5e0i - Revision history

OCA at 22:08, 28 June 2023

OCA — Wed, 28 Jun 2023 22:08:39 GMT

←Older revision		Revision as of 22:08, 28 June 2023
Line 3:		Line 3:
	<StructureSection load='5e0i' size='340' side='right'caption='[[5e0i]], [[Resolution\|resolution]] 1.95Å' scene=''>		<StructureSection load='5e0i' size='340' side='right'caption='[[5e0i]], [[Resolution\|resolution]] 1.95Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5e0i]] is a 6 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Hbv-d Hbv-d~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5E0I OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=5E0I FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5e0i]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Hepatitis_B_virus_subtype_adyw Hepatitis B virus subtype adyw]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5E0I OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5E0I FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=5J6:METHYL+4-(2-BROMO-4-FLUOROPHENYL)-6-(MORPHOLIN-4-YLMETHYL)-2-(1,3-THIAZOL-2-YL)PYRIMIDINE-5-CARBOXYLATE'>5J6</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]] 1.95Å</td></tr>
-	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://proteopedia.org/fgij/fg.htm?mol=5e0i FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5e0i OCA], [~~http~~://pdbe.org/5e0i PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5e0i RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5e0i PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5e0i ProSAT]</span></td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=5J6:METHYL+4-(2-BROMO-4-FLUOROPHENYL)-6-(MORPHOLIN-4-YLMETHYL)-2-(1,3-THIAZOL-2-YL)PYRIMIDINE-5-CARBOXYLATE'>5J6</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=5e0i FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5e0i OCA], [https://pdbe.org/5e0i PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5e0i RCSB], [https://www.ebi.ac.uk/pdbsum/5e0i PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5e0i ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/CAPSD_HBVD1 CAPSD_HBVD1]] Self assembles to form an icosahedral capsid. Most capsid appear to be large particles with a icosahedral symmetry of T=4 and consist of 240 copies of capsid protein, though a fraction forms smaller T=3 particles consisting of 180 capsid proteins. Entering capsid are transported along microtubules to the nucleus. Phosphorylation of the capsid is thought to induce exposure of nuclear localization signal in the C-terminal portion of the capsid protein that allows binding to the nuclear pore complex via the importin (karyopherin-) alpha and beta. Capsids are imported in intact form through the nuclear pore into the nuclear basket, where it probably binds NUP153. Only capsids that contain the mature viral genome can release the viral DNA and capsid protein into the nucleoplasm. Immature capsids get stucked in the basket. Capsids encapsulate the pre-genomic RNA and the P protein. Pre-genomic RNA is reverse transcribed into DNA while the capsid is still in the cytoplasm. The capsid can then either be directed to the nucleus, providing more genome for transcription, or bud through the endoplasmic reticulum to provide new virions (By similarity).<ref>PMID:7711014</ref> Encapsidates hepatitis delta genome (By similarity).<ref>PMID:7711014</ref>	+	[https://www.uniprot.org/uniprot/CAPSD_HBVD1 CAPSD_HBVD1] Self assembles to form an icosahedral capsid. Most capsid appear to be large particles with a icosahedral symmetry of T=4 and consist of 240 copies of capsid protein, though a fraction forms smaller T=3 particles consisting of 180 capsid proteins. Entering capsid are transported along microtubules to the nucleus. Phosphorylation of the capsid is thought to induce exposure of nuclear localization signal in the C-terminal portion of the capsid protein that allows binding to the nuclear pore complex via the importin (karyopherin-) alpha and beta. Capsids are imported in intact form through the nuclear pore into the nuclear basket, where it probably binds NUP153. Only capsids that contain the mature viral genome can release the viral DNA and capsid protein into the nucleoplasm. Immature capsids get stucked in the basket. Capsids encapsulate the pre-genomic RNA and the P protein. Pre-genomic RNA is reverse transcribed into DNA while the capsid is still in the cytoplasm. The capsid can then either be directed to the nucleus, providing more genome for transcription, or bud through the endoplasmic reticulum to provide new virions (By similarity).<ref>PMID:7711014</ref> Encapsidates hepatitis delta genome (By similarity).<ref>PMID:7711014</ref>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 22:		Line 23:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Hbv-d~~]]	+	[[Category: Hepatitis B virus subtype adyw]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Abendroth, J]]	+	[[Category: Abendroth J]]
-	[[Category: Klumpp, K]]	+	[[Category: Klumpp K]]
-	[[Category: Lukacs~~, C M]]~~	+	[[Category: Lukacs CM]]
-	~~[[Category: Nvr10-001e2]]~~	+
-	~~[[Category: Viral protein~~]]	+

