3BIA | pdb_00003bia

Tim-4 in complex with sodium potassium tartrate

• PDB DOI: https://doi.org/10.2210/pdb3BIA/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Mus musculus
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 2007-11-30 Released: 2008-01-01 
• Deposition Author(s): Santiago, C., Ballesteros, A., Kaplan, G.G., Freeman, G.J., Casasnovas, J.M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 
  0.238 (Depositor), 0.239 (DCC) 
• R-Value Work: 
  0.218 (Depositor), 0.218 (DCC) 
• R-Value Observed: 
  0.219 (Depositor) 

Starting Model: experimental

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

• PubMed: 18083575 
• DOI: https://doi.org/10.1016/j.immuni.2007.11.008
• Primary Citation Related Structures: 
  3BI9, 3BIA, 3BIB


• 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 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.

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Organizational Affiliation: 
• Centro Nacional de Biotecnología, CSIC, Campus Universidad Autónoma, 28049 Madrid, Spain.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 13.23 kDa 
• Atom Count: 955 
• Modeled Residue Count: 110 
• Deposited Residue Count: 116 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
T-cell immunoglobulin and mucin domain-containing protein 4	A [auth X]	116	Mus musculus	Mutation(s): 0  Gene Names: Timd4, Tim4
UniProt
Find proteins for Q6U7R4 (Mus musculus) Explore Q6U7R4  Go to UniProtKB:  Q6U7R4

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
TLA	C [auth X]	L(+)-TARTARIC ACID C4 H6 O6 FEWJPZIEWOKRBE-JCYAYHJZSA-N
NA	B [auth X]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free:  0.238 (Depositor), 0.239 (DCC) 
• R-Value Work:  0.218 (Depositor), 0.218 (DCC) 
• R-Value Observed: 0.219 (Depositor) 

Space Group: P 6₃ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 67.77	α = 90
b = 67.77	β = 90
c = 129.09	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
SCALA	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-01-01 
Deposition Author(s): Santiago, C., Ballesteros, A., Kaplan, G.G., Freeman, G.J., Casasnovas, J.M.

Revision History  

• Version 1.0: 2008-01-01
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2024-04-03
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.3: 2024-10-16
  Changes: Structure summary