3fxi: Difference between revisions

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-{{Seed}}
-[[Image:3fxi.png|left|200px]]
-<!--
+==Crystal structure of the human TLR4-human MD-2-E.coli LPS Ra complex==
-The line below this paragraph, containing "STRUCTURE_3fxi", creates the "Structure Box" on the page.
+<StructureSection load='3fxi' size='340' side='right'caption='[[3fxi]], [[Resolution|resolution]] 3.10&Aring;' scene=''>
-You may change the PDB parameter (which sets the PDB file loaded into the applet)
+== Structural highlights ==
-or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
+<table><tr><td colspan='2'>[[3fxi]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. The November 2011 RCSB PDB [https://pdb.rcsb.org/pdb/static.do?p=education_discussion/molecule_of_the_month/index.html Molecule of the Month] feature on ''Toll-like Receptors''  by David Goodsell is [https://dx.doi.org/10.2210/rcsb_pdb/mom_2011_11 10.2210/rcsb_pdb/mom_2011_11]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3FXI OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3FXI FirstGlance]. <br>
-or leave the SCENE parameter empty for the default display.
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 3.1&#8491;</td></tr>
--->
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=DAO:LAURIC+ACID'>DAO</scene>, <scene name='pdbligand=FTT:3-HYDROXY-TETRADECANOIC+ACID'>FTT</scene>, <scene name='pdbligand=GCS:D-GLUCOSAMINE'>GCS</scene>, <scene name='pdbligand=GMH:L-GLYCERO-D-MANNO-HEPTOPYRANOSE'>GMH</scene>, <scene name='pdbligand=KDO:3-DEOXY-D-MANNO-OCT-2-ULOSONIC+ACID'>KDO</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=MYR:MYRISTIC+ACID'>MYR</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene>, <scene name='pdbligand=PA1:2-AMINO-2-DEOXY-ALPHA-D-GLUCOPYRANOSE'>PA1</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>
-{{STRUCTURE_3fxi|  PDB=3fxi  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3fxi FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3fxi OCA], [https://pdbe.org/3fxi PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3fxi RCSB], [https://www.ebi.ac.uk/pdbsum/3fxi PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3fxi ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/LY96_HUMAN LY96_HUMAN] Cooperates with TLR4 in the innate immune response to bacterial lipopolysaccharide (LPS), and with TLR2 in the response to cell wall components from Gram-positive and Gram-negative bacteria. Enhances TLR4-dependent activation of NF-kappa-B. Cells expressing both MD2 and TLR4, but not TLR4 alone, respond to LPS.
+== 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/fx/3fxi_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=3fxi ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+The lipopolysaccharide (LPS) of Gram negative bacteria is a well-known inducer of the innate immune response. Toll-like receptor (TLR) 4 and myeloid differentiation factor 2 (MD-2) form a heterodimer that recognizes a common 'pattern' in structurally diverse LPS molecules. To understand the ligand specificity and receptor activation mechanism of the TLR4-MD-2-LPS complex we determined its crystal structure. LPS binding induced the formation of an m-shaped receptor multimer composed of two copies of the TLR4-MD-2-LPS complex arranged symmetrically. LPS interacts with a large hydrophobic pocket in MD-2 and directly bridges the two components of the multimer. Five of the six lipid chains of LPS are buried deep inside the pocket and the remaining chain is exposed to the surface of MD-2, forming a hydrophobic interaction with the conserved phenylalanines of TLR4. The F126 loop of MD-2 undergoes localized structural change and supports this core hydrophobic interface by making hydrophilic interactions with TLR4. Comparison with the structures of tetra-acylated antagonists bound to MD-2 indicates that two other lipid chains in LPS displace the phosphorylated glucosamine backbone by approximately 5 A towards the solvent area. This structural shift allows phosphate groups of LPS to contribute to receptor multimerization by forming ionic interactions with a cluster of positively charged residues in TLR4 and MD-2. The TLR4-MD-2-LPS structure illustrates the remarkable versatility of the ligand recognition mechanisms employed by the TLR family, which is essential for defence against diverse microbial infection.
-===Crystal structure of the human TLR4-human MD-2-E.coli LPS Ra complex===
+The structural basis of lipopolysaccharide recognition by the TLR4-MD-2 complex.,Park BS, Song DH, Kim HM, Choi BS, Lee H, Lee JO Nature. 2009 Apr 30;458(7242):1191-5. Epub 2009 Mar 1. PMID:19252480<ref>PMID:19252480</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 3fxi" style="background-color:#fffaf0;"></div>
-<!--
+==See Also==
-The line below this paragraph, {{ABSTRACT_PUBMED_19252480}}, adds the Publication Abstract to the page
+*[[Toll-like Receptor 3D structures|Toll-like Receptor 3D structures]]
-(as it appears on PubMed at http://www.pubmed.gov), where 19252480 is the PubMed ID number.
+== References ==
--->
+<references/>
-{{ABSTRACT_PUBMED_19252480}}
+__TOC__
+</StructureSection>
-==Disease==
-Known disease associated with this structure: Endotoxin hyporesponsiveness OMIM:[[http://www.ncbi.nlm.nih.gov/entrez/dispomim.cgi?id=603030 603030]], Colorectal cancer, susceptibility to OMIM:[[http://www.ncbi.nlm.nih.gov/entrez/dispomim.cgi?id=603030 603030]], Macular degeneration, age-related, 10 OMIM:[[http://www.ncbi.nlm.nih.gov/entrez/dispomim.cgi?id=603030 603030]]
-==About this Structure==
-FXI is a 4 chains structure of sequences from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli] and [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3FXI OCA].
-==Reference==
-<ref group="xtra">PMID:19252480</ref><references group="xtra"/>
-[[Category: Escherichia coli]]
 [[Category: Homo sapiens]]
-[[Category: Kim, H M.]]
+[[Category: Large Structures]]
-[[Category: Lee, J O.]]
+[[Category: RCSB PDB Molecule of the Month]]
-[[Category: Park, B S.]]
+[[Category: Toll-like Receptors]]
-[[Category: Song, D H.]]
+[[Category: Kim HM]]
-[[Category: Alternative splicing]]
+[[Category: Lee J-O]]
-[[Category: Glycoprotein]]
+[[Category: Park BS]]
-[[Category: Immune response]]
+[[Category: Song DH]]
-[[Category: Immune system]]
-[[Category: Inflammatory response]]
-[[Category: Innate immunity]]
-[[Category: Leucine rich repeat]]
-[[Category: Membrane]]
-[[Category: Polymorphism]]
-[[Category: Receptor]]
-[[Category: Secreted]]
-[[Category: Transmembrane]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed May 13 09:03:42 2009''