3KAA

Structure of Tim-3 in complex with phosphatidylserine


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.245 
  • R-Value Work: 0.235 
  • R-Value Observed: 0.236 

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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

T cell/transmembrane, Ig, and mucin-3 allelic variants differentially recognize phosphatidylserine and mediate phagocytosis of apoptotic cells.

DeKruyff, R.H.Bu, X.Ballesteros, A.Santiago, C.Chim, Y.L.Lee, H.H.Karisola, P.Pichavant, M.Kaplan, G.G.Umetsu, D.T.Freeman, G.J.Casasnovas, J.M.

(2010) J Immunol 184: 1918-1930

  • DOI: 10.4049/jimmunol.0903059
  • Primary Citation of Related Structures:  
    3KAA

  • PubMed Abstract: 
  • T cell/transmembrane, Ig, and mucin (TIM) proteins, identified using a congenic mouse model of asthma, critically regulate innate and adaptive immunity. TIM-1 and TIM-4 are receptors for phosphatidylserine (PtdSer), exposed on the surfaces of apoptotic cells ...

    T cell/transmembrane, Ig, and mucin (TIM) proteins, identified using a congenic mouse model of asthma, critically regulate innate and adaptive immunity. TIM-1 and TIM-4 are receptors for phosphatidylserine (PtdSer), exposed on the surfaces of apoptotic cells. Herein, we show with structural and biological studies that TIM-3 is also a receptor for PtdSer that binds in a pocket on the N-terminal IgV domain in coordination with a calcium ion. The TIM-3/PtdSer structure is similar to that of TIM-4/PtdSer, reflecting a conserved PtdSer binding mode by TIM family members. Fibroblastic cells expressing mouse or human TIM-3 bound and phagocytosed apoptotic cells, with the BALB/c allelic variant of mouse TIM-3 showing a higher capacity than the congenic C.D2 Es-Hba-allelic variant. These functional differences were due to structural differences in the BC loop of the IgV domain of the TIM-3 polymorphic variants. In contrast to fibroblastic cells, T or B cells expressing TIM-3 formed conjugates with but failed to engulf apoptotic cells. Together these findings indicate that TIM-3-expressing cells can respond to apoptotic cells, but the consequence of TIM-3 engagement of PtdSer depends on the polymorphic variants of and type of cell expressing TIM-3. These findings establish a new paradigm for TIM proteins as PtdSer receptors and unify the function of the TIM gene family, which has been associated with asthma and autoimmunity and shown to modulate peripheral tolerance.


    Organizational Affiliation

    Division of Immunology, Children's Hospital Boston, e, Boston, MA, USA.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Hepatitis A virus cellular receptor 2A, B118Mus musculusMutation(s): 0 
Gene Names: Havcr2Hepatitis A virus cellular receptor 2Tim3Timd3
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for Q8VIM0 (Mus musculus)
Explore Q8VIM0 
Go to UniProtKB:  Q8VIM0
IMPC:  MGI:2159682
Protein Feature View
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  • 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 
D [auth B]1,2-DICAPROYL-SN-PHOSPHATIDYL-L-SERINE
C18 H34 N O10 P
MIQYPPGTNIFAPO-CABCVRRESA-N
 Ligand Interaction
CA
Query on CA

Download Ideal Coordinates CCD File 
C [auth B]CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.245 
  • R-Value Work: 0.235 
  • R-Value Observed: 0.236 
  • Space Group: H 3 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 71.922α = 90
b = 71.922β = 90
c = 263.579γ = 120
Software Package:
Software NamePurpose
MxCuBEdata collection
PHASERphasing
PHENIXrefinement
XDSdata reduction
SCALAdata scaling

Structure Validation

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Ligand Structure Quality Assessment  



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2010-01-26
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2013-12-04
    Changes: Database references