5vzt - Revision history

OCA at 14:13, 13 March 2024

OCA — Wed, 13 Mar 2024 14:13:10 GMT

←Older revision		Revision as of 14:13, 13 March 2024
Line 3:		Line 3:
	<StructureSection load='5vzt' size='340' side='right'caption='[[5vzt]], [[Resolution\|resolution]] 2.70Å' scene=''>		<StructureSection load='5vzt' size='340' side='right'caption='[[5vzt]], [[Resolution\|resolution]] 2.70Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5vzt]] is a 4 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=5VZT OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5VZT FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5vzt]] is a 4 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=5VZT OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5VZT FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=DTT:2,3-DIHYDROXY-1,4-DITHIOBUTANE'>DTT</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</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]] 2.7Å</td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">SKP1, EMC19, OCP2, SKP1A, TCEB1L ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN]), FBXO31, FBX14, FBX31, PP2386 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])</td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=DTT:2,3-DIHYDROXY-1,4-DITHIOBUTANE'>DTT</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</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=5vzt FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5vzt OCA], [~~http~~://pdbe.org/5vzt PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5vzt RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5vzt PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5vzt 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=5vzt FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5vzt OCA], [https://pdbe.org/5vzt PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5vzt RCSB], [https://www.ebi.ac.uk/pdbsum/5vzt PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5vzt ProSAT]</span></td></tr>
	</table>		</table>
-	== Disease ==
-	[[http://www.uniprot.org/uniprot/FBX31_HUMAN FBX31_HUMAN]] Autosomal recessive non-syndromic intellectual disability. The disease is caused by mutations affecting the gene represented in this entry.
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/SKP1_HUMAN SKP1_HUMAN]] Essential component of the SCF (SKP1-CUL1-F-box protein) ubiquitin ligase complex, which mediates the ubiquitination of proteins involved in cell cycle progression, signal transduction and transcription. In the SCF complex, serves as an adapter that links the F-box protein to CUL1. SCF(BTRC) mediates the ubiquitination of NFKBIA at 'Lys-21' and 'Lys-22'; the degradation frees the associated NFKB1-RELA dimer to translocate into the nucleus and to activate transcription. SCF(Cyclin F) directs ubiquitination of CP110.<ref>PMID:16209941</ref> <ref>PMID:20181953</ref> [[http://www.uniprot.org/uniprot/FBX31_HUMAN FBX31_HUMAN]] Component of some SCF (SKP1-cullin-F-box) protein ligase complex that plays a central role in G1 arrest following DNA damage. Specifically recognizes phosphorylated cyclin-D1 (CCND1), promoting its ubiquitination and degradation by the proteasome, resulting in G1 arrest. May act as a tumor suppressor.<ref>PMID:16357137</ref> <ref>PMID:19412162</ref>	+	[https://www.uniprot.org/uniprot/SKP1_HUMAN SKP1_HUMAN] Essential component of the SCF (SKP1-CUL1-F-box protein) ubiquitin ligase complex, which mediates the ubiquitination of proteins involved in cell cycle progression, signal transduction and transcription. In the SCF complex, serves as an adapter that links the F-box protein to CUL1. SCF(BTRC) mediates the ubiquitination of NFKBIA at 'Lys-21' and 'Lys-22'; the degradation frees the associated NFKB1-RELA dimer to translocate into the nucleus and to activate transcription. SCF(Cyclin F) directs ubiquitination of CP110.<ref>PMID:16209941</ref> <ref>PMID:20181953</ref>
-	~~<div style="background-color:#fffaf0;">~~	+
-	~~== Publication Abstract from PubMed ==~~	+
-	Ubiquitin-dependent proteolysis of cyclin D1 is associated with normal and tumor cell proliferation and survival. The SCF(FBXO31) (Skp1-Cul1-Rbx1-FBXO31) ubiquitin ligase complex mediates genotoxic stress-induced cyclin D1 degradation. Previous studies have suggested that cyclin D1 levels are maintained at steady state by phosphorylation-dependent nuclear export and subsequent proteolysis in the cytoplasm. Here we present the crystal structures of the Skp1-FBXO31 complex alone and bound to a phosphorylated cyclin D1 C-terminal peptide. FBXO31 possesses a unique substrate-binding domain consisting of two beta-barrel motifs, whereas cyclin D1 binds to FBXO31 by tucking its free C-terminal carboxylate tail into an open cavity of the C-terminal FBXO31 beta-barrel. Biophysical and functional studies demonstrate that SCF(FBXO31) is capable of recruiting and ubiquitinating cyclin D1 in a phosphorylation-independent manner. Our findings provide a conceptual framework for understanding the substrate specificity of the F-box protein FBXO31 and the mechanism of FBXO31-regulated cyclin D1 protein turnover.	+
-		+
-	Structural basis of the phosphorylation-independent recognition of cyclin D1 by the SCF(FBXO31) ubiquitin ligase.,Li Y, Jin K, Bunker E, Zhang X, Luo X, Liu X, Hao B Proc Natl Acad Sci U S A. 2018 Jan 9;115(2):319-324. doi:, 10.1073/pnas.1708677115. Epub 2017 Dec 26. PMID:29279382<ref>PMID:29279382</ref>	+
-		+
-	~~From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>~~	+
-	~~</div>~~	+
-	~~<div class="pdbe-citations 5vzt" style="background-color:#fffaf0;"></div~~>	+
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Human~~]]	+	[[Category: Homo sapiens]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Hao, B]]	+	[[Category: Hao B]]
-	[[Category: Jin, K]]	+	[[Category: Jin K]]
-	[[Category: Li, Y]]	+	[[Category: Li Y]]
-	~~[[Category: Cell cycle]]~~	+
-	~~[[Category: Ubiquitin ligase~~]]	+

