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3bi9

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[[Image:3bi9.jpg|left|200px]]
 
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{{Structure
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==Tim-4==
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|PDB= 3bi9 |SIZE=350|CAPTION= <scene name='initialview01'>3bi9</scene>, resolution 2.95&Aring;
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<StructureSection load='3bi9' size='340' side='right'caption='[[3bi9]], [[Resolution|resolution]] 2.95&Aring;' scene=''>
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|SITE=
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== Structural highlights ==
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|LIGAND= <scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>
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<table><tr><td colspan='2'>[[3bi9]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Mus_musculus Mus musculus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3BI9 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3BI9 FirstGlance]. <br>
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|ACTIVITY=
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</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.95&#8491;</td></tr>
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|GENE= Timd4, Tim4 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10090 Mus musculus])
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<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene></td></tr>
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|DOMAIN=
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3bi9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3bi9 OCA], [https://pdbe.org/3bi9 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3bi9 RCSB], [https://www.ebi.ac.uk/pdbsum/3bi9 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3bi9 ProSAT]</span></td></tr>
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|RELATEDENTRY=[[2or8|2or8]], [[2or7|2or7]], [[2oyp|2oyp]], [[3bia|3BIA]], [[3bib|3BIB]]
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</table>
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|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3bi9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3bi9 OCA], [http://www.ebi.ac.uk/pdbsum/3bi9 PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=3bi9 RCSB]</span>
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== Function ==
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}}
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[https://www.uniprot.org/uniprot/TIMD4_MOUSE TIMD4_MOUSE] Phosphatidylserine receptor that enhances the engulfment of apoptotic cells. Involved in regulating T-cell proliferation and lymphotoxin signaling. Ligand for HAVCR1/TIMD1.<ref>PMID:14768054</ref> <ref>PMID:15793576</ref> <ref>PMID:17960135</ref>
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== Evolutionary Conservation ==
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'''Tim-4'''
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[[Image:Consurf_key_small.gif|200px|right]]
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Check<jmol>
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<jmolCheckbox>
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==Overview==
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<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/bi/3bi9_consurf.spt"</scriptWhenChecked>
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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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<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
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<text>to colour the structure by Evolutionary Conservation</text>
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==About this Structure==
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</jmolCheckbox>
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3BI9 is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Mus_musculus Mus musculus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3BI9 OCA].
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</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=3bi9 ConSurf].
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<div style="clear:both"></div>
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==Reference==
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== References ==
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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 GG, Freeman GJ, Casasnovas JM, Immunity. 2007 Dec;27(6):941-51. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/18083575 18083575]
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<references/>
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__TOC__
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</StructureSection>
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[[Category: Large Structures]]
[[Category: Mus musculus]]
[[Category: Mus musculus]]
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[[Category: Single protein]]
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[[Category: Ballesteros A]]
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[[Category: Ballesteros, A.]]
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[[Category: Casasnovas JM]]
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[[Category: Casasnovas, J M.]]
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[[Category: Freeman GJ]]
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[[Category: Freeman, G J.]]
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[[Category: Kaplan GG]]
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[[Category: Kaplan, G G.]]
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[[Category: Santiago C]]
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[[Category: Santiago, C.]]
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[[Category: beta barrel]]
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[[Category: glycoprotein]]
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[[Category: igv domain]]
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[[Category: immune system]]
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[[Category: immunoglobulin domain]]
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[[Category: immunoglobulin fold]]
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[[Category: membrane]]
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[[Category: polymorphism]]
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[[Category: tim]]
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[[Category: transmembrane]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Mar 31 05:26:29 2008''
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Current revision

Tim-4

PDB ID 3bi9

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