5o9j - Revision history

OCA at 11:22, 3 January 2024

OCA — Wed, 03 Jan 2024 11:22:16 GMT

←Older revision		Revision as of 11:22, 3 January 2024
Line 3:		Line 3:
	<StructureSection load='5o9j' size='340' side='right'caption='[[5o9j]], [[Resolution\|resolution]] 2.00Å' scene=''>		<StructureSection load='5o9j' size='340' side='right'caption='[[5o9j]], [[Resolution\|resolution]] 2.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5o9j]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/~~Metja Metja~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5O9J OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5O9J FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5o9j]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Methanocaldococcus_jannaschii_DSM_2661 Methanocaldococcus jannaschii DSM 2661]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5O9J OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5O9J FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=DIO:1,4-DIETHYLENE+DIOXIDE'>DIO</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MES:2-(N-MORPHOLINO)-ETHANESULFONIC+ACID'>MES</scene>, <scene name='pdbligand=NH4:AMMONIUM+ION'>NH4</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]] 2Å</td></tr>
-	~~<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">tfb, MJ0782 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=243232 METJA])~~</td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=DIO:1,4-DIETHYLENE+DIOXIDE'>DIO</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MES:2-(N-MORPHOLINO)-ETHANESULFONIC+ACID'>MES</scene>, <scene name='pdbligand=NH4:AMMONIUM+ION'>NH4</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=5o9j FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5o9j OCA], [https://pdbe.org/5o9j PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5o9j RCSB], [https://www.ebi.ac.uk/pdbsum/5o9j PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5o9j 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=5o9j FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5o9j OCA], [https://pdbe.org/5o9j PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5o9j RCSB], [https://www.ebi.ac.uk/pdbsum/5o9j PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5o9j ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/TF2B_METJA TF2B_METJA]] Stabilizes TBP binding to an archaeal box-A promoter. Also responsible for recruiting RNA polymerase II to the pre-initiation complex (DNA-TBP-TFIIB).	+	[https://www.uniprot.org/uniprot/TF2B_METJA TF2B_METJA] Stabilizes TBP binding to an archaeal box-A promoter. Also responsible for recruiting RNA polymerase II to the pre-initiation complex (DNA-TBP-TFIIB).
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
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	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Metja~~]]	+	[[Category: Methanocaldococcus jannaschii DSM 2661]]
-	[[Category: Iwai, H]]	+	[[Category: Iwai H]]
-	[[Category: Mikula~~, K M~~]]	+	[[Category: Mikula KM]]
-	[[Category: Wlodawer, A]]	+	[[Category: Wlodawer A]]
-	[[Category: Zhou, D]]	+	[[Category: Zhou D]]
-	~~[[Category: Hint fold]]~~	+
-	~~[[Category: Hydrolase]]~~	+
-	~~[[Category: Mini-intein]]~~	+
-	~~[[Category: Transcription factor iib~~]]	+

OCA at 10:56, 30 March 2022

OCA — Wed, 30 Mar 2022 10:56:09 GMT

←Older revision		Revision as of 10:56, 30 March 2022
Line 1:		Line 1:

