2zhm: Difference between revisions

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 ==Crystal structure of human galectin-9 N-terminal CRD in complex with N-acetyllactosamine trimer (crystal 1)==
-<StructureSection load='2zhm' size='340' side='right' caption='[[2zhm]], [[Resolution|resolution]] 1.84&Aring;' scene=''>
+<StructureSection load='2zhm' size='340' side='right'caption='[[2zhm]], [[Resolution|resolution]] 1.84&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[2zhm]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2ZHM OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2ZHM FirstGlance]. <br>
+<table><tr><td colspan='2'>[[2zhm]] is a 4 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=2ZHM OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2ZHM FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=RPN:(R)-1-PARA-NITRO-PHENYL-2-AZIDO-ETHANOL'>RPN</scene>, <scene name='pdbligand=GAL:BETA-D-GALACTOSE'>GAL</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</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]] 1.84&#8491;</td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[2zhk|2zhk]], [[2zhl|2zhl]], [[2zhn|2zhn]]</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GAL:BETA-D-GALACTOSE'>GAL</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene>, <scene name='pdbligand=RPN:(R)-1-PARA-NITRO-PHENYL-2-AZIDO-ETHANOL'>RPN</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=2zhm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2zhm OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2zhm RCSB], [http://www.ebi.ac.uk/pdbsum/2zhm PDBsum]</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=2zhm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2zhm OCA], [https://pdbe.org/2zhm PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2zhm RCSB], [https://www.ebi.ac.uk/pdbsum/2zhm PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2zhm ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/LEG9_HUMAN LEG9_HUMAN]] Binds galactosides. Has high affinity for the Forssman pentasaccharide. May play a role in thymocyte-epithelial interactions relevant to the biology of the thymus. Inhibits cell proliferation. It is a ligand for HAVCR2/TIM3. Induces T-helper type 1 lymphocyte (Th1) death. Isoform Short acts as an eosinophil chemoattractant.<ref>PMID:16286920</ref> <ref>PMID:18005988</ref> <ref>PMID:18977853</ref>
+[https://www.uniprot.org/uniprot/LEG9_HUMAN LEG9_HUMAN] Binds galactosides. Has high affinity for the Forssman pentasaccharide. May play a role in thymocyte-epithelial interactions relevant to the biology of the thymus. Inhibits cell proliferation. It is a ligand for HAVCR2/TIM3. Induces T-helper type 1 lymphocyte (Th1) death. Isoform Short acts as an eosinophil chemoattractant.<ref>PMID:16286920</ref> <ref>PMID:18005988</ref> <ref>PMID:18977853</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/zh/2zhm_consurf.spt"</scriptWhenChecked>
+     <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/zh/2zhm_consurf.spt"</scriptWhenChecked>
      <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.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/chain_selection.php?pdb_ID=2ata ConSurf].
+</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=2zhm ConSurf].
 <div style="clear:both"></div>
-<div style="background-color:#fffaf0;">
-== Publication Abstract from PubMed ==
-Galectins are a family of beta-galactoside-specific lectins bearing a conserved carbohydrate recognition domain. Interactions between galectins and poly-N-acetyllactosamine sequences are critical in a variety of biological processes. Galectin-9, a member of the galectin family, has two carbohydrate recognition domains at both the N- and C-terminal regions. Here we report the crystal structure of the human galectin-9 N-terminal carbohydrate recognition domain in complex with N-acetyllactosamine dimers and trimers. These complex structures revealed that the galectin-9 N-terminal carbohydrate recognition domain can recognize internal N-acetyllactosamine units within poly-N-acetyllactosamine chains. Based on these complex structures, we propose two putative recognition modes for poly-N-acetyllactosamine binding by galectins.
-Structural analysis of the recognition mechanism of poly-N-acetyllactosamine by the human galectin-9 N-terminal carbohydrate recognition domain.,Nagae M, Nishi N, Murata T, Usui T, Nakamura T, Wakatsuki S, Kato R Glycobiology. 2009 Feb;19(2):112-7. Epub 2008 Oct 31. PMID:18977853<ref>PMID:18977853</ref>
-From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-</div>
 ==See Also==
-*[[Galectin|Galectin]]
+*[[Galectin 3D structures|Galectin 3D structures]]
 == References ==
 <references/>
@@ Line 35: / Line 28: @@
 </StructureSection>
 [[Category: Homo sapiens]]
-[[Category: Kato, R]]
+[[Category: Large Structures]]
-[[Category: Murata, T]]
+[[Category: Kato R]]
-[[Category: Nagae, M]]
+[[Category: Murata T]]
-[[Category: Nakamura, T]]
+[[Category: Nagae M]]
-[[Category: Nishi, N]]
+[[Category: Nakamura T]]
-[[Category: Usui, T]]
+[[Category: Nishi N]]
-[[Category: Wakatsuki, S]]
+[[Category: Usui T]]
-[[Category: Beta sandwich]]
+[[Category: Wakatsuki S]]
-[[Category: Carbohydrate binding protein]]
-[[Category: Galectin]]
-[[Category: Sugar binding protein]]