1qnb - Revision history

OCA at 09:02, 9 May 2024

OCA — Thu, 09 May 2024 09:02:45 GMT

←Older revision		Revision as of 09:02, 9 May 2024
Line 19:		Line 19:
	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=1qnb ConSurf].		</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=1qnb ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Cocrystal structures of wild-type TATA box-binding protein (TBP) recognizing 10 naturally occurring TATA elements have been determined at 2.3-1.8 A resolution, and compared with our 1.9 A resolution structure of TBP bound to the Adenovirus major late promoter (AdMLP) TATA box (5'-TATAAAAG-3'). Minor-groove recognition by the saddle-shaped protein induces the same conformational change in each of these oligonucleotides, despite variations in promoter sequence that reduce the efficiency of transcription initiation. Three molecular mechanisms explain assembly of diverse TBP-TATA element complexes. (1) T --> A and A --> T transversions leave the minor-groove face unchanged, permitting formation of TBP-DNA complexes on many A/T-rich core promoter sequences. (2) Cavities in the interface between TBP and the minor-groove face of the AdMLP TATA box accommodate the exocyclic NH(2) groups of G in a TACA box and in a TATAAG box. (3) Formation of a C:G Hoogsteen basepair in a TATAAAC box eliminates steric clashes that would be produced by the Watson-Crick base pair. We conclude that the structure of the TBP-TATA box complex found at the heart of the polymerase II (pol II) transcription machinery has remained constant over the course of evolution, despite variations in TBP and its DNA targets.
		+
		+	TATA element recognition by the TATA box-binding protein has been conserved throughout evolution.,Patikoglou GA, Kim JL, Sun L, Yang SH, Kodadek T, Burley SK Genes Dev. 1999 Dec 15;13(24):3217-30. PMID:10617571<ref>PMID:10617571</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 1qnb" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
	*[[TATA-binding protein 3D structures\|TATA-binding protein 3D structures]]		*[[TATA-binding protein 3D structures\|TATA-binding protein 3D structures]]
	*[[Transcription initiation factors 3D structures\|Transcription initiation factors 3D structures]]		*[[Transcription initiation factors 3D structures\|Transcription initiation factors 3D structures]]
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 06:05, 17 April 2024

OCA — Wed, 17 Apr 2024 06:05:22 GMT

←Older revision		Revision as of 06:05, 17 April 2024
Line 1:		Line 1:

-	====	+	==Crystal structure of the T(-25) Adenovirus major late promoter TATA box variant bound to wild-type TBP (Arabidopsis thaliana TBP isoform 2). TATA element recognition by the TATA box-binding protein has been conserved throughout evolution.==
-	<StructureSection load='1qnb' size='340' side='right'caption='[[1qnb]]' scene=''>	+	<StructureSection load='1qnb' size='340' side='right'caption='[[1qnb]], [[Resolution\|resolution]] 2.23Å' 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= OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol= FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1qnb]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Arabidopsis_thaliana Arabidopsis thaliana]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1QNB OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1QNB FirstGlance]. <br>
-	</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=1qnb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1qnb OCA], [https://pdbe.org/1qnb PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1qnb RCSB], [https://www.ebi.ac.uk/pdbsum/1qnb PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1qnb ProSAT]</span></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]] 2.23Å</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=1qnb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1qnb OCA], [https://pdbe.org/1qnb PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1qnb RCSB], [https://www.ebi.ac.uk/pdbsum/1qnb PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1qnb ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/TBP1_ARATH TBP1_ARATH] General transcription factor that functions at the core of the DNA-binding multiprotein factor TFIID. Binding of TFIID to the TATA box is the initial transcriptional step of the pre-initiation complex (PIC), playing a role in the activation of eukaryotic genes transcribed by RNA polymerase II.
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 16:		Line 19:
	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=1qnb ConSurf].		</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=1qnb ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
		+
		+	==See Also==
		+	*[[TATA-binding protein 3D structures\|TATA-binding protein 3D structures]]
		+	*[[Transcription initiation factors 3D structures\|Transcription initiation factors 3D structures]]
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Arabidopsis thaliana]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Z-~~disk~~]]	+	[[Category: Burley SK]]
		+	[[Category: Kim JL]]
		+	[[Category: Kodadek T]]
		+	[[Category: Patikoglou GA]]
		+	[[Category: Sun L]]
		+	[[Category: Yang S-H]]

