6dhb: Difference between revisions

Latest revision as of 06:06, 11 October 2023

Crystal structure of the human TIM-3 with bound Calcium

Structural highlights

6dhb is a 1 chain structure with sequence from Homo sapiens. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 1.7Å
Ligands:	BEZ, CA, EDO
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

HAVR2_HUMAN Regulates macrophage activation. Inhibits T-helper type 1 lymphocyte (Th1)-mediated auto- and alloimmune responses and promotes immunological tolerance. May be also involved in T-cell homing. Receptor for LGALS9.^[1] ^[2]

Publication Abstract from PubMed

T-cell immunoglobulin and mucin domain containing protein-3 (TIM-3) is an important immune regulator. Here, we describe a novel high resolution (1.7 A) crystal structure of the human (h)TIM-3 N-terminal variable immunoglobulin (IgV) domain with bound calcium (Ca(++)) that was confirmed by nuclear magnetic resonance (NMR) spectroscopy. Significant conformational differences were observed in the B-C, C'-C and C'-D loops of hTIM-3 compared to mouse (m)TIM-3, hTIM-1 and hTIM-4. Further, the conformation of the C-C' loop of hTIM-3 was notably different from hTIM-4. Consistent with the known metal ion-dependent binding of phosphatidylserine (PtdSer) to mTIM-3 and mTIM-4, the NMR spectral analysis and crystal structure of Ca(++)-bound hTIM-3 revealed that residues in the hTIM-3 F-G loop coordinate binding to Ca(++). In addition, we established a novel biochemical assay to define hTIM-3 functionality as determined by binding to human carcinoembryonic antigen cell adhesion molecule 1 (CEACAM1). These studies provide new insights useful for understanding and targeting hTIM-3.

High resolution X-ray and NMR structural study of human T-cell immunoglobulin and mucin domain containing protein-3.,Gandhi AK, Kim WM, Sun ZJ, Huang YH, Bonsor DA, Sundberg EJ, Kondo Y, Wagner G, Kuchroo VK, Petsko G, Blumberg RS Sci Rep. 2018 Nov 30;8(1):17512. doi: 10.1038/s41598-018-35754-0. PMID:30504845^[3]

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

References

↑ Sanchez-Fueyo A, Tian J, Picarella D, Domenig C, Zheng XX, Sabatos CA, Manlongat N, Bender O, Kamradt T, Kuchroo VK, Gutierrez-Ramos JC, Coyle AJ, Strom TB. Tim-3 inhibits T helper type 1-mediated auto- and alloimmune responses and promotes immunological tolerance. Nat Immunol. 2003 Nov;4(11):1093-101. Epub 2003 Oct 12. PMID:14556005 doi:https://dx.doi.org/10.1038/ni987
↑ Zhu C, Anderson AC, Schubart A, Xiong H, Imitola J, Khoury SJ, Zheng XX, Strom TB, Kuchroo VK. The Tim-3 ligand galectin-9 negatively regulates T helper type 1 immunity. Nat Immunol. 2005 Dec;6(12):1245-52. Epub 2005 Nov 13. PMID:16286920 doi:https://dx.doi.org/10.1038/ni1271
↑ Gandhi AK, Kim WM, Sun ZJ, Huang YH, Bonsor DA, Sundberg EJ, Kondo Y, Wagner G, Kuchroo VK, Petsko G, Blumberg RS. High resolution X-ray and NMR structural study of human T-cell immunoglobulin and mucin domain containing protein-3. Sci Rep. 2018 Nov 30;8(1):17512. doi: 10.1038/s41598-018-35754-0. PMID:30504845 doi:https://dx.doi.org/10.1038/s41598-018-35754-0

Proteopedia Page Contributors and Editors (what is this?)

