1gqb: Difference between revisions

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-{{Seed}}
-[[Image:1gqb.png|left|200px]]
-<!--
+==HUMAN MIR-RECEPTOR, REPEAT 11==
-The line below this paragraph, containing "STRUCTURE_1gqb", creates the "Structure Box" on the page.
+<StructureSection load='1gqb' size='340' side='right'caption='[[1gqb]], [[Resolution|resolution]] 1.80&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'>[[1gqb]] is a 2 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=1GQB OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1GQB 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]] 1.8&#8491;</td></tr>
--->
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BR:BROMIDE+ION'>BR</scene></td></tr>
-{{STRUCTURE_1gqb|  PDB=1gqb  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1gqb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1gqb OCA], [https://pdbe.org/1gqb PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1gqb RCSB], [https://www.ebi.ac.uk/pdbsum/1gqb PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1gqb ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/MPRI_HUMAN MPRI_HUMAN] Transport of phosphorylated lysosomal enzymes from the Golgi complex and the cell surface to lysosomes. Lysosomal enzymes bearing phosphomannosyl residues bind specifically to mannose-6-phosphate receptors in the Golgi apparatus and the resulting receptor-ligand complex is transported to an acidic prelyosomal compartment where the low pH mediates the dissociation of the complex. This receptor also binds IGF2. Acts as a positive regulator of T-cell coactivation, by binding DPP4.<ref>PMID:10900005</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/gq/1gqb_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=1gqb ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Improved data quality now makes it feasible to exploit the weak anomalous signal derived only from the sulfurs inherent to the protein or in particular from halide ions incorporated by soaking. The latter technique requires the location of a high number of partially occupied halide sites. This number appears to be roughly proportional to the exposed protein surface. This paper explores the application of dual-space ab initio methods as implemented in the program SHELXD to the location of substructures of sulfur in SAD experiments, bromide in SAD and MAD experiments and iodide using SAD and SIRAS to determine the anomalous-atom substructure. Sets of atoms consistent with the Patterson function were generated as a starting point for the dual-space recycling procedure in SHELXD. The substructure is then expanded to the full structure by maximum-likelihood phasing with SHARP and density modification with the program DM. Success in the location of the substructures and subsequent phasing depends critically on the quality of the data and on the extent of the anomalous signal. This varies with each crystal and soak, but for the same crystal the significance of the anomalous signal was found to be highly sensitive to the redundancy of the intensity measurements, which in some cases made all the difference. This is illustrated by the determination of the previously unknown structure of repeat 11 of the human mannose-6-phosphate/insulin-like growth factor II receptor (Man6P/IGFII-receptor), with 310 amino acids in the asymmetric unit, which was phased by soaking the crystals in a cryoprotectant solution containing halide anions.
-===HUMAN MIR-RECEPTOR, REPEAT 11===
+Locating the anomalous scatterer substructures in halide and sulfur phasing.,Uson I, Schmidt B, von Bulow R, Grimme S, von Figura K, Dauter M, Rajashankar KR, Dauter Z, Sheldrick GM Acta Crystallogr D Biol Crystallogr. 2003 Jan;59(Pt 1):57-66. Epub 2002, Dec 19. PMID:12499540<ref>PMID:12499540</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 1gqb" style="background-color:#fffaf0;"></div>
-<!--
+==See Also==
-The line below this paragraph, {{ABSTRACT_PUBMED_12499540}}, adds the Publication Abstract to the page
+*[[Insulin-like growth factor receptor|Insulin-like growth factor receptor]]
-(as it appears on PubMed at http://www.pubmed.gov), where 12499540 is the PubMed ID number.
+== References ==
--->
+<references/>
-{{ABSTRACT_PUBMED_12499540}}
+__TOC__
+</StructureSection>
-==About this Structure==
-GQB is a [[Single protein]] structure of 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=1GQB OCA].
-==Reference==
-Locating the anomalous scatterer substructures in halide and sulfur phasing., Uson I, Schmidt B, von Bulow R, Grimme S, von Figura K, Dauter M, Rajashankar KR, Dauter Z, Sheldrick GM, Acta Crystallogr D Biol Crystallogr. 2003 Jan;59(Pt 1):57-66. Epub 2002, Dec 19. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/12499540 12499540]
 [[Category: Homo sapiens]]
-[[Category: Single protein]]
+[[Category: Large Structures]]
-[[Category: Buelow, R Von.]]
+[[Category: Dauter M]]
-[[Category: Dauter, M.]]
+[[Category: Dauter Z]]
-[[Category: Dauter, Z.]]
+[[Category: Grimme S]]
-[[Category: Figura, K Von.]]
+[[Category: Rajashankar KR]]
-[[Category: Grimme, S.]]
+[[Category: Schmidt B]]
-[[Category: Rajashankar, K R.]]
+[[Category: Uson I]]
-[[Category: Schmidt, B.]]
+[[Category: Von Buelow R]]
-[[Category: Uson, I.]]
+[[Category: Von Figura K]]
-[[Category: Glycoprotein]]
-[[Category: Igf-ii receptor]]
-[[Category: Mir-receptor]]
-[[Category: Transport]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Jul  1 05:53:19 2008''