OCA at 09:59, 15 September 2021

OCA — Wed, 15 Sep 2021 09:59:44 GMT

←Older revision		Revision as of 09:59, 15 September 2021
Line 1:		Line 1:

-	==Crystal structure of the T(-25) Adenovirus major late promoter TATA box variant bound to wild-type TBP (Arabidopsis thaliana TBP isoform 2). TATA element recognition by the TATA box-binding protein has been conserved throughout evolution.==	+	====
-	<StructureSection load='1qnb' size='340' side='right'caption='[[1qnb]]~~, [[Resolution\|resolution]] 2.23Å~~' scene=''>	+	<StructureSection load='1qnb' size='340' side='right'caption='[[1qnb]]' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>~~[[1qnb]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/Arath Arath].~~ Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=~~1QNB~~ OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=~~1QNB~~ FirstGlance]. <br>	+	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id= OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol= FirstGlance]. <br>
-	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1qn3\|1qn3]], [[1qn4\|1qn4]], [[1qn5\|1qn5]], [[1qn6\|1qn6]], [[1qn7\|1qn7]], [[1qn8\|1qn8]], [[1qn9\|1qn9]], [[1qna\|1qna]], [[1qnc\|1qnc]], [[1qne\|1qne]]</td></tr>	+	</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=1qnb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1qnb OCA], [https://pdbe.org/1qnb PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1qnb RCSB], [https://www.ebi.ac.uk/pdbsum/1qnb PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1qnb 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=1qnb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1qnb OCA], [~~http~~://pdbe.org/1qnb PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=1qnb RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/1qnb PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=1qnb ProSAT]</span></td></tr>	+
	</table>		</table>
-	== Function ==
-	[[http://www.uniprot.org/uniprot/TBP1_ARATH TBP1_ARATH]] General transcription factor that functions at the core of the DNA-binding multiprotein factor TFIID. Binding of TFIID to the TATA box is the initial transcriptional step of the pre-initiation complex (PIC), playing a role in the activation of eukaryotic genes transcribed by RNA polymerase II.
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 19:		Line 16:
	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=1qnb ConSurf].		</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=1qnb ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	Cocrystal structures of wild-type TATA box-binding protein (TBP) recognizing 10 naturally occurring TATA elements have been determined at 2.3-1.8 A resolution, and compared with our 1.9 A resolution structure of TBP bound to the Adenovirus major late promoter (AdMLP) TATA box (5'-TATAAAAG-3'). Minor-groove recognition by the saddle-shaped protein induces the same conformational change in each of these oligonucleotides, despite variations in promoter sequence that reduce the efficiency of transcription initiation. Three molecular mechanisms explain assembly of diverse TBP-TATA element complexes. (1) T --> A and A --> T transversions leave the minor-groove face unchanged, permitting formation of TBP-DNA complexes on many A/T-rich core promoter sequences. (2) Cavities in the interface between TBP and the minor-groove face of the AdMLP TATA box accommodate the exocyclic NH(2) groups of G in a TACA box and in a TATAAG box. (3) Formation of a C:G Hoogsteen basepair in a TATAAAC box eliminates steric clashes that would be produced by the Watson-Crick base pair. We conclude that the structure of the TBP-TATA box complex found at the heart of the polymerase II (pol II) transcription machinery has remained constant over the course of evolution, despite variations in TBP and its DNA targets.
-
-	TATA element recognition by the TATA box-binding protein has been conserved throughout evolution.,Patikoglou GA, Kim JL, Sun L, Yang SH, Kodadek T, Burley SK Genes Dev. 1999 Dec 15;13(24):3217-30. PMID:10617571<ref>PMID:10617571</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 1qnb" style="background-color:#fffaf0;"></div>
-
-	==See Also==
-	*[[TATA-Binding Protein\|TATA-Binding Protein]]
-	*[[Transcription initiation factor\|Transcription initiation factor]]
-	== References ==
-	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Arath]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Burley, S K]]~~	+	[[Category: Z-disk]]
-	~~[[Category: Kim, J L]]~~	+
-	~~[[Category: Kodadek, T]]~~	+
-	~~[[Category: Patikoglou, G A]]~~	+
-	~~[[Category: Sun, L]]~~	+
-	~~[[Category: Yang, S H]]~~	+
-	~~[[Category: Tbp~~-~~tata element complex~~]]	+

