6u8k - Revision history

OCA at 07:46, 11 October 2023

OCA — Wed, 11 Oct 2023 07:46:11 GMT

←Older revision		Revision as of 07:46, 11 October 2023
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	<StructureSection load='6u8k' size='340' side='right'caption='[[6u8k]], [[Resolution\|resolution]] 2.75Å' scene=''>		<StructureSection load='6u8k' size='340' side='right'caption='[[6u8k]], [[Resolution\|resolution]] 2.75Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6u8k]] is a 9 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=6U8K OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=6U8K FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6u8k]] is a 9 chain structure with sequence from [https://en.wikipedia.org/wiki/Hepacivirus_C Hepacivirus C] and [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6U8K OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6U8K FirstGlance]. <br>
-	</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=6u8k FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6u8k OCA], [~~http~~://pdbe.org/6u8k PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6u8k RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6u8k PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6u8k 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]] 2.75Å</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=6u8k FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6u8k OCA], [https://pdbe.org/6u8k PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6u8k RCSB], [https://www.ebi.ac.uk/pdbsum/6u8k PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6u8k ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
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	</div>		</div>
	<div class="pdbe-citations 6u8k" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 6u8k" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Antibody 3D structures\|Antibody 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Human~~]]	+	[[Category: Hepacivirus C]]
		+	[[Category: Homo sapiens]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Huang, H]]	+	[[Category: Huang H]]
-	[[Category: Koirala, D]]	+	[[Category: Koirala D]]
-	[[Category: Koldobskaya, Y]]	+	[[Category: Koldobskaya Y]]
-	[[Category: Lewicka, A]]	+	[[Category: Lewicka A]]
-	[[Category: Piccirilli~~, J A]]~~	+	[[Category: Piccirilli JA]]
-	~~[[Category: Antibody-assisted rna crystallography]]~~	+
-	~~[[Category: Hepatitis c virus]]~~	+
-	~~[[Category: Junction iiiabc]]~~	+
-	~~[[Category: Rna]]~~	+
-	~~[[Category: Rna-immune system complex]]~~	+
-	~~[[Category: Viral rna domain]]~~	+
-	~~[[Category: Viral translation~~]]	+

OCA at 13:19, 25 December 2019

OCA — Wed, 25 Dec 2019 13:19:36 GMT

←Older revision		Revision as of 13:19, 25 December 2019
Line 3:		Line 3:
	<StructureSection load='6u8k' size='340' side='right'caption='[[6u8k]], [[Resolution\|resolution]] 2.75Å' scene=''>		<StructureSection load='6u8k' size='340' side='right'caption='[[6u8k]], [[Resolution\|resolution]] 2.75Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6u8k]] is a 9 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6U8K OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6U8K FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6u8k]] is a 9 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=6U8K OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6U8K FirstGlance]. <br>
	</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=6u8k FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6u8k OCA], [http://pdbe.org/6u8k PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6u8k RCSB], [http://www.ebi.ac.uk/pdbsum/6u8k PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6u8k ProSAT]</span></td></tr>		</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=6u8k FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6u8k OCA], [http://pdbe.org/6u8k PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6u8k RCSB], [http://www.ebi.ac.uk/pdbsum/6u8k PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6u8k ProSAT]</span></td></tr>
	</table>		</table>
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Human]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: Huang, H]]		[[Category: Huang, H]]

OCA at 08:21, 4 December 2019

OCA — Wed, 04 Dec 2019 08:21:00 GMT

←Older revision		Revision as of 08:21, 4 December 2019
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-	'''Unreleased structure'''

