4j2r - Revision history

OCA at 14:19, 8 November 2023

OCA — Wed, 08 Nov 2023 14:19:35 GMT

←Older revision		Revision as of 14:19, 8 November 2023
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	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4j2r]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Influenza_A_virus_(A/Puerto_Rico/8/1934(H1N1)) Influenza A virus (A/Puerto Rico/8/1934(H1N1))]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4J2R OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4J2R FirstGlance]. <br>		<table><tr><td colspan='2'>[[4j2r]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Influenza_A_virus_(A/Puerto_Rico/8/1934(H1N1)) Influenza A virus (A/Puerto Rico/8/1934(H1N1))]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4J2R OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4J2R 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=4j2r FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4j2r OCA], [https://pdbe.org/4j2r PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4j2r RCSB], [https://www.ebi.ac.uk/pdbsum/4j2r PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4j2r 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]] 2.42Å</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=4j2r FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4j2r OCA], [https://pdbe.org/4j2r PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4j2r RCSB], [https://www.ebi.ac.uk/pdbsum/4j2r PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4j2r ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==

OCA at 21:27, 16 November 2022

OCA — Wed, 16 Nov 2022 21:27:43 GMT

←Older revision		Revision as of 21:27, 16 November 2022
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	==Middle domain of influenza A virus RNA-dependent polymerase PB2==		==Middle domain of influenza A virus RNA-dependent polymerase PB2==
-	<StructureSection load='4j2r' size='340' side='right' caption='[[4j2r]], [[Resolution\|resolution]] 2.42Å' scene=''>	+	<StructureSection load='4j2r' size='340' side='right'caption='[[4j2r]], [[Resolution\|resolution]] 2.42Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4j2r]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~I34a1 I34a1~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4J2R OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=4J2R FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4j2r]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Influenza_A_virus_(A/Puerto_Rico/8/1934(H1N1)) Influenza A virus (A/Puerto Rico/8/1934(H1N1))]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4J2R OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4J2R FirstGlance]. <br>
-	</td></tr>~~<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3cw4\|3cw4]]</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=4j2r FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4j2r OCA], [https://pdbe.org/4j2r PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4j2r RCSB], [https://www.ebi.ac.uk/pdbsum/4j2r PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4j2r ProSAT]</span></td></tr>
-	~~<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">PB2 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=211044 I34A1])</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=4j2r FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4j2r OCA], [~~http~~://pdbe.org/4j2r PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=4j2r RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/4j2r PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=4j2r ProSAT]</span></td></tr>	+
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/PB2_I34A1 PB2_I34A1]] Involved in transcription initiation and cap-stealing mechanism, in which cellular capped pre-mRNA are used to generate primers for viral transcription. Binds the cap of the target pre-RNA which is subsequently cleaved by PB1. May play a role in genome replication (By similarity).	+	[https://www.uniprot.org/uniprot/PB2_I34A1 PB2_I34A1] Involved in transcription initiation and cap-stealing mechanism, in which cellular capped pre-mRNA are used to generate primers for viral transcription. Binds the cap of the target pre-RNA which is subsequently cleaved by PB1. May play a role in genome replication (By similarity).
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
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	==See Also==		==See Also==
-	*[[RNA polymerase\|RNA polymerase]]	+	*[[RNA polymerase 3D structures\|RNA polymerase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~I34a1~~]]	+	[[Category: Large Structures]]
-	[[Category: Hatakeyama, D]]	+	[[Category: Hatakeyama D]]
-	[[Category: Kuzuhara, T]]	+	[[Category: Kuzuhara T]]
-	[[Category: Qiu, H]]	+	[[Category: Qiu H]]
-	[[Category: Tsuge, H]]	+	[[Category: Tsuge H]]
-	[[Category: Tsumori, Y]]	+	[[Category: Tsumori Y]]
-	[[Category: Tsurumura, T]]	+	[[Category: Tsurumura T]]
-	~~[[Category: Cap-binding domain]]~~	+
-	~~[[Category: Cap-snatching]]~~	+
-	~~[[Category: Viral protein~~]]	+

OCA at 12:06, 5 August 2016

OCA — Fri, 05 Aug 2016 12:06:58 GMT

←Older revision		Revision as of 12:06, 5 August 2016
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		+
	==Middle domain of influenza A virus RNA-dependent polymerase PB2==		==Middle domain of influenza A virus RNA-dependent polymerase PB2==
	<StructureSection load='4j2r' size='340' side='right' caption='[[4j2r]], [[Resolution\|resolution]] 2.42Å' scene=''>		<StructureSection load='4j2r' size='340' side='right' caption='[[4j2r]], [[Resolution\|resolution]] 2.42Å' scene=''>
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	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3cw4\|3cw4]]</td></tr>		</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3cw4\|3cw4]]</td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">PB2 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=211044 I34A1])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">PB2 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=211044 I34A1])</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=4j2r FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4j2r OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4j2r RCSB], [http://www.ebi.ac.uk/pdbsum/4j2r 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=4j2r FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4j2r OCA], [http://pdbe.org/4j2r PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4j2r RCSB], [http://www.ebi.ac.uk/pdbsum/4j2r PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4j2r ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 17:		Line 18:
	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 4j2r" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[RNA polymerase\|RNA polymerase]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 18:42, 25 December 2014