OCA at 11:42, 4 December 2019

OCA — Wed, 04 Dec 2019 11:42:58 GMT

←Older revision		Revision as of 11:42, 4 December 2019
Line 1:		Line 1:

	==Crystal structure of the T(-25) Adenovirus major late promoter TATA box variant bound to wild-type TBP (Arabidopsis thaliana TBP isoform 2). TATA element recognition by the TATA box-binding protein has been conserved throughout evolution.==		==Crystal structure of the T(-25) Adenovirus major late promoter TATA box variant bound to wild-type TBP (Arabidopsis thaliana TBP isoform 2). TATA element recognition by the TATA box-binding protein has been conserved throughout evolution.==
-	<StructureSection load='1qnb' size='340' side='right' caption='[[1qnb]], [[Resolution\|resolution]] 2.23Å' scene=''>	+	<StructureSection load='1qnb' size='340' side='right'caption='[[1qnb]], [[Resolution\|resolution]] 2.23Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1qnb]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/Arath Arath]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1QNB OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1QNB FirstGlance]. <br>		<table><tr><td colspan='2'>[[1qnb]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/Arath Arath]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1QNB OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1QNB FirstGlance]. <br>
Line 37:		Line 37:
	</StructureSection>		</StructureSection>
	[[Category: Arath]]		[[Category: Arath]]
		+	[[Category: Large Structures]]
	[[Category: Burley, S K]]		[[Category: Burley, S K]]
	[[Category: Kim, J L]]		[[Category: Kim, J L]]

OCA at 08:07, 28 February 2018

OCA — Wed, 28 Feb 2018 08:07:14 GMT

←Older revision		Revision as of 08:07, 28 February 2018
Line 1:		Line 1:
-	==~~CRYSTAL STRUCTURE OF THE~~ T(-25) ~~ADENOVIRUS MAJOR LATE PROMOTER~~ TATA ~~BOX VARIANT BOUND TO WILD~~-~~TYPE~~ TBP (~~ARABIDOPSIS THALIANA~~ TBP ~~ISOFORM~~ 2). TATA ~~ELEMENT RECOGNITION BY THE~~ TATA ~~BOX~~-~~BINDING PROTEIN HAS BEEN CONSERVED THROUGHOUT EVOLUTION~~.==	+
		+	==Crystal structure of the T(-25) Adenovirus major late promoter TATA box variant bound to wild-type TBP (Arabidopsis thaliana TBP isoform 2). TATA element recognition by the TATA box-binding protein has been conserved throughout evolution.==
	<StructureSection load='1qnb' size='340' side='right' caption='[[1qnb]], [[Resolution\|resolution]] 2.23Å' scene=''>		<StructureSection load='1qnb' size='340' side='right' caption='[[1qnb]], [[Resolution\|resolution]] 2.23Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1qnb]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/Arath Arath]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1QNB OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1QNB FirstGlance]. <br>		<table><tr><td colspan='2'>[[1qnb]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/Arath Arath]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1QNB OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1QNB FirstGlance]. <br>
	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1qn3\|1qn3]], [[1qn4\|1qn4]], [[1qn5\|1qn5]], [[1qn6\|1qn6]], [[1qn7\|1qn7]], [[1qn8\|1qn8]], [[1qn9\|1qn9]], [[1qna\|1qna]], [[1qnc\|1qnc]], [[1qne\|1qne]]</td></tr>		</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1qn3\|1qn3]], [[1qn4\|1qn4]], [[1qn5\|1qn5]], [[1qn6\|1qn6]], [[1qn7\|1qn7]], [[1qn8\|1qn8]], [[1qn9\|1qn9]], [[1qna\|1qna]], [[1qnc\|1qnc]], [[1qne\|1qne]]</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=1qnb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1qnb OCA], [http://pdbe.org/1qnb PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1qnb RCSB], [http://www.ebi.ac.uk/pdbsum/1qnb 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=1qnb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1qnb OCA], [http://pdbe.org/1qnb PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1qnb RCSB], [http://www.ebi.ac.uk/pdbsum/1qnb PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1qnb ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 12:		Line 13:
	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/qn/1qnb_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/qn/1qnb_consurf.spt"</scriptWhenChecked>
	<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>		<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
	<text>to colour the structure by Evolutionary Conservation</text>		<text>to colour the structure by Evolutionary Conservation</text>
	</jmolCheckbox>		</jmolCheckbox>
-	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/~~chain_selection~~.php?pdb_ID=~~2ata~~ ConSurf].	+	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=1qnb ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 00:10, 12 September 2015

