6us1 - Revision history

OCA at 14:58, 13 March 2024

2024-03-13T14:58:05Z

←Older revision		Revision as of 14:58, 13 March 2024
Line 3:		Line 3:
	<StructureSection load='6us1' size='340' side='right'caption='[[6us1]], [[Resolution\|resolution]] 1.65Å' scene=''>		<StructureSection load='6us1' size='340' side='right'caption='[[6us1]], [[Resolution\|resolution]] 1.65Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6us1]] 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=6US1 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=6US1 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6us1]] 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=6US1 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6US1 FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=EOH:ETHANOL'>EOH</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]] 1.653Å</td></tr>
-	<tr id='~~related~~'><td class="sblockLbl"><b>[[~~Related_structure~~\|~~Related~~:]]</b></td><td class="sblockDat"~~>[[6ure\|6ure]], [[6unt\|6unt]], [[6urj\|6urj]], [[6urk\|6urk]], [[6url\|6url]], [[6urn\|6urn]], [[6urr\|6urr]], [[6urz\|6urz]], [[6us0\|6us0]]</td></tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=EOH:ETHANOL'>EOH</scene></td></tr>
-	~~<tr~~ id~~='gene'><td class~~="~~sblockLbl~~"><~~b>[[Gene\|Gene~~:~~]]</b~~></td>~~<td class="sblockDat">BANF1, BAF, BCRG1 ([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'>[https://proteopedia.org/fgij/fg.htm?mol=6us1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6us1 OCA], [https://pdbe.org/6us1 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6us1 RCSB], [https://www.ebi.ac.uk/pdbsum/6us1 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6us1 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=6us1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6us1 OCA], [~~http~~://pdbe.org/6us1 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6us1 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6us1 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6us1 ProSAT]</span></td></tr>	+
	</table>		</table>
	== Disease ==		== Disease ==
-	[~~[http~~://www.uniprot.org/uniprot/BAF_HUMAN BAF_HUMAN]] Defects in BANF1 are the cause of Nestor-Guillermo progeria syndrome (NGPS) [MIM:[~~http~~://omim.org/entry/614008 614008]]. NGPS is an atypical progeroid syndrome characterized by normal development in the first years of life, later followed by the emergence of generalized lipoatrophy, severe osteoporosis, and marked osteolysis. The atrophic facial subcutaneous fat pad and the marked osteolysis of the maxilla and mandible result in a typical pseudosenile facial appearance with micrognatia, prominent subcutaneous venous patterning, a convex nasal ridge, and proptosis. Cognitive development is completely normal. Patients do not have cardiovascular dysfunction, atherosclerosis, or metabolic anomalies.<ref>PMID:21549337</ref>	+	[https://www.uniprot.org/uniprot/BAF_HUMAN BAF_HUMAN] Defects in BANF1 are the cause of Nestor-Guillermo progeria syndrome (NGPS) [MIM:[https://omim.org/entry/614008 614008]. NGPS is an atypical progeroid syndrome characterized by normal development in the first years of life, later followed by the emergence of generalized lipoatrophy, severe osteoporosis, and marked osteolysis. The atrophic facial subcutaneous fat pad and the marked osteolysis of the maxilla and mandible result in a typical pseudosenile facial appearance with micrognatia, prominent subcutaneous venous patterning, a convex nasal ridge, and proptosis. Cognitive development is completely normal. Patients do not have cardiovascular dysfunction, atherosclerosis, or metabolic anomalies.<ref>PMID:21549337</ref>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/BAF_HUMAN BAF_HUMAN]] Plays fundamental roles in nuclear assembly, chromatin organization, gene expression and gonad development. May potently compress chromatin structure and be involved in membrane recruitment and chromatin decondensation during nuclear assembly. Contains 2 non-specific dsDNA-binding sites which may promote DNA cross-bridging. Exploited by retroviruses for inhibiting self-destructing autointegration of retroviral DNA, thereby promoting integration of viral DNA into the host chromosome. EMD and BAF are cooperative cofactors of HIV-1 infection. Association of EMD with the viral DNA requires the presence of BAF and viral integrase. The association of viral DNA with chromatin requires the presence of BAF and EMD.