OCA at 08:16, 15 April 2020

OCA — Wed, 15 Apr 2020 08:16:35 GMT

←Older revision		Revision as of 08:16, 15 April 2020
Line 1:		Line 1:
		+
	==Crystal structure of the HBV capsid Y132A mutant (VCID 8772) in complex with NVR10-001E2 at 1.95A resolution==		==Crystal structure of the HBV capsid Y132A mutant (VCID 8772) in complex with NVR10-001E2 at 1.95A resolution==
-	<StructureSection load='5e0i' size='340' side='right' caption='[[5e0i]], [[Resolution\|resolution]] 1.95Å' scene=''>	+	<StructureSection load='5e0i' size='340' side='right'caption='[[5e0i]], [[Resolution\|resolution]] 1.95Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5e0i]] is a 6 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5E0I OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5E0I FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5e0i]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/Hbv-d Hbv-d]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5E0I OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5E0I FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=5J6:METHYL+4-(2-BROMO-4-FLUOROPHENYL)-6-(MORPHOLIN-4-YLMETHYL)-2-(1,3-THIAZOL-2-YL)PYRIMIDINE-5-CARBOXYLATE'>5J6</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=5J6:METHYL+4-(2-BROMO-4-FLUOROPHENYL)-6-(MORPHOLIN-4-YLMETHYL)-2-(1,3-THIAZOL-2-YL)PYRIMIDINE-5-CARBOXYLATE'>5J6</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=5e0i FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5e0i OCA], [http://pdbe.org/5e0i PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5e0i RCSB], [http://www.ebi.ac.uk/pdbsum/5e0i PDBsum]</span></td></tr>	+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=5e0i FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5e0i OCA], [http://pdbe.org/5e0i PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5e0i RCSB], [http://www.ebi.ac.uk/pdbsum/5e0i PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5e0i ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 21:		Line 22:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Hbv-d]]
		+	[[Category: Large Structures]]
	[[Category: Abendroth, J]]		[[Category: Abendroth, J]]
	[[Category: Klumpp, K]]		[[Category: Klumpp, K]]

