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 1.2 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: 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 ...

    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)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Syntenin 1A, B166Homo sapiensMutation(s): 3 
Gene Names: SDCBP OR MDA9 OR SYCLSDCBPMDA9SYCL
Find proteins for O00560 (Homo sapiens)
Explore O00560 
Go to UniProtKB:  O00560
NIH Common Fund Data Resources
PHAROS  O00560
Protein Feature View
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  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A,BL-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 

  • 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