4csr - Revision history

OCA at 12:15, 20 December 2023

2023-12-20T12:15:55Z

←Older revision		Revision as of 12:15, 20 December 2023
Line 4:		Line 4:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4csr]] 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=4CSR OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4CSR FirstGlance]. <br>		<table><tr><td colspan='2'>[[4csr]] 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=4CSR OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4CSR FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</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]] 1.5Å</td></tr>
		+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</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=4csr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4csr OCA], [https://pdbe.org/4csr PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4csr RCSB], [https://www.ebi.ac.uk/pdbsum/4csr PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4csr ProSAT]</span></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=4csr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4csr OCA], [https://pdbe.org/4csr PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4csr RCSB], [https://www.ebi.ac.uk/pdbsum/4csr PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4csr ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/NFYB_HUMAN NFYB_HUMAN]] Stimulates the transcription of various genes by recognizing and binding to a CCAAT motif in promoters, for example in type 1 collagen, albumin and beta-actin genes.	+	[https://www.uniprot.org/uniprot/NFYB_HUMAN NFYB_HUMAN] Stimulates the transcription of various genes by recognizing and binding to a CCAAT motif in promoters, for example in type 1 collagen, albumin and beta-actin genes.

	==See Also==		==See Also==

OCA at 07:31, 14 September 2022

2022-09-14T07:31:19Z

←Older revision		Revision as of 07:31, 14 September 2022
Line 3:		Line 3:
	<StructureSection load='4csr' size='340' side='right'caption='[[4csr]], [[Resolution\|resolution]] 1.50Å' scene=''>		<StructureSection load='4csr' size='340' side='right'caption='[[4csr]], [[Resolution\|resolution]] 1.50Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4csr]] 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=4CSR OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=4CSR FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4csr]] 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=4CSR OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4CSR FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</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=4csr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4csr OCA], [~~http~~://pdbe.org/4csr PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=4csr RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/4csr PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=4csr ProSAT]</span></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=4csr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4csr OCA], [https://pdbe.org/4csr PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4csr RCSB], [https://www.ebi.ac.uk/pdbsum/4csr PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4csr ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[~~http~~://www.uniprot.org/uniprot/NFYB_HUMAN NFYB_HUMAN]] Stimulates the transcription of various genes by recognizing and binding to a CCAAT motif in promoters, for example in type 1 collagen, albumin and beta-actin genes. [[http://www.uniprot.org/uniprot/NFYC_HUMAN NFYC_HUMAN]] Stimulates the transcription of various genes by recognizing and binding to a CCAAT motif in promoters, for example in type 1 collagen, albumin and beta-actin genes.	+	[[https://www.uniprot.org/uniprot/NFYB_HUMAN NFYB_HUMAN]] Stimulates the transcription of various genes by recognizing and binding to a CCAAT motif in promoters, for example in type 1 collagen, albumin and beta-actin genes.
-	~~<div style="background-color:#fffaf0;">~~	+
-	~~== Publication Abstract from PubMed ==~~	+
-	The sequence-specific transcription factor NF-Y binds the CCAAT box, one of the sequence elements most frequently found in eukaryotic promoters. NF-Y is composed of the NF-YA and NF-YB/NF-YC subunits, the latter two hosting histone-fold domains (HFDs). The crystal structure of NF-Y bound to a 25 bp CCAAT oligonucleotide shows that the HFD dimer binds to the DNA sugar-phosphate backbone, mimicking the nucleosome H2A/H2B-DNA assembly. NF-YA both binds to NF-YB/NF-YC and inserts an alpha helix deeply into the DNA minor groove, providing sequence-specific contacts to the CCAAT box. Structural considerations and mutational data indicate that NF-YB ubiquitination at Lys138 precedes and is equivalent to H2B Lys120 monoubiquitination, important in transcriptional activation. Thus, NF-Y is a sequence-specific transcription factor with nucleosome-like properties of nonspecific DNA binding and helps establish permissive chromatin modifications at CCAAT promoters. Our findings suggest that other HFD-containing proteins may function in similar ways.	+
-		+
-	Sequence-Specific Transcription Factor NF-Y Displays Histone-like DNA Binding and H2B-like Ubiquitination.,Nardini M, Gnesutta N, Donati G, Gatta R, Forni C, Fossati A, Vonrhein C, Moras D, Romier C, Bolognesi M, Mantovani R Cell. 2013 Jan 17;152(1-2):132-43. doi: 10.1016/j.cell.2012.11.047. PMID:23332751<ref>PMID:23332751</ref>	+
-		+
-	~~From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>~~	+
-	~~</div>~~	+
-	~~<div class="pdbe-citations 4csr" style="background-color:#fffaf0;"></div>~~	+