-	~~The entry~~ 6u8k is ~~ON HOLD until Paper~~ Publication	+	==Crystal structure of hepatitis C virus IRES junction IIIabc in complex with Fab HCV3==
		+	<StructureSection load='6u8k' size='340' side='right'caption='[[6u8k]], [[Resolution\|resolution]] 2.75Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[6u8k]] is a 9 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6U8K OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6U8K FirstGlance]. <br>
		+	</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=6u8k FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6u8k OCA], [http://pdbe.org/6u8k PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6u8k RCSB], [http://www.ebi.ac.uk/pdbsum/6u8k PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6u8k ProSAT]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Structured RNA elements within the internal ribosome entry site (IRES) of hepatitis C virus (HCV) genome hijack host cell machinery for translation initiation through a cap-independent mechanism. Here, using a phage display selection, we obtained two antibody fragments (Fabs), HCV2 and HCV3, against HCV IRES that bind the RNA with dissociation constants of 32 +/- 7 nM and 37 +/- 8 nM respectively, specifically recognizing the so-called junction IIIabc (JIIIabc). We used these Fabs as crystallization chaperones and determined the high-resolution crystal structures of JIIIabc - HCV2 and - HCV3 complexes at 1.81-A and 2.75-A resolution respectively, revealing an anti-parallel four-way junction with the so-called IIIa and IIIc sub-domains brought together through tertiary interactions. The RNA conformation observed in the structures supports the structural model for this region derived from cryo-EM data for the HCV IRES - 40S ribosome complex, suggesting that the tertiary fold of the RNA pre-organizes the domain for interactions with the 40S ribosome. Strikingly, both Fabs and the ribosomal protein eS27 not only interact with a common subset of nucleotides within the JIIIabc but also use physio-chemically similar sets of protein residues to do so, suggesting that the RNA surface is well-suited for interactions with proteins, perhaps analogous to the 'hot spot' concept elaborated for protein-protein interactions. Using a rabbit reticulocyte lysate-based translation assay with a bicistronic reporter construct, we further demonstrated that Fabs HCV2 and HCV3 specifically inhibit the HCV IRES-directed translation, implicating disruption of the JIIIabc - ribosome interaction as a potential therapeutic strategy against HCV.

-	~~Authors:~~ Koirala, D., Lewicka, A., Koldobskaya, Y., Huang, H., Piccirilli~~, J~~.A.	+	Synthetic antibody binding to a pre-organized IRES RNA domain of hepatitis C virus inhibits translation.,Koirala D, Lewicka A, Koldobskaya Y, Huang H, Piccirilli JA ACS Chem Biol. 2019 Nov 25. doi: 10.1021/acschembio.9b00785. PMID:31765566<ref>PMID:31765566</ref>

-	~~Description: Crystal structure~~ of ~~hepatitis C virus IRES junction IIIabc in complex with Fab HCV3~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased~~ Structures]]	+	</div>
		+	<div class="pdbe-citations 6u8k" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Huang, H]]
		+	[[Category: Koirala, D]]
	[[Category: Koldobskaya, Y]]		[[Category: Koldobskaya, Y]]
	[[Category: Lewicka, A]]		[[Category: Lewicka, A]]
-	[[Category: ~~Koirala~~, D]]	+	[[Category: Piccirilli, J A]]
-	[[Category: ~~Huang, H~~]]	+	[[Category: Antibody-assisted rna crystallography]]
-	[[Category: ~~Piccirilli, J.A~~]]	+	[[Category: Hepatitis c virus]]
		+	[[Category: Junction iiiabc]]
		+	[[Category: Rna]]
		+	[[Category: Rna-immune system complex]]
		+	[[Category: Viral rna domain]]
		+	[[Category: Viral translation]]

OCA at 13:45, 20 November 2019

OCA — Wed, 20 Nov 2019 13:45:17 GMT

←Older revision		Revision as of 13:45, 20 November 2019
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 6u8k is ON HOLD	+	The entry 6u8k is ON HOLD until Paper Publication

	Authors: Koirala, D., Lewicka, A., Koldobskaya, Y., Huang, H., Piccirilli, J.A.		Authors: Koirala, D., Lewicka, A., Koldobskaya, Y., Huang, H., Piccirilli, J.A.

OCA: Protected "6u8k" [edit=sysop:move=sysop]

OCA — Wed, 02 Oct 2019 08:23:33 GMT

Protected "6u8k" [edit=sysop:move=sysop]

←Older revision

Revision as of 08:23, 2 October 2019

OCA: New page: '''Unreleased structure''' The entry 6u8k is ON HOLD Authors: Koirala, D., Lewicka, A., Koldobskaya, Y., Huang, H., Piccirilli, J.A. Description: Crystal structure of hepatitis C virus...

OCA — Wed, 02 Oct 2019 08:23:31 GMT

New page: '''Unreleased structure''' The entry 6u8k is ON HOLD Authors: Koirala, D., Lewicka, A., Koldobskaya, Y., Huang, H., Piccirilli, J.A. Description: Crystal structure of hepatitis C virus...

New page

'''Unreleased structure'''

The entry 6u8k is ON HOLD

Authors: Koirala, D., Lewicka, A., Koldobskaya, Y., Huang, H., Piccirilli, J.A.

Description: Crystal structure of hepatitis C virus IRES junction IIIabc in complex with Fab HCV3
[[Category: Unreleased Structures]]
[[Category: Koldobskaya, Y]]
[[Category: Lewicka, A]]
[[Category: Koirala, D]]
[[Category: Huang, H]]
[[Category: Piccirilli, J.A]]