OCA — Thu, 25 Dec 2014 18:42:01 GMT

←Older revision		Revision as of 18:42, 25 December 2014
Line 1:		Line 1:
-	~~{{STRUCTURE_4j2r\| PDB=4j2r \| SCENE= }}~~	+	==Middle domain of influenza A virus RNA-dependent polymerase PB2==
-	===Middle domain of influenza A virus RNA-dependent polymerase PB2===	+	<StructureSection load='4j2r' size='340' side='right' caption='[[4j2r]], [[Resolution\|resolution]] 2.42Å' scene=''>
-	~~{{ABSTRACT_PUBMED_24419622}}~~	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[4j2r]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/I34a1 I34a1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4J2R OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4J2R FirstGlance]. <br>
-	==Function==	+	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3cw4\|3cw4]]</td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">PB2 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=211044 I34A1])</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=4j2r FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4j2r OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4j2r RCSB], [http://www.ebi.ac.uk/pdbsum/4j2r PDBsum]</span></td></tr>
		+	</table>
		+	== Function ==
	[[http://www.uniprot.org/uniprot/PB2_I34A1 PB2_I34A1]] Involved in transcription initiation and cap-stealing mechanism, in which cellular capped pre-mRNA are used to generate primers for viral transcription. Binds the cap of the target pre-RNA which is subsequently cleaved by PB1. May play a role in genome replication (By similarity).		[[http://www.uniprot.org/uniprot/PB2_I34A1 PB2_I34A1]] Involved in transcription initiation and cap-stealing mechanism, in which cellular capped pre-mRNA are used to generate primers for viral transcription. Binds the cap of the target pre-RNA which is subsequently cleaved by PB1. May play a role in genome replication (By similarity).
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	In the last hundred years, four influenza pandemics have been experienced, beginning with that in Spain in 1918. Influenza A virus causes severe pneumonia and its RNA polymerase is an important target for drug design. The influenza A (H1N1) virus has eight ribonucleoprotein complexes, which are composed of viral RNA, RNA polymerases and nucleoproteins. PB2 forms part of the RNA polymerase complex and plays an important role in binding to the cap structure of host mRNA. The middle domain of PB2 includes a cap-binding site. The structure of PB2 from H1N1 complexed with m(7)GTP has not been reported. Plate-like crystals of the middle domain of PB2 from H1N1 were obtained, but the quality of these crystals was not good. An attempt was made to crystallize the middle domain of PB2 complexed with m(7)GTP using a soaking method; however, electron density for m(7)GTP was not observed on preliminary X-ray diffraction analysis. This protein has hydrophobic residues on its surface and is stable in the presence of high salt concentrations. To improve the solubility, a surface double mutant (P453H and I471T) was prepared. These mutations change the surface electrostatic potential drastically. The protein was successfully prepared at a lower salt concentration and good cube-shaped crystals were obtained using this protein. Here, the crystallization and preliminary X-ray diffraction analysis of this mutant of the middle domain of PB2 are reported.

-	~~==About this Structure==~~	+	Crystallization and preliminary X-ray diffraction studies of a surface mutant of the middle domain of PB2 from human influenza A (H1N1) virus.,Tsurumura T, Qiu H, Yoshida T, Tsumori Y, Tsuge H Acta Crystallogr F Struct Biol Commun. 2014 Jan;70(Pt 1):72-5. doi:, 10.1107/S2053230X13032603. Epub 2013 Dec 24. PMID:24419622<ref>PMID:24419622</ref>
-	~~[[4j2r]] is~~ a ~~2 chain structure. Full crystallographic information is available~~ from ~~[http://oca~~.~~weizmann~~.ac.il/~~oca-bin/ocashort?id=4J2R OCA]~~.	+

-	==~~Reference~~==	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	~~<ref group="xtra">PMID:024419622</ref>~~<references ~~group="xtra"~~/><~~references~~/>	+	</div>
-	[[Category: Hatakeyama, D.]]	+	== References ==
-	[[Category: Kuzuhara, T.]]	+	<references/>
-	[[Category: Qiu, H.]]	+	__TOC__
-	[[Category: Tsuge, H.]]	+	</StructureSection>
-	[[Category: Tsumori, Y.]]	+	[[Category: I34a1]]
-	[[Category: Tsurumura, T.]]	+	[[Category: Hatakeyama, D]]
		+	[[Category: Kuzuhara, T]]
		+	[[Category: Qiu, H]]
		+	[[Category: Tsuge, H]]
		+	[[Category: Tsumori, Y]]
		+	[[Category: Tsurumura, T]]
	[[Category: Cap-binding domain]]		[[Category: Cap-binding domain]]
	[[Category: Cap-snatching]]		[[Category: Cap-snatching]]
	[[Category: Viral protein]]		[[Category: Viral protein]]