	==See Also==		==See Also==
	*[[Nuclear transcription factor Y\|Nuclear transcription factor Y]]		*[[Nuclear transcription factor Y\|Nuclear transcription factor Y]]
-	== References ==
-	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Human~~]]	+	[[Category: Homo sapiens]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Bolognesi, M]]	+	[[Category: Bolognesi M]]
-	[[Category: Cocolo, S]]	+	[[Category: Cocolo S]]
-	[[Category: Gnesutta, N]]	+	[[Category: Gnesutta N]]
-	[[Category: Mantovani, R]]	+	[[Category: Mantovani R]]
-	[[Category: Nardini, M]]	+	[[Category: Nardini M]]
-	~~[[Category: Ccaat-box]]~~	+
-	~~[[Category: Dna-binding]]~~	+
-	~~[[Category: Nf-y]]~~	+
-	~~[[Category: Transcription~~]]	+

OCA at 08:55, 20 March 2019

2019-03-20T08:55:35Z

←Older revision		Revision as of 08:55, 20 March 2019
Line 1:		Line 1:

	==High resolution crystal structure of the histone fold dimer (NF-YB)-(NF-YC)==		==High resolution crystal structure of the histone fold dimer (NF-YB)-(NF-YC)==
-	<StructureSection load='4csr' size='340' side='right' caption='[[4csr]], [[Resolution\|resolution]] 1.50Å' scene=''>	+	<StructureSection load='4csr' size='340' side='right'caption='[[4csr]], [[Resolution\|resolution]] 1.50Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4csr]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4CSR OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4CSR FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4csr]] 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=4CSR OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4CSR FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</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=4csr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4csr OCA], [http://pdbe.org/4csr PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4csr RCSB], [http://www.ebi.ac.uk/pdbsum/4csr PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4csr ProSAT]</span></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=4csr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4csr OCA], [http://pdbe.org/4csr PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4csr RCSB], [http://www.ebi.ac.uk/pdbsum/4csr PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4csr ProSAT]</span></td></tr>
Line 25:		Line 25:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Human]]
		+	[[Category: Large Structures]]
	[[Category: Bolognesi, M]]		[[Category: Bolognesi, M]]
	[[Category: Cocolo, S]]		[[Category: Cocolo, S]]

OCA at 07:18, 23 December 2016

2016-12-23T07:18:12Z

←Older revision		Revision as of 07:18, 23 December 2016
Line 1:		Line 1:
		+
	==High resolution crystal structure of the histone fold dimer (NF-YB)-(NF-YC)==		==High resolution crystal structure of the histone fold dimer (NF-YB)-(NF-YC)==
	<StructureSection load='4csr' size='340' side='right' caption='[[4csr]], [[Resolution\|resolution]] 1.50Å' scene=''>		<StructureSection load='4csr' size='340' side='right' caption='[[4csr]], [[Resolution\|resolution]] 1.50Å' scene=''>
Line 4:		Line 5:
	<table><tr><td colspan='2'>[[4csr]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4CSR OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4CSR FirstGlance]. <br>		<table><tr><td colspan='2'>[[4csr]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4CSR OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4CSR FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</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=4csr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4csr OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4csr RCSB], [http://www.ebi.ac.uk/pdbsum/4csr PDBsum]</span></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=4csr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4csr OCA], [http://pdbe.org/4csr PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4csr RCSB], [http://www.ebi.ac.uk/pdbsum/4csr PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4csr ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 16:		Line 17:
	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>		From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
	</div>		</div>
		+	<div class="pdbe-citations 4csr" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Nuclear transcription factor Y\|Nuclear transcription factor Y]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 12:05, 18 March 2015

2015-03-18T12:05:42Z

←Older revision		Revision as of 12:05, 18 March 2015
Line 1:		Line 1:
-	'''~~Unreleased~~ structure'''	+	==High resolution crystal structure of the histone fold dimer (NF-YB)-(NF-YC)==
		+	<StructureSection load='4csr' size='340' side='right' caption='[[4csr]], [[Resolution\|resolution]] 1.50Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[4csr]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4CSR OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4CSR FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</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=4csr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4csr OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4csr RCSB], [http://www.ebi.ac.uk/pdbsum/4csr PDBsum]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/NFYB_HUMAN NFYB_HUMAN]] Stimulates the transcription of various genes by recognizing and binding to a CCAAT motif in promoters, for example in type 1 collagen, albumin and beta-actin genes. [[http://www.uniprot.org/uniprot/NFYC_HUMAN NFYC_HUMAN]] Stimulates the transcription of various genes by recognizing and binding to a CCAAT motif in promoters, for example in type 1 collagen, albumin and beta-actin genes.
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The sequence-specific transcription factor NF-Y binds the CCAAT box, one of the sequence elements most frequently found in eukaryotic promoters. NF-Y is composed of the NF-YA and NF-YB/NF-YC subunits, the latter two hosting histone-fold domains (HFDs). The crystal structure of NF-Y bound to a 25 bp CCAAT oligonucleotide shows that the HFD dimer binds to the DNA sugar-phosphate backbone, mimicking the nucleosome H2A/H2B-DNA assembly. NF-YA both binds to NF-YB/NF-YC and inserts an alpha helix deeply into the DNA minor groove, providing sequence-specific contacts to the CCAAT box. Structural considerations and mutational data indicate that NF-YB ubiquitination at Lys138 precedes and is equivalent to H2B Lys120 monoubiquitination, important in transcriptional activation. Thus, NF-Y is a sequence-specific transcription factor with nucleosome-like properties of nonspecific DNA binding and helps establish permissive chromatin modifications at CCAAT promoters. Our findings suggest that other HFD-containing proteins may function in similar ways.

