1rdi: Difference between revisions

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-[[Image:1rdi.jpg|left|200px]]
-<!--
-The line below this paragraph, containing "STRUCTURE_1rdi", creates the "Structure Box" on the page.
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-{{STRUCTURE_1rdi|  PDB=1rdi  |  SCENE=  }}
-'''MANNOSE-BINDING PROTEIN, SUBTILISIN DIGEST FRAGMENT COMPLEX WITH ALPHA-METHYL-L-FUCOPYRANOSIDE'''
+==MANNOSE-BINDING PROTEIN, SUBTILISIN DIGEST FRAGMENT COMPLEX WITH ALPHA-METHYL-L-FUCOPYRANOSIDE==
+<StructureSection load='1rdi' size='340' side='right'caption='[[1rdi]], [[Resolution|resolution]] 1.80&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[1rdi]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Rattus_rattus Rattus rattus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1RDI OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1RDI 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]] 1.8&#8491;</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=MFU:ALPHA-L-METHYL-FUCOSE'>MFU</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=1rdi FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1rdi OCA], [https://pdbe.org/1rdi PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1rdi RCSB], [https://www.ebi.ac.uk/pdbsum/1rdi PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1rdi ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/MBL2_RAT MBL2_RAT] Calcium-dependent lectin involved in innate immune defense. Binds mannose, fucose and N-acetylglucosamine on different microorganisms and activates the lectin complement pathway. Binds to late apoptotic cells, as well as to apoptotic blebs and to necrotic cells, but not to early apoptotic cells, facilitating their uptake by macrophages (By similarity).
+== 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/rd/1rdi_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=1rdi ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+The structural basis of carbohydrate recognition by rat liver mannose-binding protein (MBP-C) has been explored by determining the three-dimensional structure of the C-type carbohydrate-recognition domain (CRD) of MBP-C using x-ray crystallography. The structure was solved by molecular replacement using rat serum mannose-binding protein (MBP-A) as a search model and was refined to maximum Bragg spacings of 1.7 A. Despite their almost identical folds, the dimeric structures formed by the two MBP CRDs differ dramatically. Complexes of MBP-C with methyl glycosides of mannose, N-acetylglucosamine, and fucose were prepared by soaking MBP-C crystals in solutions containing these sugars. Surprisingly, the pyranose ring of mannose is rotated 180 degrees relative to the orientation observed previously in MBP-A, but the local interactions between sugar and protein are preserved. For each of the bound sugars, vicinal, equatorial hydroxyl groups equivalent to the 3- and 4-OH groups of mannose directly coordinate Ca2+ and form hydrogen bonds with residues also serving as Ca2+ ligands. Few interactions are observed between other parts of the sugar and the protein. A complex formed between free galactose and MBP-C reveals a similar mode of binding, with the anomeric hydroxyl group serving as one of the Ca2+ ligands. A second binding site for mannose has also been observed in one of two copies in the asymmetric unit at a sugar concentration of 1.3 M. These structures explain how MBPs recognize a wide range of monosaccharides and suggest how fine specificity differences between MBP-A and MBP-C may be achieved.
-==Overview==
+Structural analysis of monosaccharide recognition by rat liver mannose-binding protein.,Ng KK, Drickamer K, Weis WI J Biol Chem. 1996 Jan 12;271(2):663-74. PMID:8557671<ref>PMID:8557671</ref>
-The structural basis of carbohydrate recognition by rat liver mannose-binding protein (MBP-C) has been explored by determining the three-dimensional structure of the C-type carbohydrate-recognition domain (CRD) of MBP-C using x-ray crystallography. The structure was solved by molecular replacement using rat serum mannose-binding protein (MBP-A) as a search model and was refined to maximum Bragg spacings of 1.7 A. Despite their almost identical folds, the dimeric structures formed by the two MBP CRDs differ dramatically. Complexes of MBP-C with methyl glycosides of mannose, N-acetylglucosamine, and fucose were prepared by soaking MBP-C crystals in solutions containing these sugars. Surprisingly, the pyranose ring of mannose is rotated 180 degrees relative to the orientation observed previously in MBP-A, but the local interactions between sugar and protein are preserved. For each of the bound sugars, vicinal, equatorial hydroxyl groups equivalent to the 3- and 4-OH groups of mannose directly coordinate Ca2+ and form hydrogen bonds with residues also serving as Ca2+ ligands. Few interactions are observed between other parts of the sugar and the protein. A complex formed between free galactose and MBP-C reveals a similar mode of binding, with the anomeric hydroxyl group serving as one of the Ca2+ ligands. A second binding site for mannose has also been observed in one of two copies in the asymmetric unit at a sugar concentration of 1.3 M. These structures explain how MBPs recognize a wide range of monosaccharides and suggest how fine specificity differences between MBP-A and MBP-C may be achieved.
-==About this Structure==
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-RDI is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Rattus_rattus Rattus rattus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1RDI OCA].
+</div>
+<div class="pdbe-citations 1rdi" style="background-color:#fffaf0;"></div>
-==Reference==
+==See Also==
-Structural analysis of monosaccharide recognition by rat liver mannose-binding protein., Ng KK, Drickamer K, Weis WI, J Biol Chem. 1996 Jan 12;271(2):663-74. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/8557671 8557671]
+*[[Mannose-binding protein|Mannose-binding protein]]
+== References ==
+<references/>
+__TOC__
+</StructureSection>
+[[Category: Large Structures]]
 [[Category: Rattus rattus]]
-[[Category: Single protein]]
+[[Category: Drickamer K]]
-[[Category: Drickamer, K.]]
+[[Category: Ng KK-S]]
-[[Category: Ng, K K.S.]]
+[[Category: Weis WI]]
-[[Category: Weis, W I.]]
-[[Category: C-type lectin]]
-[[Category: Calcium-binding protein]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sat May  3 07:22:00 2008''