OCA at 09:43, 1 January 2020

OCA — Wed, 01 Jan 2020 09:43:33 GMT

←Older revision		Revision as of 09:43, 1 January 2020
Line 1:		Line 1:

	==Crystal structure of the Skp1-FBXO31 complex==		==Crystal structure of the Skp1-FBXO31 complex==
-	<StructureSection load='5vzt' size='340' side='right' caption='[[5vzt]], [[Resolution\|resolution]] 2.70Å' scene=''>	+	<StructureSection load='5vzt' size='340' side='right'caption='[[5vzt]], [[Resolution\|resolution]] 2.70Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5vzt]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5VZT OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5VZT FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5vzt]] is a 4 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=5VZT OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5VZT FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=DTT:2,3-DIHYDROXY-1,4-DITHIOBUTANE'>DTT</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=DTT:2,3-DIHYDROXY-1,4-DITHIOBUTANE'>DTT</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">SKP1, EMC19, OCP2, SKP1A, TCEB1L ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN]), FBXO31, FBX14, FBX31, PP2386 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])</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=5vzt FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5vzt OCA], [http://pdbe.org/5vzt PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5vzt RCSB], [http://www.ebi.ac.uk/pdbsum/5vzt PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5vzt 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=5vzt FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5vzt OCA], [http://pdbe.org/5vzt PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5vzt RCSB], [http://www.ebi.ac.uk/pdbsum/5vzt PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5vzt ProSAT]</span></td></tr>
	</table>		</table>
Line 24:		Line 25:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Human]]
		+	[[Category: Large Structures]]
	[[Category: Hao, B]]		[[Category: Hao, B]]
	[[Category: Jin, K]]		[[Category: Jin, K]]

