1I7E | pdb_00001i7e

C-Terminal Domain Of Mouse Brain Tubby Protein bound to Phosphatidylinositol 4,5-bis-phosphate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 
    0.261 (Depositor), 0.260 (DCC) 
  • R-Value Work: 
    0.212 (Depositor), 0.212 (DCC) 
  • R-Value Observed: 
    0.212 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.4 of the entry. See complete history

Literature

G-protein signaling through tubby proteins.

Santagata, S.Boggon, T.J.Baird, C.L.Gomez, C.A.Zhao, J.Shan, W.S.Myszka, D.G.Shapiro, L.

(2001) Science 292: 2041-2050

  • DOI: https://doi.org/10.1126/science.1061233
  • Primary Citation Related Structures: 
    1I7E

  • PubMed Abstract: 

    Dysfunction of the tubby protein results in maturity-onset obesity in mice. Tubby has been implicated as a transcription regulator, but details of the molecular mechanism underlying its function remain unclear. Here we show that tubby functions in signal transduction from heterotrimeric GTP-binding protein (G protein)-coupled receptors. Tubby localizes to the plasma membrane by binding phosphatidylinositol 4,5-bisphosphate through its carboxyl terminal "tubby domain." X-ray crystallography reveals the atomic-level basis of this interaction and implicates tubby domains as phosphorylated-phosphatidyl- inositol binding factors. Receptor-mediated activation of G protein alphaq (Galphaq) releases tubby from the plasma membrane through the action of phospholipase C-beta, triggering translocation of tubby to the cell nucleus. The localization of tubby-like protein 3 (TULP3) is similarly regulated. These data suggest that tubby proteins function as membrane-bound transcription regulators that translocate to the nucleus in response to phosphoinositide hydrolysis, providing a direct link between G-protein signaling and the regulation of gene expression.


  • Organizational Affiliation
    • Ruttenberg Cancer Center, Structural Biology Program, Department of Physiology and Biophysics, Mount Sinai School of Medicine of New York University, 1425 Madison Avenue New York, NY 10029, USA.

Macromolecule Content 

  • Total Structure Weight: 30.49 kDa 
  • Atom Count: 2,267 
  • Modeled Residue Count: 237 
  • Deposited Residue Count: 265 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
TUBBY PROTEIN265Mus musculusMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P50586 (Mus musculus)
Explore P50586 
Go to UniProtKB:  P50586
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP50586
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
IBS

Query on IBS



Download:Ideal Coordinates CCD File
B [auth A]L-ALPHA-GLYCEROPHOSPHO-D-MYO-INOSITOL-4,5-BIS-PHOSPHATE
C9 H19 O17 P3
JBQPYAMQMBKZDT-WKBARDANSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free:  0.261 (Depositor), 0.260 (DCC) 
  • R-Value Work:  0.212 (Depositor), 0.212 (DCC) 
  • R-Value Observed: 0.212 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 43.102α = 90
b = 51.469β = 90
c = 120.834γ = 90
Software Package:
Software NamePurpose
X-PLORmodel building
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLORphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2001-06-27
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2018-01-31
    Changes: Experimental preparation
  • Version 1.4: 2023-08-09
    Changes: Data collection, Database references, Derived calculations, Refinement description