5pyq

From Proteopedia

(Difference between revisions)

Revision as of 07:52, 2 September 2020

PanDDA analysis group deposition -- Crystal Structure of SP100 after initial refinement with no ligand modelled (structure 86)

Structural highlights

5pyq is a 2 chain structure. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:	, ,
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

[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.^[1] ^[2] ^[3] ^[4] ^[5] ^[6] ^[7] ^[8] ^[9]

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^[10]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

↑ Wasylyk C, Schlumberger SE, Criqui-Filipe P, Wasylyk B. Sp100 interacts with ETS-1 and stimulates its transcriptional activity. Mol Cell Biol. 2002 Apr;22(8):2687-702. PMID:11909962
↑ Moller A, Sirma H, Hofmann TG, Staege H, Gresko E, Ludi KS, Klimczak E, Droge W, Will H, Schmitz ML. Sp100 is important for the stimulatory effect of homeodomain-interacting protein kinase-2 on p53-dependent gene expression. Oncogene. 2003 Nov 27;22(54):8731-7. PMID:14647468 doi:http://dx.doi.org/10.1038/sj.onc.1207079
↑ Yordy JS, Li R, Sementchenko VI, Pei H, Muise-Helmericks RC, Watson DK. SP100 expression modulates ETS1 transcriptional activity and inhibits cell invasion. Oncogene. 2004 Aug 26;23(39):6654-65. PMID:15247905 doi:http://dx.doi.org/10.1038/sj.onc.1207891
↑ Yordy JS, Moussa O, Pei H, Chaussabel D, Li R, Watson DK. SP100 inhibits ETS1 activity in primary endothelial cells. Oncogene. 2005 Jan 27;24(5):916-31. PMID:15592518 doi:http://dx.doi.org/10.1038/sj.onc.1208245
↑ Jiang WQ, Zhong ZH, Henson JD, Neumann AA, Chang AC, Reddel RR. Suppression of alternative lengthening of telomeres by Sp100-mediated sequestration of the MRE11/RAD50/NBS1 complex. Mol Cell Biol. 2005 Apr;25(7):2708-21. PMID:15767676 doi:http://dx.doi.org/10.1128/MCB.25.7.2708-2721.2005
↑ Ling PD, Peng RS, Nakajima A, Yu JH, Tan J, Moses SM, Yang WH, Zhao B, Kieff E, Bloch KD, Bloch DB. Mediation of Epstein-Barr virus EBNA-LP transcriptional coactivation by Sp100. EMBO J. 2005 Oct 19;24(20):3565-75. Epub 2005 Sep 22. PMID:16177824 doi:http://dx.doi.org/7600820
↑ Milovic-Holm K, Krieghoff E, Jensen K, Will H, Hofmann TG. FLASH links the CD95 signaling pathway to the cell nucleus and nuclear bodies. EMBO J. 2007 Jan 24;26(2):391-401. PMID:17245429 doi:http://dx.doi.org/10.1038/sj.emboj.7601504
↑ Held-Feindt J, Hattermann K, Knerlich-Lukoschus F, Mehdorn HM, Mentlein R. SP100 reduces malignancy of human glioma cells. Int J Oncol. 2011 Apr;38(4):1023-30. doi: 10.3892/ijo.2011.927. Epub 2011 Jan 27. PMID:21274506 doi:http://dx.doi.org/10.3892/ijo.2011.927
↑ Kim YE, Lee JH, Kim ET, Shin HJ, Gu SY, Seol HS, Ling PD, Lee CH, Ahn JH. Human cytomegalovirus infection causes degradation of Sp100 proteins that suppress viral gene expression. J Virol. 2011 Nov;85(22):11928-37. doi: 10.1128/JVI.00758-11. Epub 2011 Aug 31. PMID:21880768 doi:http://dx.doi.org/10.1128/JVI.00758-11
↑ Pearce NM, Krojer T, Bradley AR, Collins P, Nowak RP, Talon R, Marsden BD, Kelm S, Shi J, Deane CM, von Delft F. A multi-crystal method for extracting obscured crystallographic states from conventionally uninterpretable electron density. Nat Commun. 2017 Apr 24;8:15123. doi: 10.1038/ncomms15123. PMID:28436492 doi:http://dx.doi.org/10.1038/ncomms15123

1 Structural highlights
2 Function
3 Publication Abstract from PubMed
4 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/5pyq"

@@ Line 1: / Line 1: @@
 ==PanDDA analysis group deposition -- Crystal Structure of SP100 after initial refinement with no ligand modelled (structure 86)==
-<StructureSection load='5pyq' size='340' side='right' caption='[[5pyq]], [[Resolution|resolution]] 1.97&Aring;' scene=''>
+<StructureSection load='5pyq' size='340' side='right'caption='[[5pyq]], [[Resolution|resolution]] 1.97&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[5pyq]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5PYQ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5PYQ FirstGlance]. <br>
+<table><tr><td colspan='2'>[[5pyq]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5PYQ OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5PYQ 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='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'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5pyq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5pyq OCA], [http://pdbe.org/5pyq PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5pyq RCSB], [http://www.ebi.ac.uk/pdbsum/5pyq PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5pyq ProSAT]</span></td></tr>
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=5pyq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5pyq OCA], [http://pdbe.org/5pyq PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5pyq RCSB], [http://www.ebi.ac.uk/pdbsum/5pyq PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5pyq ProSAT]</span></td></tr>
 </table>
 == Function ==
@@ Line 22: / Line 22: @@
 __TOC__
 </StructureSection>
+[[Category: Large Structures]]
 [[Category: Arrowsmith, C H]]
 [[Category: Bountra, C]]

5pyq

From Proteopedia

Revision as of 07:52, 2 September 2020

PanDDA analysis group deposition -- Crystal Structure of SP100 after initial refinement with no ligand modelled (structure 86)

Structural highlights

Function

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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