	==Crystal structure of transcription factor IIB Mja mini-intein==		==Crystal structure of transcription factor IIB Mja mini-intein==
-	<StructureSection load='5o9j' size='340' side='right' caption='[[5o9j]], [[Resolution\|resolution]] 2.00Å' scene=''>	+	<StructureSection load='5o9j' size='340' side='right'caption='[[5o9j]], [[Resolution\|resolution]] 2.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5o9j]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Metja Metja]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5O9J OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5O9J FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5o9j]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Metja Metja]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5O9J OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5O9J FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=DIO:1,4-DIETHYLENE+DIOXIDE'>DIO</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MES:2-(N-MORPHOLINO)-ETHANESULFONIC+ACID'>MES</scene>, <scene name='pdbligand=NH4:AMMONIUM+ION'>NH4</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=DIO:1,4-DIETHYLENE+DIOXIDE'>DIO</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MES:2-(N-MORPHOLINO)-ETHANESULFONIC+ACID'>MES</scene>, <scene name='pdbligand=NH4:AMMONIUM+ION'>NH4</scene></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">tfb, MJ0782 ([~~http~~://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=243232 METJA])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">tfb, MJ0782 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=243232 METJA])</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=5o9j FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5o9j OCA], [~~http~~://pdbe.org/5o9j PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5o9j RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5o9j PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5o9j 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=5o9j FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5o9j OCA], [https://pdbe.org/5o9j PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5o9j RCSB], [https://www.ebi.ac.uk/pdbsum/5o9j PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5o9j ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[~~http~~://www.uniprot.org/uniprot/TF2B_METJA TF2B_METJA]] Stabilizes TBP binding to an archaeal box-A promoter. Also responsible for recruiting RNA polymerase II to the pre-initiation complex (DNA-TBP-TFIIB).	+	[[https://www.uniprot.org/uniprot/TF2B_METJA TF2B_METJA]] Stabilizes TBP binding to an archaeal box-A promoter. Also responsible for recruiting RNA polymerase II to the pre-initiation complex (DNA-TBP-TFIIB).
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 19:		Line 19:
	</div>		</div>
	<div class="pdbe-citations 5o9j" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 5o9j" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Transcription initiation factors 3D structures\|Transcription initiation factors 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
	[[Category: Metja]]		[[Category: Metja]]
	[[Category: Iwai, H]]		[[Category: Iwai, H]]

OCA at 07:44, 6 December 2017

OCA — Wed, 06 Dec 2017 07:44:06 GMT

←Older revision		Revision as of 07:44, 6 December 2017
Line 3:		Line 3:
	<StructureSection load='5o9j' size='340' side='right' caption='[[5o9j]], [[Resolution\|resolution]] 2.00Å' scene=''>		<StructureSection load='5o9j' size='340' side='right' caption='[[5o9j]], [[Resolution\|resolution]] 2.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5o9j]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5O9J OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5O9J FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5o9j]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Metja Metja]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5O9J OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5O9J FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=DIO:1,4-DIETHYLENE+DIOXIDE'>DIO</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MES:2-(N-MORPHOLINO)-ETHANESULFONIC+ACID'>MES</scene>, <scene name='pdbligand=NH4:AMMONIUM+ION'>NH4</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=DIO:1,4-DIETHYLENE+DIOXIDE'>DIO</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MES:2-(N-MORPHOLINO)-ETHANESULFONIC+ACID'>MES</scene>, <scene name='pdbligand=NH4:AMMONIUM+ION'>NH4</scene></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">tfb, MJ0782 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=243232 METJA])</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=5o9j FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5o9j OCA], [http://pdbe.org/5o9j PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5o9j RCSB], [http://www.ebi.ac.uk/pdbsum/5o9j PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5o9j 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=5o9j FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5o9j OCA], [http://pdbe.org/5o9j PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5o9j RCSB], [http://www.ebi.ac.uk/pdbsum/5o9j PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5o9j ProSAT]</span></td></tr>
	</table>		</table>
Line 22:		Line 23:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Metja]]
	[[Category: Iwai, H]]		[[Category: Iwai, H]]
	[[Category: Mikula, K M]]		[[Category: Mikula, K M]]

