8bb5 - Revision history

OCA at 11:07, 22 November 2023

2023-11-22T11:07:03Z

←Older revision		Revision as of 11:07, 22 November 2023
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	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[8bb5]] 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=8BB5 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=8BB5 FirstGlance]. <br>		<table><tr><td colspan='2'>[[8bb5]] 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=8BB5 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=8BB5 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=Q43:~{N}-[5-[4-[[4-[2-[[(2~{S})-3,3-dimethyl-1-[(2~{S},4~{R})-2-[[4-(4-methyl-1,3-thiazol-5-yl)phenyl]methylcarbamoyl]-4-oxidanyl-pyrrolidin-1-yl]-1-oxidanylidene-butan-2-yl]amino]-2-oxidanylidene-ethyl]phenyl]methylcarbamoyl]phenyl]-2-(4-methylpiperazin-1-yl)phenyl]-6-oxidanyl-4-(trifluoromethyl)pyridine-3-carboxamide'>Q43</scene>, <scene name='pdbligand=SCN:THIOCYANATE+ION'>SCN</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]] 2.2Å</td></tr>
		+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=Q43:~{N}-[5-[4-[[4-[2-[[(2~{S})-3,3-dimethyl-1-[(2~{S},4~{R})-2-[[4-(4-methyl-1,3-thiazol-5-yl)phenyl]methylcarbamoyl]-4-oxidanyl-pyrrolidin-1-yl]-1-oxidanylidene-butan-2-yl]amino]-2-oxidanylidene-ethyl]phenyl]methylcarbamoyl]phenyl]-2-(4-methylpiperazin-1-yl)phenyl]-6-oxidanyl-4-(trifluoromethyl)pyridine-3-carboxamide'>Q43</scene>, <scene name='pdbligand=SCN:THIOCYANATE+ION'>SCN</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=8bb5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=8bb5 OCA], [https://pdbe.org/8bb5 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=8bb5 RCSB], [https://www.ebi.ac.uk/pdbsum/8bb5 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=8bb5 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=8bb5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=8bb5 OCA], [https://pdbe.org/8bb5 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=8bb5 RCSB], [https://www.ebi.ac.uk/pdbsum/8bb5 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=8bb5 ProSAT]</span></td></tr>
	</table>		</table>
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	== Function ==		== Function ==
	[https://www.uniprot.org/uniprot/VHL_HUMAN VHL_HUMAN] Involved in the ubiquitination and subsequent proteasomal degradation via the von Hippel-Lindau ubiquitination complex. Seems to act as target recruitment subunit in the E3 ubiquitin ligase complex and recruits hydroxylated hypoxia-inducible factor (HIF) under normoxic conditions. Involved in transcriptional repression through interaction with HIF1A, HIF1AN and histone deacetylases. Ubiquitinates, in an oxygen-responsive manner, ADRB2.<ref>PMID:9751722</ref> <ref>PMID:10944113</ref> <ref>PMID:19584355</ref>		[https://www.uniprot.org/uniprot/VHL_HUMAN VHL_HUMAN] Involved in the ubiquitination and subsequent proteasomal degradation via the von Hippel-Lindau ubiquitination complex. Seems to act as target recruitment subunit in the E3 ubiquitin ligase complex and recruits hydroxylated hypoxia-inducible factor (HIF) under normoxic conditions. Involved in transcriptional repression through interaction with HIF1A, HIF1AN and histone deacetylases. Ubiquitinates, in an oxygen-responsive manner, ADRB2.<ref>PMID:9751722</ref> <ref>PMID:10944113</ref> <ref>PMID:19584355</ref>
		+
		+	==See Also==
		+	*[[Elongation factor 3D structures\|Elongation factor 3D structures]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 07:32, 9 November 2022

2022-11-09T07:32:53Z

←Older revision		Revision as of 07:32, 9 November 2022
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-	'''Unreleased structure'''