OCA at 11:18, 5 February 2014

OCA — Wed, 05 Feb 2014 11:18:00 GMT

←Older revision		Revision as of 11:18, 5 February 2014
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-	~~'''Unreleased structure'''~~	+	{{STRUCTURE_4j2r\| PDB=4j2r \| SCENE= }}
		+	===Middle domain of influenza A virus RNA-dependent polymerase PB2===
		+	{{ABSTRACT_PUBMED_24419622}}

-	~~The entry 4j2r~~ is ~~ON HOLD until Paper Publication~~	+	==Function==
		+	[[http://www.uniprot.org/uniprot/PB2_I34A1 PB2_I34A1]] Involved in transcription initiation and cap-stealing mechanism, in which cellular capped pre-mRNA are used to generate primers for viral transcription. Binds the cap of the target pre-RNA which is subsequently cleaved by PB1. May play a role in genome replication (By similarity).

-	~~Authors~~: ~~Qiu, H., Tsurumura, T., Tsumori, Y~~.~~, Hatakeyama, D~~.~~, Kuzuhara, T~~.~~, Tsuge, H~~.	+	==About this Structure==
		+	[[4j2r]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4J2R OCA].

-	~~Description~~: ~~Middle~~ domain ~~of influenza A virus RNA~~-~~dependent polymerase PB2~~	+	==Reference==
		+	<ref group="xtra">PMID:024419622</ref><references group="xtra"/><references/>
		+	[[Category: Hatakeyama, D.]]
		+	[[Category: Kuzuhara, T.]]
		+	[[Category: Qiu, H.]]
		+	[[Category: Tsuge, H.]]
		+	[[Category: Tsumori, Y.]]
		+	[[Category: Tsurumura, T.]]
		+	[[Category: Cap-binding domain]]
		+	[[Category: Cap-snatching]]
		+	[[Category: Viral protein]]

OCA at 14:23, 27 February 2013

OCA — Wed, 27 Feb 2013 14:23:05 GMT

←Older revision		Revision as of 14:23, 27 February 2013
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 4j2r is ON HOLD	+	The entry 4j2r is ON HOLD until Paper Publication

	Authors: Qiu, H., Tsurumura, T., Tsumori, Y., Hatakeyama, D., Kuzuhara, T., Tsuge, H.		Authors: Qiu, H., Tsurumura, T., Tsumori, Y., Hatakeyama, D., Kuzuhara, T., Tsuge, H.

	Description: Middle domain of influenza A virus RNA-dependent polymerase PB2		Description: Middle domain of influenza A virus RNA-dependent polymerase PB2

OCA at 13:29, 20 February 2013

OCA — Wed, 20 Feb 2013 13:29:15 GMT

←Older revision		Revision as of 13:29, 20 February 2013
Line 3:		Line 3:
	The entry 4j2r is ON HOLD		The entry 4j2r is ON HOLD

-	Authors: H. ~~Qiu~~, T. ~~Tsurumura~~, Y. ~~Tsumori~~, D. ~~Hatakeyama~~, T. ~~Kuzuhara~~, H. ~~Tsuge~~	+	Authors: Qiu, H., Tsurumura, T., Tsumori, Y., Hatakeyama, D., Kuzuhara, T., Tsuge, H.

	Description: Middle domain of influenza A virus RNA-dependent polymerase PB2		Description: Middle domain of influenza A virus RNA-dependent polymerase PB2

OCA: Protected "4j2r" [edit=sysop:move=sysop]

OCA — Wed, 13 Feb 2013 10:10:36 GMT

Protected "4j2r" [edit=sysop:move=sysop]

←Older revision

Revision as of 10:10, 13 February 2013

OCA: New page: '''Unreleased structure''' The entry 4j2r is ON HOLD Authors: H. Qiu, T. Tsurumura, Y. Tsumori, D. Hatakeyama, T. Kuzuhara, H. Tsuge Description: Middle domain of influenza A virus RNA...

OCA — Wed, 13 Feb 2013 10:10:35 GMT

New page: '''Unreleased structure''' The entry 4j2r is ON HOLD Authors: H. Qiu, T. Tsurumura, Y. Tsumori, D. Hatakeyama, T. Kuzuhara, H. Tsuge Description: Middle domain of influenza A virus RNA...

New page

'''Unreleased structure'''

The entry 4j2r is ON HOLD

Authors: H. Qiu, T. Tsurumura, Y. Tsumori, D. Hatakeyama, T. Kuzuhara, H. Tsuge

Description: Middle domain of influenza A virus RNA-dependent polymerase PB2