-	~~The entry 4csr is ON HOLD until Paper Publication~~	+	Sequence-Specific Transcription Factor NF-Y Displays Histone-like DNA Binding and H2B-like Ubiquitination.,Nardini M, Gnesutta N, Donati G, Gatta R, Forni C, Fossati A, Vonrhein C, Moras D, Romier C, Bolognesi M, Mantovani R Cell. 2013 Jan 17;152(1-2):132-43. doi: 10.1016/j.cell.2012.11.047. PMID:23332751<ref>PMID:23332751</ref>

-	~~Authors: Gnesutta~~, N.~~, Cocolo,~~ S.~~, Mantovani, R., Bolognesi, M., Nardini, M~~.	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~Description: High resolution crystal structure of the histone fold dimer (NF-YB)-( NF-YC)~~	+	== References ==
-	[[Category: ~~Unreleased Structures~~]]	+	<references/>
-	[[Category: ~~Nardini~~, M]]	+	__TOC__
		+	</StructureSection>
		+	[[Category: Bolognesi, M]]
		+	[[Category: Cocolo, S]]
	[[Category: Gnesutta, N]]		[[Category: Gnesutta, N]]
	[[Category: Mantovani, R]]		[[Category: Mantovani, R]]
-	[[Category: ~~Cocolo~~, S]]	+	[[Category: Nardini, M]]
-	[[Category: ~~Bolognesi, M~~]]	+	[[Category: Ccaat-box]]
		+	[[Category: Dna-binding]]
		+	[[Category: Nf-y]]
		+	[[Category: Transcription]]

OCA at 13:31, 24 December 2014

2014-12-24T13:31:17Z

←Older revision		Revision as of 13:31, 24 December 2014
Line 6:		Line 6:

	Description: High resolution crystal structure of the histone fold dimer (NF-YB)-( NF-YC)		Description: High resolution crystal structure of the histone fold dimer (NF-YB)-( NF-YC)
		+	[[Category: Unreleased Structures]]
		+	[[Category: Nardini, M]]
		+	[[Category: Gnesutta, N]]
		+	[[Category: Mantovani, R]]
		+	[[Category: Cocolo, S]]
		+	[[Category: Bolognesi, M]]

OCA at 07:28, 21 May 2014

2014-05-21T07:28:04Z

←Older revision		Revision as of 07:28, 21 May 2014
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 4csr is ON HOLD	+	The entry 4csr is ON HOLD until Paper Publication

	Authors: Gnesutta, N., Cocolo, S., Mantovani, R., Bolognesi, M., Nardini, M.		Authors: Gnesutta, N., Cocolo, S., Mantovani, R., Bolognesi, M., Nardini, M.

	Description: High resolution crystal structure of the histone fold dimer (NF-YB)-( NF-YC)		Description: High resolution crystal structure of the histone fold dimer (NF-YB)-( NF-YC)

OCA: Protected "4csr" [edit=sysop:move=sysop]

2014-03-19T06:51:31Z

Protected "4csr" [edit=sysop:move=sysop]

←Older revision

Revision as of 06:51, 19 March 2014

OCA: New page: '''Unreleased structure''' The entry 4csr is ON HOLD Authors: Gnesutta, N., Cocolo, S., Mantovani, R., Bolognesi, M., Nardini, M. Description: High resolution crystal structure of the ...

2014-03-19T06:51:29Z

New page: '''Unreleased structure''' The entry 4csr is ON HOLD Authors: Gnesutta, N., Cocolo, S., Mantovani, R., Bolognesi, M., Nardini, M. Description: High resolution crystal structure of the ...

New page

'''Unreleased structure'''

The entry 4csr is ON HOLD

Authors: Gnesutta, N., Cocolo, S., Mantovani, R., Bolognesi, M., Nardini, M.

Description: High resolution crystal structure of the histone fold dimer (NF-YB)-( NF-YC)