OCA at 06:53, 17 January 2018

OCA — Wed, 17 Jan 2018 06:53:56 GMT

←Older revision		Revision as of 06:53, 17 January 2018
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5vzt is ~~ON HOLD~~ ~~until Paper~~ Publication	+	==Crystal structure of the Skp1-FBXO31 complex==
		+	<StructureSection load='5vzt' size='340' side='right' caption='[[5vzt]], [[Resolution\|resolution]] 2.70Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[5vzt]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5VZT OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5VZT FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=DTT:2,3-DIHYDROXY-1,4-DITHIOBUTANE'>DTT</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</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=5vzt FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5vzt OCA], [http://pdbe.org/5vzt PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5vzt RCSB], [http://www.ebi.ac.uk/pdbsum/5vzt PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5vzt ProSAT]</span></td></tr>
		+	</table>
		+	== Disease ==
		+	[[http://www.uniprot.org/uniprot/FBX31_HUMAN FBX31_HUMAN]] Autosomal recessive non-syndromic intellectual disability. The disease is caused by mutations affecting the gene represented in this entry.
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/SKP1_HUMAN SKP1_HUMAN]] Essential component of the SCF (SKP1-CUL1-F-box protein) ubiquitin ligase complex, which mediates the ubiquitination of proteins involved in cell cycle progression, signal transduction and transcription. In the SCF complex, serves as an adapter that links the F-box protein to CUL1. SCF(BTRC) mediates the ubiquitination of NFKBIA at 'Lys-21' and 'Lys-22'; the degradation frees the associated NFKB1-RELA dimer to translocate into the nucleus and to activate transcription. SCF(Cyclin F) directs ubiquitination of CP110.<ref>PMID:16209941</ref> <ref>PMID:20181953</ref> [[http://www.uniprot.org/uniprot/FBX31_HUMAN FBX31_HUMAN]] Component of some SCF (SKP1-cullin-F-box) protein ligase complex that plays a central role in G1 arrest following DNA damage. Specifically recognizes phosphorylated cyclin-D1 (CCND1), promoting its ubiquitination and degradation by the proteasome, resulting in G1 arrest. May act as a tumor suppressor.<ref>PMID:16357137</ref> <ref>PMID:19412162</ref>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Ubiquitin-dependent proteolysis of cyclin D1 is associated with normal and tumor cell proliferation and survival. The SCF(FBXO31) (Skp1-Cul1-Rbx1-FBXO31) ubiquitin ligase complex mediates genotoxic stress-induced cyclin D1 degradation. Previous studies have suggested that cyclin D1 levels are maintained at steady state by phosphorylation-dependent nuclear export and subsequent proteolysis in the cytoplasm. Here we present the crystal structures of the Skp1-FBXO31 complex alone and bound to a phosphorylated cyclin D1 C-terminal peptide. FBXO31 possesses a unique substrate-binding domain consisting of two beta-barrel motifs, whereas cyclin D1 binds to FBXO31 by tucking its free C-terminal carboxylate tail into an open cavity of the C-terminal FBXO31 beta-barrel. Biophysical and functional studies demonstrate that SCF(FBXO31) is capable of recruiting and ubiquitinating cyclin D1 in a phosphorylation-independent manner. Our findings provide a conceptual framework for understanding the substrate specificity of the F-box protein FBXO31 and the mechanism of FBXO31-regulated cyclin D1 protein turnover.

-	~~Authors~~:	+	Structural basis of the phosphorylation-independent recognition of cyclin D1 by the SCF(FBXO31) ubiquitin ligase.,Li Y, Jin K, Bunker E, Zhang X, Luo X, Liu X, Hao B Proc Natl Acad Sci U S A. 2018 Jan 9;115(2):319-324. doi:, 10.1073/pnas.1708677115. Epub 2017 Dec 26. PMID:29279382<ref>PMID:29279382</ref>

-	~~Description~~:	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased Structures~~]]	+	</div>
		+	<div class="pdbe-citations 5vzt" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Hao, B]]
		+	[[Category: Jin, K]]
		+	[[Category: Li, Y]]
		+	[[Category: Cell cycle]]
		+	[[Category: Ubiquitin ligase]]

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

OCA — Wed, 27 Sep 2017 14:17:50 GMT

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

←Older revision

Revision as of 14:17, 27 September 2017

OCA: New page: '''Unreleased structure''' The entry 5vzt is ON HOLD until Paper Publication Authors: Description: Category: Unreleased Structures

OCA — Wed, 27 Sep 2017 14:17:49 GMT

New page: '''Unreleased structure''' The entry 5vzt is ON HOLD until Paper Publication Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 5vzt is ON HOLD until Paper Publication

Authors:

Description:
[[Category: Unreleased Structures]]