4GVC

Crystal Structure of T-cell Lymphoma Invasion and Metastasis-1 PDZ in complex with phosphorylated Syndecan1 Peptide

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.54 Å
  • R-Value Free: 0.200 
  • R-Value Work: 0.166 
  • R-Value Observed: 0.167 

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Literature

The structure of the Tiam1 PDZ domain/ phospho-syndecan1 complex reveals a ligand conformation that modulates protein dynamics.

Liu, X., Shepherd, T.R., Murray, A.M., Xu, Z., Fuentes, E.J.

(2013) Structure 21: 342-354

  • DOI: 10.1016/j.str.2013.01.004
  • Primary Citation of Related Structures:  
    4GVC, 4GVD

  • PubMed Abstract: 

    • PDZ (PSD-95/Dlg/ZO-1) domains are protein-protein interaction modules often regulated by ligand phosphorylation. Here, we investigated the specificity, structure, and dynamics of Tiam1 PDZ domain/ligand interactions. We show that the PDZ domain specifically binds syndecan1 (SDC1), phosphorylated SDC1 (pSDC1), and SDC3 but not other syndecan isoforms ...

    PDZ (PSD-95/Dlg/ZO-1) domains are protein-protein interaction modules often regulated by ligand phosphorylation. Here, we investigated the specificity, structure, and dynamics of Tiam1 PDZ domain/ligand interactions. We show that the PDZ domain specifically binds syndecan1 (SDC1), phosphorylated SDC1 (pSDC1), and SDC3 but not other syndecan isoforms. The crystal structure of the PDZ/SDC1 complex indicates that syndecan affinity is derived from amino acids beyond the four C-terminal residues. Remarkably, the crystal structure of the PDZ/pSDC1 complex reveals a binding pocket that accommodates the phosphoryl group. Methyl relaxation experiments of PDZ/SCD1 and PDZ/pSDC1 complexes reveal that PDZ-phosphoryl interactions dampen dynamic motions in a distal region of the PDZ domain by decoupling them from the ligand-binding site. Our data are consistent with a selection model by which specificity and phosphorylation regulate PDZ/syndecan interactions and signaling events. Importantly, our relaxation data demonstrate that PDZ/phospho-ligand interactions regulate protein dynamics and their coupling to distal sites.

    Organizational Affiliation: 

    Department of Biochemistry, University of Iowa, Carver College of Medicine, Iowa City, IA 52242, USA.



Macromolecules
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(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
T-lymphoma invasion and metastasis-inducing protein 1A94Homo sapiensMutation(s): 0 
Gene Names: TIAM1
UniProt & NIH Common Fund Data Resources
Find proteins for Q13009 (Homo sapiens)
Explore Q13009 
Go to UniProtKB:  Q13009
PHAROS:  Q13009
GTEx:  ENSG00000156299
Protein Feature View
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  • Reference Sequence
  • Find similar proteins by:  Sequence   |   Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Syndecan-1B8Homo sapiensMutation(s): 0 
Gene Names: SDC1, SDC
UniProt & NIH Common Fund Data Resources
Find proteins for P18827 (Homo sapiens)
Explore P18827 
Go to UniProtKB:  P18827
PHAROS:  P18827
GTEx:  ENSG00000115884
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ANS (Subject of Investigation/LOI)
Query on ANS
Download Ideal Coordinates CCD File 
 D [auth B]5-(DIMETHYLAMINO)-1-NAPHTHALENESULFONIC ACID(DANSYL ACID)
C12 H13 N O3 S
BBEQQKBWUHCIOU-UHFFFAOYSA-N		 Ligand Interaction
CL
Query on CL
Download Ideal Coordinates CCD File 
 C [auth A], E [auth B]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M		 Ligand Interaction
NA
Query on NA
Download Ideal Coordinates CCD File 
 F [auth B]SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N		 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
PTR
Query on PTR		BL-PEPTIDE LINKINGC9 H12 N O6 PTYR
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.54 Å
  • R-Value Free: 0.200 
  • R-Value Work: 0.166 
  • R-Value Observed: 0.167 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 26.717α = 90
b = 50.135β = 90
c = 57.712γ = 90
Software Package:
Software NamePurpose
StructureStudiodata collection
PHASERphasing
REFMACrefinement
XDSdata reduction
SCALAdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-03-13
    Type: Initial release
  • Version 1.1: 2015-05-27
    Changes: Database references