OCA — Sat, 12 Sep 2015 00:10:44 GMT

←Older revision		Revision as of 00:10, 12 September 2015
Line 2:		Line 2:
	<StructureSection load='1qnb' size='340' side='right' caption='[[1qnb]], [[Resolution\|resolution]] 2.23Å' scene=''>		<StructureSection load='1qnb' size='340' side='right' caption='[[1qnb]], [[Resolution\|resolution]] 2.23Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1qnb]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Arabidopsis_thaliana Arabidopsis thaliana~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1QNB OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1QNB FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1qnb]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/Arath Arath]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1QNB OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1QNB FirstGlance]. <br>
	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1qn3\|1qn3]], [[1qn4\|1qn4]], [[1qn5\|1qn5]], [[1qn6\|1qn6]], [[1qn7\|1qn7]], [[1qn8\|1qn8]], [[1qn9\|1qn9]], [[1qna\|1qna]], [[1qnc\|1qnc]], [[1qne\|1qne]]</td></tr>		</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1qn3\|1qn3]], [[1qn4\|1qn4]], [[1qn5\|1qn5]], [[1qn6\|1qn6]], [[1qn7\|1qn7]], [[1qn8\|1qn8]], [[1qn9\|1qn9]], [[1qna\|1qna]], [[1qnc\|1qnc]], [[1qne\|1qne]]</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=1qnb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1qnb OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1qnb RCSB], [http://www.ebi.ac.uk/pdbsum/1qnb 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=1qnb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1qnb OCA], [http://pdbe.org/1qnb PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1qnb RCSB], [http://www.ebi.ac.uk/pdbsum/1qnb PDBsum]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/TBP1_ARATH TBP1_ARATH]] General transcription factor that functions at the core of the DNA-binding multiprotein factor TFIID. Binding of TFIID to the TATA box is the initial transcriptional step of the pre-initiation complex (PIC), playing a role in the activation of eukaryotic genes transcribed by RNA polymerase II.
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 24:		Line 26:
	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 1qnb" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
Line 32:		Line 35:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Arabidopsis thaliana~~]]	+	[[Category: Arath]]
	[[Category: Burley, S K]]		[[Category: Burley, S K]]
	[[Category: Kim, J L]]		[[Category: Kim, J L]]

OCA at 07:24, 6 January 2015

OCA — Tue, 06 Jan 2015 07:24:30 GMT

←Older revision		Revision as of 07:24, 6 January 2015
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1qnb]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/Arabidopsis_thaliana Arabidopsis thaliana]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1QNB OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1QNB FirstGlance]. <br>		<table><tr><td colspan='2'>[[1qnb]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/Arabidopsis_thaliana Arabidopsis thaliana]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1QNB OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1QNB FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1qn3\|1qn3]], [[1qn4\|1qn4]], [[1qn5\|1qn5]], [[1qn6\|1qn6]], [[1qn7\|1qn7]], [[1qn8\|1qn8]], [[1qn9\|1qn9]], [[1qna\|1qna]], [[1qnc\|1qnc]], [[1qne\|1qne]]</td></tr>	+	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1qn3\|1qn3]], [[1qn4\|1qn4]], [[1qn5\|1qn5]], [[1qn6\|1qn6]], [[1qn7\|1qn7]], [[1qn8\|1qn8]], [[1qn9\|1qn9]], [[1qna\|1qna]], [[1qnc\|1qnc]], [[1qne\|1qne]]</td></tr>
-	<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1qnb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1qnb OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1qnb RCSB], [http://www.ebi.ac.uk/pdbsum/1qnb 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=1qnb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1qnb OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1qnb RCSB], [http://www.ebi.ac.uk/pdbsum/1qnb PDBsum]</span></td></tr>
-	<table>	+	</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 33:		Line 33:
	</StructureSection>		</StructureSection>
	[[Category: Arabidopsis thaliana]]		[[Category: Arabidopsis thaliana]]
-	[[Category: Burley, S K.]]	+	[[Category: Burley, S K]]
-	[[Category: Kim, J L.]]	+	[[Category: Kim, J L]]
-	[[Category: Kodadek, T.]]	+	[[Category: Kodadek, T]]
-	[[Category: Patikoglou, G A.]]	+	[[Category: Patikoglou, G A]]
-	[[Category: Sun, L.]]	+	[[Category: Sun, L]]
-	[[Category: Yang, S H.]]	+	[[Category: Yang, S H]]
	[[Category: Tbp-tata element complex]]		[[Category: Tbp-tata element complex]]