<ref>PMID:11005805</ref> <ref>PMID:12163470</ref> <ref>PMID:16680152</ref>	+	[https://www.uniprot.org/uniprot/BAF_HUMAN BAF_HUMAN] Plays fundamental roles in nuclear assembly, chromatin organization, gene expression and gonad development. May potently compress chromatin structure and be involved in membrane recruitment and chromatin decondensation during nuclear assembly. Contains 2 non-specific dsDNA-binding sites which may promote DNA cross-bridging. Exploited by retroviruses for inhibiting self-destructing autointegration of retroviral DNA, thereby promoting integration of viral DNA into the host chromosome. EMD and BAF are cooperative cofactors of HIV-1 infection. Association of EMD with the viral DNA requires the presence of BAF and viral integrase. The association of viral DNA with chromatin requires the presence of BAF and EMD.<ref>PMID:11005805</ref> <ref>PMID:12163470</ref> <ref>PMID:16680152</ref>
-	~~<div style="background-color:#fffaf0;">~~	+
-	~~== Publication Abstract from PubMed ==~~	+
-	The multiple-solvent crystal structure (MSCS) approach uses high concentrations of organic solvents to characterize the interactions and effects of solvents on proteins. Here, the method has been further developed and an MSCS data-handling pipeline is presented that uses the Detection of Related Solvent Positions (DRoP) program to improve data quality. DRoP is used to selectively model conserved water molecules, so that an advanced stage of structural refinement is reached quickly. This allows the placement of organic molecules more accurately and convergence on high-quality maps and structures. This pipeline was applied to the chromatin-associated protein barrier-to-autointegration factor (BAF), resulting in structural models with better than average statistics. DRoP and Phenix Structure Comparison were used to characterize the data sets and to identify a binding site that overlaps with the interaction site of BAF with emerin. The conserved water-mediated networks identified by DRoP suggested a mechanism by which water molecules are used to drive the binding of DNA. Normalized and differential B-factor analysis is shown to be a valuable tool to characterize the effects of specific solvents on defined regions of BAF. Specific solvents are identified that cause stabilization of functionally important regions of the protein. This work presents tools and a standardized approach for the analysis and comprehension of MSCS data sets.	+
-		+
-	Development of a structure-analysis pipeline using multiple-solvent crystal structures of barrier-to-autointegration factor.,Agarwal S, Smith M, De La Rosa I, Verba KA, Swartz P, Segura-Totten M, Mattos C Acta Crystallogr D Struct Biol. 2020 Oct 1;76(Pt 10):1001-1014. doi:, 10.1107/S2059798320011341. Epub 2020 Sep 17. PMID:33021502<ref>PMID:33021502</ref>	+
-		+
-	~~From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>~~	+
-	~~</div>~~	+
-	~~<div class="pdbe-citations 6us1" style="background-color:#fffaf0;"></div~~>	+
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Human~~]]	+	[[Category: Homo sapiens]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Agarwal, S]]	+	[[Category: Agarwal S]]
-	[[Category: ~~Kliment, A V~~]]	+	[[Category: De La Rosa I]]
-	[[Category: ~~Mattos, C~~]]	+	[[Category: Kliment AV]]
-	[[Category: ~~Rosa, I De La~~]]	+	[[Category: Mattos C]]
-	[[Category: Segura-Totten, M]]	+	[[Category: Segura-Totten M]]
-	[[Category: Smith, M]]	+	[[Category: Smith M]]
-	[[Category: Swartz, P]]	+	[[Category: Swartz P]]
-	~~[[Category: Alpha helical]]~~	+
-	~~[[Category: Dna binding protein]]~~	+
-	~~[[Category: Minor groove binder]]~~	+
-	~~[[Category: Msc~~]]	+

