barral K, Egea-Jimenez AL, Kovalskyy D, Feracci M, Garcia M, Derviaux C, Betzi S, Ghossoub R, Platonov M, Roche P, Morelli X, Hoffer L, Zimmermann P
J Extracell Vesicles 10 e12039 (2020)
PMID: 33343836

Function and Biology Details

Biochemical function:
  • not assigned
Biological process:
  • not assigned
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
homo dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-126347 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Syntenin-1 Chains: A, B, C, D
Molecule details ›
Chains: A, B, C, D
Length: 166 amino acids
Theoretical weight: 18.02 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli K-12
UniProt:
  • Canonical: O00560 (Residues: 113-273; Coverage: 54%)
Gene names: MDA9, SDCBP, SYCL
Sequence domains: PDZ domain

Ligands and Environments

2 bound ligands:
Ligand K7Z 4 x K7Z
Ligand ACT 3 x ACT
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: ESRF BEAMLINE ID30B
Spacegroup: P1
Unit cell:
a: 29.23Å b: 57.512Å c: 101.094Å
α: 93.99° β: 96.08° γ: 107.7°
R-values:
R R work R free
0.261 0.259 0.301
Expression system: Escherichia coli K-12

Quick links

Citations

10 review citations

Exosome biogenesis: machinery, regulation, and therapeutic implications in cancer.
Han et al. (2022)
9 more

1 mention without citation

Pharmacological inhibition of syntenin PDZ2 domain impairs breast cancer cell activities and exosome loading with syndecan and EpCAM cargo.
Leblanc et al. (2020)