OCA at 22:32, 28 September 2014

OCA — Sun, 28 Sep 2014 22:32:58 GMT

←Older revision		Revision as of 22:32, 28 September 2014
Line 1:		Line 1:
-	[[~~Image:~~1qnb.~~png~~\|~~left~~\|200px]]	+	==CRYSTAL STRUCTURE OF THE T(-25) ADENOVIRUS MAJOR LATE PROMOTER TATA BOX VARIANT BOUND TO WILD-TYPE TBP (ARABIDOPSIS THALIANA TBP ISOFORM 2). TATA ELEMENT RECOGNITION BY THE TATA BOX-BINDING PROTEIN HAS BEEN CONSERVED THROUGHOUT EVOLUTION.==
		+	<StructureSection load='1qnb' size='340' side='right' caption='[[1qnb]], [[Resolution\|resolution]] 2.23Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[1qnb]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/Arabidopsis_thaliana Arabidopsis thaliana]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1QNB OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1QNB FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1qn3\|1qn3]], [[1qn4\|1qn4]], [[1qn5\|1qn5]], [[1qn6\|1qn6]], [[1qn7\|1qn7]], [[1qn8\|1qn8]], [[1qn9\|1qn9]], [[1qna\|1qna]], [[1qnc\|1qnc]], [[1qne\|1qne]]</td></tr>
		+	<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1qnb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1qnb OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1qnb RCSB], [http://www.ebi.ac.uk/pdbsum/1qnb PDBsum]</span></td></tr>
		+	<table>
		+	== Evolutionary Conservation ==
		+	[[Image:Consurf_key_small.gif\|200px\|right]]
		+	Check<jmol>
		+	<jmolCheckbox>
		+	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/qn/1qnb_consurf.spt"</scriptWhenChecked>
		+	<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
		+	<text>to colour the structure by Evolutionary Conservation</text>
		+	</jmolCheckbox>
		+	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/chain_selection.php?pdb_ID=2ata ConSurf].
		+	<div style="clear:both"></div>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Cocrystal structures of wild-type TATA box-binding protein (TBP) recognizing 10 naturally occurring TATA elements have been determined at 2.3-1.8 A resolution, and compared with our 1.9 A resolution structure of TBP bound to the Adenovirus major late promoter (AdMLP) TATA box (5'-TATAAAAG-3'). Minor-groove recognition by the saddle-shaped protein induces the same conformational change in each of these oligonucleotides, despite variations in promoter sequence that reduce the efficiency of transcription initiation. Three molecular mechanisms explain assembly of diverse TBP-TATA element complexes. (1) T --> A and A --> T transversions leave the minor-groove face unchanged, permitting formation of TBP-DNA complexes on many A/T-rich core promoter sequences. (2) Cavities in the interface between TBP and the minor-groove face of the AdMLP TATA box accommodate the exocyclic NH(2) groups of G in a TACA box and in a TATAAG box. (3) Formation of a C:G Hoogsteen basepair in a TATAAAC box eliminates steric clashes that would be produced by the Watson-Crick base pair. We conclude that the structure of the TBP-TATA box complex found at the heart of the polymerase II (pol II) transcription machinery has remained constant over the course of evolution, despite variations in TBP and its DNA targets.

-	~~{{STRUCTURE_1qnb\| PDB=1qnb \| SCENE= }}~~	+	TATA element recognition by the TATA box-binding protein has been conserved throughout evolution.,Patikoglou GA, Kim JL, Sun L, Yang SH, Kodadek T, Burley SK Genes Dev. 1999 Dec 15;13(24):3217-30. PMID:10617571<ref>PMID:10617571</ref>