OCA at 08:36, 21 October 2020

2020-10-21T08:36:26Z

←Older revision		Revision as of 08:36, 21 October 2020
Line 1:		Line 1:

	==Barrier-to-autointegration factor soaked in isobutanol: 1 of 14 in MSCS set==		==Barrier-to-autointegration factor soaked in isobutanol: 1 of 14 in MSCS set==
-	<StructureSection load='6us1' size='340' side='right'caption='[[6us1]]' scene=''>	+	<StructureSection load='6us1' size='340' side='right'caption='[[6us1]], [[Resolution\|resolution]] 1.65Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6US1 OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6US1 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6us1]] 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=6US1 OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6US1 FirstGlance]. <br>
-	</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=6us1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6us1 OCA], [http://pdbe.org/6us1 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6us1 RCSB], [http://www.ebi.ac.uk/pdbsum/6us1 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6us1 ProSAT]</span></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=EOH:ETHANOL'>EOH</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[6ure\|6ure]], [[6unt\|6unt]], [[6urj\|6urj]], [[6urk\|6urk]], [[6url\|6url]], [[6urn\|6urn]], [[6urr\|6urr]], [[6urz\|6urz]], [[6us0\|6us0]]</td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">BANF1, BAF, BCRG1 ([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://proteopedia.org/fgij/fg.htm?mol=6us1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6us1 OCA], [http://pdbe.org/6us1 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6us1 RCSB], [http://www.ebi.ac.uk/pdbsum/6us1 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6us1 ProSAT]</span></td></tr>
	</table>		</table>
		+	== Disease ==
		+	[[http://www.uniprot.org/uniprot/BAF_HUMAN BAF_HUMAN]] Defects in BANF1 are the cause of Nestor-Guillermo progeria syndrome (NGPS) [MIM:[http://omim.org/entry/614008 614008]]. NGPS is an atypical progeroid syndrome characterized by normal development in the first years of life, later followed by the emergence of generalized lipoatrophy, severe osteoporosis, and marked osteolysis. The atrophic facial subcutaneous fat pad and the marked osteolysis of the maxilla and mandible result in a typical pseudosenile facial appearance with micrognatia, prominent subcutaneous venous patterning, a convex nasal ridge, and proptosis. Cognitive development is completely normal. Patients do not have cardiovascular dysfunction, atherosclerosis, or metabolic anomalies.<ref>PMID:21549337</ref>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/BAF_HUMAN BAF_HUMAN]] Plays fundamental roles in nuclear assembly, chromatin organization, gene expression and gonad development. May potently compress chromatin structure and be involved in membrane recruitment and chromatin decondensation during nuclear assembly. Contains 2 non-specific dsDNA-binding sites which may promote DNA cross-bridging. Exploited by retroviruses for inhibiting self-destructing autointegration of retroviral DNA, thereby promoting integration of viral DNA into the host chromosome. EMD and BAF are cooperative cofactors of HIV-1 infection. Association of EMD with the viral DNA requires the presence of BAF and viral integrase. The association of viral DNA with chromatin requires the presence of BAF and EMD.<ref>PMID:11005805</ref> <ref>PMID:12163470</ref> <ref>PMID:16680152</ref>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The multiple-solvent crystal structure (MSCS) approach uses high concentrations of organic solvents to characterize the interactions and effects of solvents on proteins. Here, the method has been further developed and an MSCS data-handling pipeline is presented that uses the Detection of Related Solvent Positions (DRoP) program to improve data quality. DRoP is used to selectively model conserved water molecules, so that an advanced stage of structural refinement is reached quickly. This allows the placement of organic molecules more accurately and convergence on high-quality maps and structures. This pipeline was applied to the chromatin-associated protein barrier-to-autointegration factor (BAF), resulting in structural models with better than average statistics. DRoP and Phenix Structure Comparison were used to characterize the data sets and to identify a binding site that overlaps with the interaction site of BAF with emerin. The conserved water-mediated networks identified by DRoP suggested a mechanism by which water molecules are used to drive the binding of DNA. Normalized and differential B-factor analysis is shown to be a valuable tool to characterize the effects of specific solvents on defined regions of BAF. Specific solvents are identified that cause stabilization of functionally important regions of the protein. This work presents tools and a standardized approach for the analysis and comprehension of MSCS data sets.
		+
		+	Development of a structure-analysis pipeline using multiple-solvent crystal structures of barrier-to-autointegration factor.,Agarwal S, Smith M, De La Rosa I, Verba KA, Swartz P, Segura-Totten M, Mattos C Acta Crystallogr D Struct Biol. 2020 Oct 1;76(Pt 10):1001-1014. doi:, 10.1107/S2059798320011341. Epub 2020 Sep 17. PMID:33021502<ref>PMID:33021502</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 6us1" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Human]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Agarwal S]]	+	[[Category: Agarwal, S]]
-	[[Category: ~~De La Rosa I~~]]	+	[[Category: Kliment, A V]]
-	[[Category: ~~Kliment AV~~]]	+	[[Category: Mattos, C]]
-	[[Category: ~~Mattos C~~]]	+	[[Category: Rosa, I De La]]
-	[[Category: Segura-Totten M]]	+	[[Category: Segura-Totten, M]]
-	[[Category: Smith M]]	+	[[Category: Smith, M]]
-	[[Category: Swartz P]]	+	[[Category: Swartz, P]]
		+	[[Category: Alpha helical]]
		+	[[Category: Dna binding protein]]
		+	[[Category: Minor groove binder]]
		+	[[Category: Msc]]

