4GVD

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.243 
  • R-Value Work: 0.196 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

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:  

  • 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 speci ...

    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

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
T-lymphoma invasion and metastasis-inducing protein 1
A, B
94Homo sapiensMutation(s): 0 
Gene Names: TIAM1
Find proteins for Q13009 (Homo sapiens)
Go to Gene View: TIAM1
Go to UniProtKB:  Q13009
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Syndecan-1
C, D
8Homo sapiensMutation(s): 0 
Gene Names: SDC1 (SDC)
Find proteins for P18827 (Homo sapiens)
Go to Gene View: SDC1
Go to UniProtKB:  P18827
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NA
Query on NA

Download SDF File 
Download CCD File 
A, B
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

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Download CCD File 
A, B
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
ANS
Query on ANS

Download SDF File 
Download CCD File 
C, D
5-(DIMETHYLAMINO)-1-NAPHTHALENESULFONIC ACID(DANSYL ACID)
DANSYL ACID
C12 H13 N O3 S
BBEQQKBWUHCIOU-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.243 
  • R-Value Work: 0.196 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 26.517α = 90.00
b = 58.106β = 90.50
c = 50.948γ = 90.00
Software Package:
Software NamePurpose
StructureStudiodata collection
d*TREKdata reduction
PHASERphasing
d*TREKdata scaling
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

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