OCA at 13:38, 9 December 2015

OCA — Wed, 09 Dec 2015 13:38:25 GMT

←Older revision		Revision as of 13:38, 9 December 2015
Line 1:		Line 1:
-	'''~~Unreleased~~ structure'''	+	==Crystal structure of the HBV capsid Y132A mutant (VCID 8772) in complex with NVR10-001E2 at 1.95A resolution==
		+	<StructureSection load='5e0i' size='340' side='right' caption='[[5e0i]], [[Resolution\|resolution]] 1.95Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[5e0i]] is a 6 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5E0I OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5E0I FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=5J6:METHYL+4-(2-BROMO-4-FLUOROPHENYL)-6-(MORPHOLIN-4-YLMETHYL)-2-(1,3-THIAZOL-2-YL)PYRIMIDINE-5-CARBOXYLATE'>5J6</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=5e0i FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5e0i OCA], [http://pdbe.org/5e0i PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5e0i RCSB], [http://www.ebi.ac.uk/pdbsum/5e0i PDBsum]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/CAPSD_HBVD1 CAPSD_HBVD1]] Self assembles to form an icosahedral capsid. Most capsid appear to be large particles with a icosahedral symmetry of T=4 and consist of 240 copies of capsid protein, though a fraction forms smaller T=3 particles consisting of 180 capsid proteins. Entering capsid are transported along microtubules to the nucleus. Phosphorylation of the capsid is thought to induce exposure of nuclear localization signal in the C-terminal portion of the capsid protein that allows binding to the nuclear pore complex via the importin (karyopherin-) alpha and beta. Capsids are imported in intact form through the nuclear pore into the nuclear basket, where it probably binds NUP153. Only capsids that contain the mature viral genome can release the viral DNA and capsid protein into the nucleoplasm. Immature capsids get stucked in the basket. Capsids encapsulate the pre-genomic RNA and the P protein. Pre-genomic RNA is reverse transcribed into DNA while the capsid is still in the cytoplasm. The capsid can then either be directed to the nucleus, providing more genome for transcription, or bud through the endoplasmic reticulum to provide new virions (By similarity).<ref>PMID:7711014</ref> Encapsidates hepatitis delta genome (By similarity).<ref>PMID:7711014</ref>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The hepatitis B virus (HBV) core protein is essential for HBV replication and an important target for antiviral drug discovery. We report the first, to our knowledge, high-resolution crystal structure of an antiviral compound bound to the HBV core protein. The compound NVR-010-001-E2 can induce assembly of the HBV core wild-type and Y132A mutant proteins and thermostabilize the proteins with a Tm increase of more than 10 degrees C. NVR-010-001-E2 binds at the dimer-dimer interface of the core proteins, forms a new interaction surface promoting protein-protein interaction, induces protein assembly, and increases stability. The impact of naturally occurring core protein mutations on antiviral activity correlates with NVR-010-001-E2 binding interactions determined by crystallography. The crystal structure provides understanding of a drug efficacy mechanism related to the induction and stabilization of protein-protein interactions and enables structure-guided design to improve antiviral potency and drug-like properties.

-	~~The entry 5e0i is ON HOLD~~	+	High-resolution crystal structure of a hepatitis B virus replication inhibitor bound to the viral core protein.,Klumpp K, Lam AM, Lukacs C, Vogel R, Ren S, Espiritu C, Baydo R, Atkins K, Abendroth J, Liao G, Efimov A, Hartman G, Flores OA Proc Natl Acad Sci U S A. 2015 Nov 23. pii: 201513803. PMID:26598693<ref>PMID:26598693</ref>

-	~~Authors: Lukacs~~, C.M.~~, Abendroth, J., Klumpp, K~~.	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~Description: Crystal structure of the HBV capsid Y132A mutant (VCID 8772) in cmoplex with NVR10~~-~~001E2 at 1.95A resolution~~	+	<div class="pdbe-citations 5e0i" style="background-color:#fffaf0;"></div>
-	[[Category: ~~Unreleased Structures~~]]	+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Abendroth, J]]
	[[Category: Klumpp, K]]		[[Category: Klumpp, K]]
-	[[Category: ~~Abendroth~~, J]]	+	[[Category: Lukacs, C M]]
-	[[Category: ~~Lukacs, C.M~~]]	+	[[Category: Nvr10-001e2]]
		+	[[Category: Viral protein]]

OCA: Protected "5e0i" [edit=sysop:move=sysop]

OCA — Wed, 07 Oct 2015 12:47:26 GMT

Protected "5e0i" [edit=sysop:move=sysop]

←Older revision

Revision as of 12:47, 7 October 2015

OCA: New page: '''Unreleased structure''' The entry 5e0i is ON HOLD Authors: Lukacs, C.M., Abendroth, J., Klumpp, K. Description: Crystal structure of the HBV capsid Y132A mutant (VCID 8772) in cmopl...

OCA — Wed, 07 Oct 2015 12:47:25 GMT

New page: '''Unreleased structure''' The entry 5e0i is ON HOLD Authors: Lukacs, C.M., Abendroth, J., Klumpp, K. Description: Crystal structure of the HBV capsid Y132A mutant (VCID 8772) in cmopl...

New page

'''Unreleased structure'''

The entry 5e0i is ON HOLD

Authors: Lukacs, C.M., Abendroth, J., Klumpp, K.

Description: Crystal structure of the HBV capsid Y132A mutant (VCID 8772) in cmoplex with NVR10-001E2 at 1.95A resolution
[[Category: Unreleased Structures]]
[[Category: Klumpp, K]]
[[Category: Abendroth, J]]
[[Category: Lukacs, C.M]]