OCA at 11:58, 1 February 2024

OCA — Thu, 01 Feb 2024 11:58:32 GMT

←Older revision		Revision as of 11:58, 1 February 2024
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-	====	+	==Crystal structure of human DDB1 bound to human DCAF1 (amino acid residues 1046-1396)==
-	<StructureSection load='6zue' size='340' side='right'caption='[[6zue]]' scene=''>	+	<StructureSection load='6zue' size='340' side='right'caption='[[6zue]], [[Resolution\|resolution]] 3.09Å' 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'>[[6zue]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6ZUE OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6ZUE 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=6zue FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6zue OCA], [https://pdbe.org/6zue PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6zue RCSB], [https://www.ebi.ac.uk/pdbsum/6zue PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6zue 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]] 3.094Å</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=6zue FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6zue OCA], [https://pdbe.org/6zue PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6zue RCSB], [https://www.ebi.ac.uk/pdbsum/6zue PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6zue ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/DDB1_HUMAN DDB1_HUMAN] Required for DNA repair. Binds to DDB2 to form the UV-damaged DNA-binding protein complex (the UV-DDB complex). The UV-DDB complex may recognize UV-induced DNA damage and recruit proteins of the nucleotide excision repair pathway (the NER pathway) to initiate DNA repair. The UV-DDB complex preferentially binds to cyclobutane pyrimidine dimers (CPD), 6-4 photoproducts (6-4 PP), apurinic sites and short mismatches. Also appears to function as a component of numerous distinct DCX (DDB1-CUL4-X-box) E3 ubiquitin-protein ligase complexes which mediate the ubiquitination and subsequent proteasomal degradation of target proteins. The functional specificity of the DCX E3 ubiquitin-protein ligase complex is determined by the variable substrate recognition component recruited by DDB1. DCX(DDB2) (also known as DDB1-CUL4-ROC1, CUL4-DDB-ROC1 and CUL4-DDB-RBX1) may ubiquitinate histone H2A, histone H3 and histone H4 at sites of UV-induced DNA damage. The ubiquitination of histones may facilitate their removal from the nucleosome and promote subsequent DNA repair. DCX(DDB2) also ubiquitinates XPC, which may enhance DNA-binding by XPC and promote NER. DCX(DTL) plays a role in PCNA-dependent polyubiquitination of CDT1 and MDM2-dependent ubiquitination of TP53 in response to radiation-induced DNA damage and during DNA replication. DCX(ERCC8) (the CSA complex) plays a role in transcription-coupled repair (TCR). May also play a role in ubiquitination of CDKN1B/p27kip when associated with CUL4 and SKP2.<ref>PMID:12732143</ref> <ref>PMID:15448697</ref> <ref>PMID:14739464</ref> <ref>PMID:15882621</ref> <ref>PMID:16260596</ref> <ref>PMID:16482215</ref> <ref>PMID:17079684</ref> <ref>PMID:16407242</ref> <ref>PMID:16407252</ref> <ref>PMID:16678110</ref> <ref>PMID:16940174</ref> <ref>PMID:17041588</ref> <ref>PMID:16473935</ref> <ref>PMID:18593899</ref> <ref>PMID:18381890</ref> <ref>PMID:18332868</ref>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Viruses have evolved means to manipulate the host's ubiquitin-proteasome system, in order to down-regulate antiviral host factors. The Vpx/Vpr family of lentiviral accessory proteins usurp the substrate receptor DCAF1 of host Cullin4-RING ligases (CRL4), a family of modular ubiquitin ligases involved in DNA replication, DNA repair and cell cycle regulation. CRL4DCAF1 specificity modulation by Vpx and Vpr from certain simian immunodeficiency viruses (SIV) leads to recruitment, poly-ubiquitylation and subsequent proteasomal degradation of the host restriction factor SAMHD1, resulting in enhanced virus replication in differentiated cells. To unravel the mechanism of SIV Vpr-induced SAMHD1 ubiquitylation, we conducted integrative biochemical and structural analyses of the Vpr protein from SIVs infecting Cercopithecus cephus (SIVmus). X-ray crystallography reveals commonalities between SIVmus Vpr and other members of the Vpx/Vpr family with regard to DCAF1 interaction, while cryo-electron microscopy and cross-linking mass spectrometry highlight a divergent molecular mechanism of SAMHD1 recruitment. In addition, these studies demonstrate how SIVmus Vpr exploits the dynamic architecture of the multi-subunit CRL4DCAF1 assembly to optimise SAMHD1 ubiquitylation. Together, the present work provides detailed molecular insight into variability and species-specificity of the evolutionary arms race between host SAMHD1 restriction and lentiviral counteraction through Vpx/Vpr proteins.
		+
		+	Structural insights into Cullin4-RING ubiquitin ligase remodelling by Vpr from simian immunodeficiency viruses.,Banchenko S, Krupp F, Gotthold C, Burger J, Graziadei A, O'Reilly FJ, Sinn L, Ruda O, Rappsilber J, Spahn CMT, Mielke T, Taylor IA, Schwefel D PLoS Pathog. 2021 Aug 2;17(8):e1009775. doi: 10.1371/journal.ppat.1009775. , eCollection 2021 Aug. PMID:34339457<ref>PMID:34339457</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 6zue" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[DNA damage-binding protein\|DNA damage-binding protein]]
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Homo sapiens]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Z-disk~~]]	+	[[Category: Schwefel D]]
		+	[[Category: Taylor IA]]

OCA at 10:31, 28 July 2021

OCA — Wed, 28 Jul 2021 10:31:34 GMT

←Older revision		Revision as of 10:31, 28 July 2021
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 6zue ~~is ON HOLD until Paper Publication~~	+	====
-		+	<StructureSection load='6zue' size='340' side='right'caption='[[6zue]]' scene=''>
-	~~Authors~~: ~~Schwefel, D~~.~~, Taylor, I~~.A.	+	== 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>
-	~~Description~~: ~~Crystal structure of human DDB1 bound to human DCAF1 (amino acid residues 1046~~-~~1396)~~	+	</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=6zue FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6zue OCA], [https://pdbe.org/6zue PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6zue RCSB], [https://www.ebi.ac.uk/pdbsum/6zue PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6zue ProSAT]</span></td></tr>
-	[[~~Category~~: ~~Unreleased Structures~~]]	+	</table>
-	[[Category: ~~Taylor, I.A~~]]	+	__TOC__
-	[[Category: ~~Schwefel, D~~]]	+	</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Z-disk]]

OCA at 09:09, 26 August 2020

OCA — Wed, 26 Aug 2020 09:09:06 GMT

←Older revision		Revision as of 09:09, 26 August 2020
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

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

	Authors: Schwefel, D., Taylor, I.A.		Authors: Schwefel, D., Taylor, I.A.

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

OCA — Wed, 29 Jul 2020 09:36:18 GMT

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

←Older revision

Revision as of 09:36, 29 July 2020

OCA: New page: '''Unreleased structure''' The entry 6zue is ON HOLD Authors: Schwefel, D., Taylor, I.A. Description: Crystal structure of human DDB1 bound to human DCAF1 (amino acid residues 1046-139...

OCA — Wed, 29 Jul 2020 09:36:16 GMT

New page: '''Unreleased structure''' The entry 6zue is ON HOLD Authors: Schwefel, D., Taylor, I.A. Description: Crystal structure of human DDB1 bound to human DCAF1 (amino acid residues 1046-139...

New page

'''Unreleased structure'''

The entry 6zue is ON HOLD

Authors: Schwefel, D., Taylor, I.A.

Description: Crystal structure of human DDB1 bound to human DCAF1 (amino acid residues 1046-1396)
[[Category: Unreleased Structures]]
[[Category: Taylor, I.A]]
[[Category: Schwefel, D]]

6zue - Revision history

OCA at 11:58, 1 February 2024

OCA at 10:31, 28 July 2021

OCA at 09:09, 26 August 2020

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

OCA: New page: '''Unreleased structure''' The entry 6zue is ON HOLD Authors: Schwefel, D., Taylor, I.A. Description: Crystal structure of human DDB1 bound to human DCAF1 (amino acid residues 1046-139...