3BIB

Tim-4 in complex with phosphatidylserine


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.248 
  • R-Value Work: 0.219 
  • R-Value Observed: 0.221 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Structures of T Cell Immunoglobulin Mucin Protein 4 Show a Metal-Ion-Dependent Ligand Binding Site where Phosphatidylserine Binds.

Santiago, C.Ballesteros, A.Martinez-Munoz, L.Mellado, M.Kaplan, G.G.Freeman, G.J.Casasnovas, J.M.

(2007) Immunity 27: 941-951

  • DOI: 10.1016/j.immuni.2007.11.008
  • Primary Citation of Related Structures:  
    3BI9, 3BIB, 3BIA

  • PubMed Abstract: 
  • The T cell immunoglobulin and mucin domain (TIM) proteins are important regulators of T cell responses. Crystal structures of the murine TIM-4 identified a metal-ion-dependent ligand binding site (MILIBS) in the immunoglobulin (Ig) domain of the TIM family ...

    The T cell immunoglobulin and mucin domain (TIM) proteins are important regulators of T cell responses. Crystal structures of the murine TIM-4 identified a metal-ion-dependent ligand binding site (MILIBS) in the immunoglobulin (Ig) domain of the TIM family. The characteristic CC' loop of the TIM domain and the hydrophobic FG loop shaped a narrow cavity where acidic compounds penetrate and coordinate to a metal ion bound to conserved residues in the TIM proteins. The structure of phosphatidylserine bound to the Ig domain showed that the hydrophilic head penetrates into the MILIBS and coordinates with the metal ion, whereas the aromatic residues on the tip of the FG loop interacted with the fatty acid chains and could insert into the lipid bilayer. Our results also revealed an important role of the MILIBS in the trafficking of TIM-1 to the cell surface.


    Organizational Affiliation

    Centro Nacional de Biotecnología, CSIC, Campus Universidad Autónoma, 28049 Madrid, Spain.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
T-cell immunoglobulin and mucin domain-containing protein 4A [auth X]116Mus musculusMutation(s): 0 
Gene Names: Timd4Tim4
Membrane Entity: Yes 
UniProt
Find proteins for Q6U7R4 (Mus musculus)
Explore Q6U7R4 
Go to UniProtKB:  Q6U7R4
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PSF (Subject of Investigation/LOI)
Query on PSF

Download Ideal Coordinates CCD File 
C [auth X]1,2-DICAPROYL-SN-PHOSPHATIDYL-L-SERINE
C18 H34 N O10 P
MIQYPPGTNIFAPO-CABCVRRESA-N
 Ligand Interaction
NA
Query on NA

Download Ideal Coordinates CCD File 
B [auth X]SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
PSF Binding MOAD:  3BIB IC50: 4.00e+6 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.248 
  • R-Value Work: 0.219 
  • R-Value Observed: 0.221 
  • Space Group: P 63 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 66.26α = 90
b = 66.26β = 90
c = 139.39γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
MxCuBEdata collection
XDSdata reduction
SCALAdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment  



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2008-01-01
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance