1YBO

Crystal structure of the PDZ tandem of human syntenin with syndecan peptide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.273 
  • R-Value Work: 0.193 

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This is version 1.3 of the entry. See complete history


Literature

The binding of the PDZ tandem of syntenin to target proteins

Grembecka, J.Cierpicki, T.Devedjiev, Y.Derewenda, U.Kang, B.S.Bushweller, J.H.Derewenda, Z.S.

(2006) Biochemistry 45: 3674-3683

  • DOI: 10.1021/bi052225y
  • Primary Citation of Related Structures:  
    1W9E, 1W9Q, 1W9O, 1V1T, 1YBO

  • PubMed Abstract: 
  • PDZ domains are among the most abundant protein modules in the known genomes. Their main function is to provide scaffolds for membrane-associated protein complexes by binding to the cytosolic, C-terminal fragments of receptors, channels, and other integral membrane proteins ...

    PDZ domains are among the most abundant protein modules in the known genomes. Their main function is to provide scaffolds for membrane-associated protein complexes by binding to the cytosolic, C-terminal fragments of receptors, channels, and other integral membrane proteins. Here, using both heteronuclear NMR and single crystal X-ray diffraction, we show how peptides with different sequences, including those corresponding to the C-termini of syndecan, neurexin, and ephrin B, can simultaneously bind to both PDZ domains of the scaffolding protein syntenin. The PDZ2 domain binds these peptides in the canonical fashion, and an induced fit mechanism allows for the accommodation of a range of side chains in the P(0) and P(-)(2) positions. However, binding to the PDZ1 domain requires that the target peptide assume a noncanonical conformation. These data help explain how syntenin, and perhaps other PDZ-containing proteins, may preferentially bind to dimeric and clustered targets, and provide a mechanistic explanation for the previously reported cooperative ligand binding by syntenin's two PDZ domains.


    Organizational Affiliation

    Department of Molecular Physiology and Biological Physics, University of Virginia School of Medicine, Charlottesville, Virginia 22908-0736, USA.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Syntenin 1A, B166Homo sapiensMutation(s): 0 
Gene Names: SDCBPMDA9SYCL
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
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Syndecan-4C, D17N/AMutation(s): 0 
Find proteins for P31431 (Homo sapiens)
Explore P31431 
Go to UniProtKB:  P31431
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PHAROS:  P31431
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.273 
  • R-Value Work: 0.193 
  • Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 72.322α = 90
b = 72.322β = 90
c = 125.921γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
AMoREphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2006-01-10
    Type: Initial release
  • Version 1.1: 2008-04-30
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Advisory, Version format compliance
  • Version 1.3: 2017-10-11
    Changes: Refinement description