OCA

[1] Sanchez-Fueyo A, Tian J, Picarella D, Domenig C, Zheng XX, Sabatos CA, Manlongat N, Bender O, Kamradt T, Kuchroo VK, Gutierrez-Ramos JC, Coyle AJ, Strom TB. Tim-3 inhibits T helper type 1-mediated auto- and alloimmune responses and promotes immunological tolerance. Nat Immunol. 2003 Nov;4(11):1093-101. Epub 2003 Oct 12. PMID:14556005 doi:https://dx.doi.org/10.1038/ni987

[2] Zhu C, Anderson AC, Schubart A, Xiong H, Imitola J, Khoury SJ, Zheng XX, Strom TB, Kuchroo VK. The Tim-3 ligand galectin-9 negatively regulates T helper type 1 immunity. Nat Immunol. 2005 Dec;6(12):1245-52. Epub 2005 Nov 13. PMID:16286920 doi:https://dx.doi.org/10.1038/ni1271

[3] Gandhi AK, Kim WM, Sun ZJ, Huang YH, Bonsor DA, Sundberg EJ, Kondo Y, Wagner G, Kuchroo VK, Petsko G, Blumberg RS. High resolution X-ray and NMR structural study of human T-cell immunoglobulin and mucin domain containing protein-3. Sci Rep. 2018 Nov 30;8(1):17512. doi: 10.1038/s41598-018-35754-0. PMID:30504845 doi:https://dx.doi.org/10.1038/s41598-018-35754-0

[1]

[2]

[3]

@@ Line 3: / Line 3: @@
 <StructureSection load='6dhb' size='340' side='right'caption='[[6dhb]], [[Resolution|resolution]] 1.70&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[6dhb]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Human Human]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6DHB OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6DHB FirstGlance]. <br>
+<table><tr><td colspan='2'>[[6dhb]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6DHB OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6DHB FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BEZ:BENZOIC+ACID'>BEZ</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene></td></tr>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.7&#8491;</td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">HAVCR2, TIM3, TIMD3 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BEZ:BENZOIC+ACID'>BEZ</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene></td></tr>
-<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6dhb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6dhb OCA], [http://pdbe.org/6dhb PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6dhb RCSB], [http://www.ebi.ac.uk/pdbsum/6dhb PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6dhb ProSAT]</span></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=6dhb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6dhb OCA], [https://pdbe.org/6dhb PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6dhb RCSB], [https://www.ebi.ac.uk/pdbsum/6dhb PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6dhb ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/HAVR2_HUMAN HAVR2_HUMAN]] Regulates macrophage activation. Inhibits T-helper type 1 lymphocyte (Th1)-mediated auto- and alloimmune responses and promotes immunological tolerance. May be also involved in T-cell homing. Receptor for LGALS9.<ref>PMID:14556005</ref> <ref>PMID:16286920</ref>
+[https://www.uniprot.org/uniprot/HAVR2_HUMAN HAVR2_HUMAN] Regulates macrophage activation. Inhibits T-helper type 1 lymphocyte (Th1)-mediated auto- and alloimmune responses and promotes immunological tolerance. May be also involved in T-cell homing. Receptor for LGALS9.<ref>PMID:14556005</ref> <ref>PMID:16286920</ref>
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==
@@ Line 23: / Line 23: @@
 __TOC__
 </StructureSection>
-[[Category: Human]]
+[[Category: Homo sapiens]]
 [[Category: Large Structures]]
-[[Category: Blumberg, R S]]
+[[Category: Blumberg RS]]
-[[Category: Bonsor, D]]
+[[Category: Bonsor D]]
-[[Category: Gandhi, A K]]
+[[Category: Gandhi AK]]
-[[Category: Huang, Y H]]
+[[Category: Huang YH]]
-[[Category: Kim, W M]]
+[[Category: Kim WM]]
-[[Category: Kuchroo, V]]
+[[Category: Kuchroo V]]
-[[Category: Petsko, G A]]
+[[Category: Petsko GA]]
-[[Category: Sun, Z Y]]
+[[Category: Sun Z-Y]]
-[[Category: Sundberg, E]]
+[[Category: Sundberg E]]
-[[Category: Immune system]]
-[[Category: T cell immunoglobulin mucin-3 immunological tolerance]]

6dhb: Difference between revisions

Latest revision as of 06:06, 11 October 2023

Crystal structure of the human TIM-3 with bound Calcium

Structural highlights

Function

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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