1N99

CRYSTAL STRUCTURE OF THE PDZ TANDEM OF HUMAN SYNTENIN


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.94 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.184 
  • R-Value Observed: 0.186 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

PDZ Tandem of Human Syntenin: Crystal Structure and Functional Properties

Kang, B.S.Cooper, D.R.Jelen, F.Devedjiev, Y.Derewenda, U.Dauter, Z.Otlewski, J.Derewenda, Z.S.

(2003) Structure 11: 459-468

  • DOI: https://doi.org/10.1016/s0969-2126(03)00052-2
  • Primary Citation of Related Structures:  
    1N99

  • PubMed Abstract: 

    Syntenin, a 33 kDa protein, interacts with several cell membrane receptors and with merlin, the product of the causal gene for neurofibromatosis type II. We report a crystal structure of the functional fragment of human syntenin containing two canonical PDZ domains, as well as binding studies for full-length syntenin, the PDZ tandem, and isolated PDZ domains. We show that the functional properties of syntenin are a result of independent interactions with target peptides, and that each domain is able to bind peptides belonging to two different classes: PDZ1 binds peptides from classes I and III, while PDZ2 interacts with classes I and II. The independent binding of merlin by PDZ1 and syndecan-4 by PDZ2 provides direct evidence for the coupling of syndecan-mediated signaling to actin regulation by merlin.


  • Organizational Affiliation

    Department of Molecular Physiology and Biological Physics and The Cancer Center, University of Virginia, Charlottesville, VA 22908, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Syntenin 1
A, B
166Homo sapiensMutation(s): 3 
Gene Names: SDCBP OR MDA9 OR SYCL
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
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
MSE
Query on MSE
A, B
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.94 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.184 
  • R-Value Observed: 0.186 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 100.727α = 90
b = 48.678β = 120.82
c = 74.69γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
TRUNCATEdata reduction
SHARPphasing
REFMACrefinement
HKL-2000data reduction
CCP4data scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2003-04-15
    Type: Initial release
  • Version 1.1: 2008-04-28
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Advisory, Version format compliance
  • Version 1.3: 2022-12-21
    Changes: Database references, Derived calculations