3bi9

From Proteopedia

(Difference between revisions)

Current revision

Tim-4

Structural highlights

3bi9 is a 1 chain structure with sequence from Mus musculus. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 2.95Å
Ligands:
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

TIMD4_MOUSE Phosphatidylserine receptor that enhances the engulfment of apoptotic cells. Involved in regulating T-cell proliferation and lymphotoxin signaling. Ligand for HAVCR1/TIMD1.^[1] ^[2] ^[3]

Evolutionary Conservation

Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.

Publication Abstract from PubMed

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.

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:18083575^[4]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

↑ Shakhov AN, Rybtsov S, Tumanov AV, Shulenin S, Dean M, Kuprash DV, Nedospasov SA. SMUCKLER/TIM4 is a distinct member of TIM family expressed by stromal cells of secondary lymphoid tissues and associated with lymphotoxin signaling. Eur J Immunol. 2004 Feb;34(2):494-503. PMID:14768054 doi:http://dx.doi.org/10.1002/eji.200324590
↑ Meyers JH, Chakravarti S, Schlesinger D, Illes Z, Waldner H, Umetsu SE, Kenny J, Zheng XX, Umetsu DT, DeKruyff RH, Strom TB, Kuchroo VK. TIM-4 is the ligand for TIM-1, and the TIM-1-TIM-4 interaction regulates T cell proliferation. Nat Immunol. 2005 May;6(5):455-64. Epub 2005 Mar 27. PMID:15793576 doi:http://dx.doi.org/10.1038/ni1185
↑ Miyanishi M, Tada K, Koike M, Uchiyama Y, Kitamura T, Nagata S. Identification of Tim4 as a phosphatidylserine receptor. Nature. 2007 Nov 15;450(7168):435-9. Epub 2007 Oct 24. PMID:17960135 doi:http://dx.doi.org/10.1038/nature06307
↑ Santiago C, Ballesteros A, Martinez-Munoz L, Mellado M, Kaplan GG, Freeman GJ, Casasnovas JM. Structures of T cell immunoglobulin mucin protein 4 show a metal-Ion-dependent ligand binding site where phosphatidylserine binds. Immunity. 2007 Dec;27(6):941-51. PMID:18083575 doi:http://dx.doi.org/10.1016/j.immuni.2007.11.008

1 Structural highlights
2 Function
3 Evolutionary Conservation
4 Publication Abstract from PubMed
5 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/3bi9"

@@ Line 1: / Line 1: @@
-[[Image:3bi9.jpg|left|200px]]<br /><applet load="3bi9" size="350" color="white" frame="true" align="right" spinBox="true"
-caption="3bi9, resolution 2.95&Aring;" />
-'''Tim-4'''<br />
-==Overview==
+==Tim-4==
-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.
+<StructureSection load='3bi9' size='340' side='right'caption='[[3bi9]], [[Resolution|resolution]] 2.95&Aring;' scene=''>
+== Structural highlights ==
+<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>
+</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>
+<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>
+<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>
+</table>
+== Function ==
+[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>
+== Evolutionary Conservation ==
+[[Image:Consurf_key_small.gif|200px|right]]
+Check<jmol>
+  <jmolCheckbox>
+    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/bi/3bi9_consurf.spt"</scriptWhenChecked>
+    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.spt</scriptWhenUnchecked>
+    <text>to colour the structure by Evolutionary Conservation</text>
+  </jmolCheckbox>
+</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].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+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.
-==About this Structure==
+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:18083575<ref>PMID:18083575</ref>
-BI9 is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Mus_musculus Mus musculus] with <scene name='pdbligand=ACT:'>ACT</scene> as [http://en.wikipedia.org/wiki/ligand ligand]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3BI9 OCA].
-==Reference==
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-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://ispc.weizmann.ac.il//pmbin/getpm?pmid=18083575 18083575]
+</div>
+<div class="pdbe-citations 3bi9" style="background-color:#fffaf0;"></div>
+== References ==
+<references/>
+__TOC__
+</StructureSection>
+[[Category: Large Structures]]
 [[Category: Mus musculus]]
-[[Category: Single protein]]
+[[Category: Ballesteros A]]
-[[Category: Ballesteros, A.]]
+[[Category: Casasnovas JM]]
-[[Category: Casasnovas, J.M.]]
+[[Category: Freeman GJ]]
-[[Category: Freeman, G.J.]]
+[[Category: Kaplan GG]]
-[[Category: Kaplan, G.G.]]
+[[Category: Santiago C]]
-[[Category: Santiago, C.]]
-[[Category: ACT]]
-[[Category: beta barrel]]
-[[Category: glycoprotein]]
-[[Category: igv domain]]
-[[Category: immune system]]
-[[Category: immunoglobulin domain]]
-[[Category: immunoglobulin fold]]
-[[Category: membrane]]
-[[Category: polymorphism]]
-[[Category: tim]]
-[[Category: transmembrane]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Jan 23 11:21:17 2008''

3bi9

From Proteopedia

Current revision

Tim-4

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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