5pvo: Difference between revisions

Revision as of 14:13, 6 November 2017

PanDDA analysis group deposition -- Crystal Structure of BRD1 after initial refinement with no ligand modelled (structure 239)

Structural highlights

5pvo is a 2 chain structure with sequence from Human. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:	EDO, NA
Gene:	BRD1, BRL, BRPF2 (HUMAN)
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

[BRD1_HUMAN] Component of the MOZ/MORF complex which has a histone H3 acetyltransferase activity.^[1] ^[2]

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^[3]

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

References

↑ Doyon Y, Cayrou C, Ullah M, Landry AJ, Cote V, Selleck W, Lane WS, Tan S, Yang XJ, Cote J. ING tumor suppressor proteins are critical regulators of chromatin acetylation required for genome expression and perpetuation. Mol Cell. 2006 Jan 6;21(1):51-64. PMID:16387653 doi:10.1016/j.molcel.2005.12.007
↑ Qin S, Jin L, Zhang J, Liu L, Ji P, Wu M, Wu J, Shi Y. Recognition of unmodified histone H3 by the first PHD finger of bromodomain-PHD finger protein 2 provides insights into the regulation of histone acetyltransferases monocytic leukemic zinc-finger protein (MOZ) and MOZ-related factor (MORF). J Biol Chem. 2011 Oct 21;286(42):36944-55. doi: 10.1074/jbc.M111.244400. Epub, 2011 Aug 31. PMID:21880731 doi:https://dx.doi.org/10.1074/jbc.M111.244400
↑ 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:https://dx.doi.org/10.1038/ncomms15123

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OCA

[1] Doyon Y, Cayrou C, Ullah M, Landry AJ, Cote V, Selleck W, Lane WS, Tan S, Yang XJ, Cote J. ING tumor suppressor proteins are critical regulators of chromatin acetylation required for genome expression and perpetuation. Mol Cell. 2006 Jan 6;21(1):51-64. PMID:16387653 doi:10.1016/j.molcel.2005.12.007

[2] Qin S, Jin L, Zhang J, Liu L, Ji P, Wu M, Wu J, Shi Y. Recognition of unmodified histone H3 by the first PHD finger of bromodomain-PHD finger protein 2 provides insights into the regulation of histone acetyltransferases monocytic leukemic zinc-finger protein (MOZ) and MOZ-related factor (MORF). J Biol Chem. 2011 Oct 21;286(42):36944-55. doi: 10.1074/jbc.M111.244400. Epub, 2011 Aug 31. PMID:21880731 doi:https://dx.doi.org/10.1074/jbc.M111.244400

[3] 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:https://dx.doi.org/10.1038/ncomms15123

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[2]

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@@ Line 3: / Line 3: @@
 <StructureSection load='5pvo' size='340' side='right' caption='[[5pvo]], [[Resolution|resolution]] 1.96&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[5pvo]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5PVO OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5PVO FirstGlance]. <br>
+<table><tr><td colspan='2'>[[5pvo]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Human Human]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5PVO OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5PVO 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=NA:SODIUM+ION'>NA</scene></td></tr>
+<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">BRD1, BRL, BRPF2 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])</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=5pvo FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5pvo OCA], [http://pdbe.org/5pvo PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5pvo RCSB], [http://www.ebi.ac.uk/pdbsum/5pvo PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5pvo ProSAT]</span></td></tr>
 </table>
@@ Line 22: / Line 23: @@
 __TOC__
 </StructureSection>
+[[Category: Human]]
 [[Category: Arrowsmith, C H]]
 [[Category: Bountra, C]]

5pvo: Difference between revisions

Revision as of 14:13, 6 November 2017

PanDDA analysis group deposition -- Crystal Structure of BRD1 after initial refinement with no ligand modelled (structure 239)

Structural highlights

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Publication Abstract from PubMed

References

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