5pxm: Difference between revisions

← Older edit

Proteopedia Page Contributors and Editors (what is this?)Proteopedia Page Contributors and Editors (what is this?)

OCA

@@ Line 1: / Line 1: @@
 ==PanDDA analysis group deposition -- Crystal Structure of SP100 after initial refinement with no ligand modelled (structure 46)==
-<StructureSection load='5pxm' size='340' side='right' caption='[[5pxm]], [[Resolution|resolution]] 1.59&Aring;' scene=''>
+<StructureSection load='5pxm' size='340' side='right'caption='[[5pxm]], [[Resolution|resolution]] 1.59&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[5pxm]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5PXM OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5PXM FirstGlance]. <br>
+<table><tr><td colspan='2'>[[5pxm]] 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=5PXM OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5PXM FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=MES:2-(N-MORPHOLINO)-ETHANESULFONIC+ACID'>MES</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</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]] 1.59&#8491;</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=5pxm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5pxm OCA], [http://pdbe.org/5pxm PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5pxm RCSB], [http://www.ebi.ac.uk/pdbsum/5pxm PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5pxm ProSAT]</span></td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=MES:2-(N-MORPHOLINO)-ETHANESULFONIC+ACID'>MES</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</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=5pxm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5pxm OCA], [https://pdbe.org/5pxm PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5pxm RCSB], [https://www.ebi.ac.uk/pdbsum/5pxm PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5pxm ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/SP100_HUMAN SP100_HUMAN]] Together with PML, this tumor suppressor is a major constituent of the PML bodies, a subnuclear organelle involved in a large number of physiological processes including cell growth, differentiation and apoptosis. Functions as a transcriptional coactivator of ETS1 and ETS2 according to PubMed:11909962. Under certain conditions, it may also act as a corepressor of ETS1 preventing its binding to DNA according to PubMed:15247905. Through the regulation of ETS1 it may play a role in angiogenesis, controlling endothelial cell motility and invasion. Through interaction with the MRN complex it may be involved in the regulation of telomeres lengthening. May also regulate TP53-mediated transcription and through CASP8AP2, regulate FAS-mediated apoptosis. Also plays a role in infection by viruses, including human cytomegalovirus and Epstein-Barr virus, through mechanisms that may involve chromatin and/or transcriptional regulation.<ref>PMID:11909962</ref> <ref>PMID:14647468</ref> <ref>PMID:15247905</ref> <ref>PMID:15592518</ref> <ref>PMID:15767676</ref> <ref>PMID:16177824</ref> <ref>PMID:17245429</ref> <ref>PMID:21274506</ref> <ref>PMID:21880768</ref>
+[https://www.uniprot.org/uniprot/SP100_HUMAN SP100_HUMAN] Together with PML, this tumor suppressor is a major constituent of the PML bodies, a subnuclear organelle involved in a large number of physiological processes including cell growth, differentiation and apoptosis. Functions as a transcriptional coactivator of ETS1 and ETS2 according to PubMed:11909962. Under certain conditions, it may also act as a corepressor of ETS1 preventing its binding to DNA according to PubMed:15247905. Through the regulation of ETS1 it may play a role in angiogenesis, controlling endothelial cell motility and invasion. Through interaction with the MRN complex it may be involved in the regulation of telomeres lengthening. May also regulate TP53-mediated transcription and through CASP8AP2, regulate FAS-mediated apoptosis. Also plays a role in infection by viruses, including human cytomegalovirus and Epstein-Barr virus, through mechanisms that may involve chromatin and/or transcriptional regulation.<ref>PMID:11909962</ref> <ref>PMID:14647468</ref> <ref>PMID:15247905</ref> <ref>PMID:15592518</ref> <ref>PMID:15767676</ref> <ref>PMID:16177824</ref> <ref>PMID:17245429</ref> <ref>PMID:21274506</ref> <ref>PMID:21880768</ref>
-<div style="background-color:#fffaf0;">
-== Publication Abstract from PubMed ==
-In macromolecular crystallography, the rigorous detection of changed states (for example, ligand binding) is difficult unless signal is strong. Ambiguous ('weak' or 'noisy') density is experimentally common, since molecular states are generally only fractionally present in the crystal. Existing methodologies focus on generating maximally accurate maps whereby minor states become discernible; in practice, such map interpretation is disappointingly subjective, time-consuming and methodologically unsound. Here we report the PanDDA method, which automatically reveals clear electron density for the changed state-even from inaccurate maps-by subtracting a proportion of the confounding 'ground state'; changed states are objectively identified from statistical analysis of density distributions. The method is completely general, implying new best practice for all changed-state studies, including the routine collection of multiple ground-state crystals. More generally, these results demonstrate: the incompleteness of atomic models; that single data sets contain insufficient information to model them fully; and that accuracy requires further map-deconvolution approaches.
-A multi-crystal method for extracting obscured crystallographic states from conventionally uninterpretable electron density.,Pearce NM, Krojer T, Bradley AR, Collins P, Nowak RP, Talon R, Marsden BD, Kelm S, Shi J, Deane CM, von Delft F Nat Commun. 2017 Apr 24;8:15123. doi: 10.1038/ncomms15123. PMID:28436492<ref>PMID:28436492</ref>
-From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-</div>
-<div class="pdbe-citations 5pxm" style="background-color:#fffaf0;"></div>
 == References ==
 <references/>
 __TOC__
 </StructureSection>
-[[Category: Arrowsmith, C H]]
+[[Category: Homo sapiens]]
-[[Category: Bountra, C]]
+[[Category: Large Structures]]
-[[Category: Bradley, A R]]
+[[Category: Arrowsmith CH]]
-[[Category: Brandao-Neto, J]]
+[[Category: Bountra C]]
-[[Category: Brennan, P E]]
+[[Category: Bradley AR]]
-[[Category: Collins, P]]
+[[Category: Brandao-Neto J]]
-[[Category: Cox, O]]
+[[Category: Brennan PE]]
-[[Category: Delft, F von]]
+[[Category: Collins P]]
-[[Category: Dias, A]]
+[[Category: Cox O]]
-[[Category: Douangamath, A]]
+[[Category: Dias A]]
-[[Category: Edwards, A]]
+[[Category: Douangamath A]]
-[[Category: Fairhead, M]]
+[[Category: Edwards A]]
-[[Category: Krojer, T]]
+[[Category: Fairhead M]]
-[[Category: MacLean, E]]
+[[Category: Krojer T]]
-[[Category: Ng, J]]
+[[Category: MacLean E]]
-[[Category: Pearce, N M]]
+[[Category: Ng J]]
-[[Category: Renjie, Z]]
+[[Category: Pearce NM]]
-[[Category: Sethi, R]]
+[[Category: Renjie Z]]
-[[Category: Talon, R]]
+[[Category: Sethi R]]
-[[Category: Wright, N]]
+[[Category: Talon R]]
-[[Category: Bromodomain]]
+[[Category: Wright N]]
-[[Category: Epigenetic]]
+[[Category: Von Delft F]]
-[[Category: Pandda]]
-[[Category: Sgc - diamond i04-1 fragment screening]]
-[[Category: Transcription]]
-[[Category: Xchemexplorer]]