-	===CRYSTAL STRUCTURE OF THE T(-25) ADENOVIRUS MAJOR LATE PROMOTER TATA BOX VARIANT BOUND TO WILD-TYPE TBP (ARABIDOPSIS THALIANA TBP ISOFORM 2). TATA ELEMENT RECOGNITION BY THE TATA BOX-BINDING PROTEIN HAS BEEN CONSERVED THROUGHOUT EVOLUTION.===	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_10617571}}~~	+
-		+
-	~~==About this Structure==~~	+
-	~~[[1qnb]] is~~ a ~~6 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Arabidopsis_thaliana Arabidopsis thaliana]~~. ~~Full crystallographic information is available from [http:~~/~~/oca.weizmann.ac.il/oca-bin/ocashort?id=1QNB OCA].~~	+

	==See Also==		==See Also==
	*[[TATA-Binding Protein\|TATA-Binding Protein]]		*[[TATA-Binding Protein\|TATA-Binding Protein]]
	*[[Transcription initiation factor\|Transcription initiation factor]]		*[[Transcription initiation factor\|Transcription initiation factor]]
-		+	== References ==
-	==~~Reference~~==	+	<references/>
-	<~~ref group="xtra">PMID:010617571<~~/~~ref~~><~~references group="xtra"~~/>	+	__TOC__
		+	</StructureSection>
	[[Category: Arabidopsis thaliana]]		[[Category: Arabidopsis thaliana]]
	[[Category: Burley, S K.]]		[[Category: Burley, S K.]]

OCA at 21:44, 20 October 2012

OCA — Sat, 20 Oct 2012 21:44:06 GMT

←Older revision		Revision as of 21:44, 20 October 2012
Line 8:		Line 8:

	==About this Structure==		==About this Structure==
-	[[1qnb]] is a 6 chain structure ~~of [[TATA-Binding Protein]]~~ with sequence from [http://en.wikipedia.org/wiki/Arabidopsis_thaliana Arabidopsis thaliana]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1QNB OCA].	+	[[1qnb]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/Arabidopsis_thaliana Arabidopsis thaliana]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1QNB OCA].

	==See Also==		==See Also==
	*[[TATA-Binding Protein\|TATA-Binding Protein]]		*[[TATA-Binding Protein\|TATA-Binding Protein]]
		+	*[[Transcription initiation factor\|Transcription initiation factor]]

	==Reference==		==Reference==

OCA at 14:07, 27 July 2012

OCA — Fri, 27 Jul 2012 14:07:08 GMT

←Older revision		Revision as of 14:07, 27 July 2012
Line 1:		Line 1:
	[[Image:1qnb.png\|left\|200px]]		[[Image:1qnb.png\|left\|200px]]

-	<!--
-	The line below this paragraph, containing "STRUCTURE_1qnb", creates the "Structure Box" on the page.
-	You may change the PDB parameter (which sets the PDB file loaded into the applet)
-	or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
-	or leave the SCENE parameter empty for the default display.
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	{{STRUCTURE_1qnb\| PDB=1qnb \| SCENE= }}		{{STRUCTURE_1qnb\| PDB=1qnb \| SCENE= }}

	===CRYSTAL STRUCTURE OF THE T(-25) ADENOVIRUS MAJOR LATE PROMOTER TATA BOX VARIANT BOUND TO WILD-TYPE TBP (ARABIDOPSIS THALIANA TBP ISOFORM 2). TATA ELEMENT RECOGNITION BY THE TATA BOX-BINDING PROTEIN HAS BEEN CONSERVED THROUGHOUT EVOLUTION.===		===CRYSTAL STRUCTURE OF THE T(-25) ADENOVIRUS MAJOR LATE PROMOTER TATA BOX VARIANT BOUND TO WILD-TYPE TBP (ARABIDOPSIS THALIANA TBP ISOFORM 2). TATA ELEMENT RECOGNITION BY THE TATA BOX-BINDING PROTEIN HAS BEEN CONSERVED THROUGHOUT EVOLUTION.===

-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_10617571}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 10617571 is the PubMed ID number.
-	-->
	{{ABSTRACT_PUBMED_10617571}}		{{ABSTRACT_PUBMED_10617571}}

Line 22:		Line 11:

	==See Also==		==See Also==
-	*[[TATA-Binding Protein]]	+	*[[TATA-Binding Protein\|TATA-Binding Protein]]

	==Reference==		==Reference==
-	<ref group="xtra">PMID:~~10617571~~</ref><references group="xtra"/>	+	<ref group="xtra">PMID:010617571</ref><references group="xtra"/>
	[[Category: Arabidopsis thaliana]]		[[Category: Arabidopsis thaliana]]
	[[Category: Burley, S K.]]		[[Category: Burley, S K.]]