OCA at 06:00, 1 November 2017

OCA — Wed, 01 Nov 2017 06:00:58 GMT

←Older revision		Revision as of 06:00, 1 November 2017
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5o9j is ~~ON HOLD until Paper~~ Publication	+	==Crystal structure of transcription factor IIB Mja mini-intein==
		+	<StructureSection load='5o9j' size='340' side='right' caption='[[5o9j]], [[Resolution\|resolution]] 2.00Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[5o9j]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5O9J OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5O9J FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=DIO:1,4-DIETHYLENE+DIOXIDE'>DIO</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MES:2-(N-MORPHOLINO)-ETHANESULFONIC+ACID'>MES</scene>, <scene name='pdbligand=NH4:AMMONIUM+ION'>NH4</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=5o9j FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5o9j OCA], [http://pdbe.org/5o9j PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5o9j RCSB], [http://www.ebi.ac.uk/pdbsum/5o9j PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5o9j ProSAT]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/TF2B_METJA TF2B_METJA]] Stabilizes TBP binding to an archaeal box-A promoter. Also responsible for recruiting RNA polymerase II to the pre-initiation complex (DNA-TBP-TFIIB).
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Inteins are mobile genetic elements that are spliced out of proteins after translation. Some inteins contain a homing endonuclease (HEN) responsible for their propagation. Hedgehog/INTein (HINT) domains catalyzing protein splicing and their nested HEN domains are thought to be functionally independent because of the existence of functional mini-inteins without HEN domains. Despite the lack of obvious mutualism between HEN and HINT domains, HEN domains are persistently found at one specific site in inteins, indicating their potential functional role in protein splicing. Here we report crystal structures of inactive and active mini-inteins derived from inteins residing in the transcription factor IIB of Methanococcus jannaschii and Methanocaldococcus vulcanius, revealing a novel modified HINT fold that might provide new insights on the mutualism between the HEN and HINT domains. We propose an evolutionary model of inteins and a functional role of HEN domains in inteins.

-	~~Authors: Mikula, K.M~~., Iwai, H., ~~Zhou~~, D., ~~Wlodawer~~, A.	+	Structural basis for the persistence of homing endonucleases in transcription factor IIB inteins.,Iwai H, Mikula KM, Oeemig JS, Zhou D, Li M, Wlodawer A J Mol Biol. 2017 Oct 18. pii: S0022-2836(17)30498-9. doi:, 10.1016/j.jmb.2017.10.016. PMID:29055778<ref>PMID:29055778</ref>

-	~~Description: Crystal structure~~ of ~~transcription factor IIB Mja mini~~-~~intein~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased Structures~~]]	+	</div>
		+	<div class="pdbe-citations 5o9j" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Iwai, H]]
		+	[[Category: Mikula, K M]]
	[[Category: Wlodawer, A]]		[[Category: Wlodawer, A]]
-	[[Category: Mikula, K.M]]
	[[Category: Zhou, D]]		[[Category: Zhou, D]]
-	[[Category: ~~Iwai, H~~]]	+	[[Category: Hint fold]]
		+	[[Category: Hydrolase]]
		+	[[Category: Mini-intein]]
		+	[[Category: Transcription factor iib]]

OCA: Protected "5o9j" [edit=sysop:move=sysop]

OCA — Wed, 27 Sep 2017 12:11:14 GMT

Protected "5o9j" [edit=sysop:move=sysop]

←Older revision

Revision as of 12:11, 27 September 2017

OCA: New page: '''Unreleased structure''' The entry 5o9j is ON HOLD until Paper Publication Authors: Mikula, K.M., Iwai, H., Zhou, D., Wlodawer, A. Description: Crystal structure of transcription fac...

OCA — Wed, 27 Sep 2017 12:11:13 GMT

New page: '''Unreleased structure''' The entry 5o9j is ON HOLD until Paper Publication Authors: Mikula, K.M., Iwai, H., Zhou, D., Wlodawer, A. Description: Crystal structure of transcription fac...

New page

'''Unreleased structure'''

The entry 5o9j is ON HOLD until Paper Publication

Authors: Mikula, K.M., Iwai, H., Zhou, D., Wlodawer, A.

Description: Crystal structure of transcription factor IIB Mja mini-intein
[[Category: Unreleased Structures]]
[[Category: Wlodawer, A]]
[[Category: Mikula, K.M]]
[[Category: Zhou, D]]
[[Category: Iwai, H]]