OCA at 06:18, 7 October 2020

2020-10-07T06:18:42Z

←Older revision		Revision as of 06:18, 7 October 2020
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry 6us1 is ON HOLD until Paper Publication~~	+	==Barrier-to-autointegration factor soaked in isobutanol: 1 of 14 in MSCS set==
-		+	<StructureSection load='6us1' size='340' side='right'caption='[[6us1]]' scene=''>
-	~~Authors: Agarwal, S., Smith, M., De La Rosa, I., Kliment, A.V., Swartz, P., Segura-Totten, M., Mattos, C.~~	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6US1 OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6US1 FirstGlance]. <br>
-	~~Description:~~ Barrier-to-autointegration factor soaked in isobutanol: 1 of 14 in MSCS set	+	</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=6us1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6us1 OCA], [http://pdbe.org/6us1 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6us1 RCSB], [http://www.ebi.ac.uk/pdbsum/6us1 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6us1 ProSAT]</span></td></tr>
-	[[~~Category~~: ~~Unreleased Structures~~]]	+	</table>
-	[[~~Category~~: ~~Kliment~~, A.V]]	+	__TOC__
-	[[Category: ~~Swartz, P~~]]	+	</StructureSection>
-	[[Category: ~~Segura-Totten, M~~]]	+	[[Category: Large Structures]]
-	[[Category: De La Rosa, I]]	+	[[Category: Agarwal S]]
-	[[Category: Mattos, C]]	+	[[Category: De La Rosa I]]
-	[[Category: Smith, M]]	+	[[Category: Kliment AV]]
-	[[Category: ~~Agarwal, S~~]]	+	[[Category: Mattos C]]
		+	[[Category: Segura-Totten M]]
		+	[[Category: Smith M]]
		+	[[Category: Swartz P]]

OCA at 13:27, 29 January 2020

2020-01-29T13:27:23Z

←Older revision		Revision as of 13:27, 29 January 2020
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 6us1 is ON HOLD	+	The entry 6us1 is ON HOLD until Paper Publication

	Authors: Agarwal, S., Smith, M., De La Rosa, I., Kliment, A.V., Swartz, P., Segura-Totten, M., Mattos, C.		Authors: Agarwal, S., Smith, M., De La Rosa, I., Kliment, A.V., Swartz, P., Segura-Totten, M., Mattos, C.
Line 7:		Line 7:
	Description: Barrier-to-autointegration factor soaked in isobutanol: 1 of 14 in MSCS set		Description: Barrier-to-autointegration factor soaked in isobutanol: 1 of 14 in MSCS set
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
		+	[[Category: Kliment, A.V]]
	[[Category: Swartz, P]]		[[Category: Swartz, P]]
	[[Category: Segura-Totten, M]]		[[Category: Segura-Totten, M]]
-	[[Category: Agarwal, S]]
	[[Category: De La Rosa, I]]		[[Category: De La Rosa, I]]
	[[Category: Mattos, C]]		[[Category: Mattos, C]]
-	[[Category: Kliment, A.V]]
	[[Category: Smith, M]]		[[Category: Smith, M]]
		+	[[Category: Agarwal, S]]

OCA: Protected "6us1" [edit=sysop:move=sysop]

2019-10-30T07:45:17Z

Protected "6us1" [edit=sysop:move=sysop]

←Older revision

Revision as of 07:45, 30 October 2019

OCA: New page: '''Unreleased structure''' The entry 6us1 is ON HOLD Authors: Agarwal, S., Smith, M., De La Rosa, I., Kliment, A.V., Swartz, P., Segura-Totten, M., Mattos, C. Description: Barrier-to-a...

2019-10-30T07:45:15Z

New page: '''Unreleased structure''' The entry 6us1 is ON HOLD Authors: Agarwal, S., Smith, M., De La Rosa, I., Kliment, A.V., Swartz, P., Segura-Totten, M., Mattos, C. Description: Barrier-to-a...

New page

'''Unreleased structure'''

The entry 6us1 is ON HOLD

Authors: Agarwal, S., Smith, M., De La Rosa, I., Kliment, A.V., Swartz, P., Segura-Totten, M., Mattos, C.

Description: Barrier-to-autointegration factor soaked in isobutanol: 1 of 14 in MSCS set
[[Category: Unreleased Structures]]
[[Category: Swartz, P]]
[[Category: Segura-Totten, M]]
[[Category: Agarwal, S]]
[[Category: De La Rosa, I]]
[[Category: Mattos, C]]
[[Category: Kliment, A.V]]
[[Category: Smith, M]]