-	~~The entry~~ 8bb5 is ~~ON HOLD~~	+	==Structure of human WDR5 and pVHL:ElonginC:ElonginB bound to PROTAC with Aryl linker==
-		+	<StructureSection load='8bb5' size='340' side='right'caption='[[8bb5]], [[Resolution\|resolution]] 2.20Å' scene=''>
-	~~Authors~~: ~~Kraemer~~, A., ~~Doelle~~, A., ~~Knapp~~, S., ~~Structural Genomics Consortium~~ (~~SGC~~)	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[8bb5]] 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=8BB5 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=8BB5 FirstGlance]. <br>
-	~~Description~~: ~~Structure~~ of ~~human WDR5~~ and ~~pVHL~~:~~ElonginC~~:~~ElonginB bound~~ to ~~PROTAC~~ with ~~Aryl linker~~	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=Q43:~{N}-[5-[4-[[4-[2-[[(2~{S})-3,3-dimethyl-1-[(2~{S},4~{R})-2-[[4-(4-methyl-1,3-thiazol-5-yl)phenyl]methylcarbamoyl]-4-oxidanyl-pyrrolidin-1-yl]-1-oxidanylidene-butan-2-yl]amino]-2-oxidanylidene-ethyl]phenyl]methylcarbamoyl]phenyl]-2-(4-methylpiperazin-1-yl)phenyl]-6-oxidanyl-4-(trifluoromethyl)pyridine-3-carboxamide'>Q43</scene>, <scene name='pdbligand=SCN:THIOCYANATE+ION'>SCN</scene></td></tr>
-	[[Category: ~~Unreleased Structures~~]]	+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=8bb5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=8bb5 OCA], [https://pdbe.org/8bb5 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=8bb5 RCSB], [https://www.ebi.ac.uk/pdbsum/8bb5 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=8bb5 ProSAT]</span></td></tr>
-	[[Category: ~~Knapp, S~~]]	+	</table>
-	[[Category: ~~Structural Genomics Consortium (Sgc)~~]]	+	== Disease ==
-	[[Category: ~~Doelle, A~~]]	+	[https://www.uniprot.org/uniprot/VHL_HUMAN VHL_HUMAN] Defects in VHL are a cause of susceptibility to pheochromocytoma (PCC) [MIM:[https://omim.org/entry/171300 171300]. A catecholamine-producing tumor of chromaffin tissue of the adrenal medulla or sympathetic paraganglia. The cardinal symptom, reflecting the increased secretion of epinephrine and norepinephrine, is hypertension, which may be persistent or intermittent. Defects in VHL are the cause of von Hippel-Lindau disease (VHLD) [MIM:[https://omim.org/entry/193300 193300]. VHLD is a dominantly inherited familial cancer syndrome characterized by the development of retinal angiomatosis, cerebellar and spinal hemangioblastoma, renal cell carcinoma (RCC), phaeochromocytoma and pancreatic tumors. VHL type 1 is without pheochromocytoma, type 2 is with pheochromocytoma. VHL type 2 is further subdivided into types 2A (pheochromocytoma, retinal angioma, and hemangioblastomas without renal cell carcinoma and pancreatic cyst) and 2B (pheochromocytoma, retinal angioma, and hemangioblastomas with renal cell carcinoma and pancreatic cyst). VHL type 2C refers to patients with isolated pheochromocytoma without hemangioblastoma or renal cell carcinoma. The estimated incidence is 3/100000 births per year and penetrance is 97% by age 60 years.<ref>PMID:10635329</ref> <ref>PMID:8493574</ref> <ref>PMID:7987306</ref> <ref>PMID:7728151</ref> <ref>PMID:8634692</ref> <ref>PMID:8592333</ref> <ref>PMID:8825918</ref> <ref>PMID:8730290</ref> <ref>PMID:8956040</ref> <ref>PMID:9452032</ref> <ref>PMID:9452106</ref> <ref>PMID:10627136</ref> <ref>PMID:9829911</ref> <ref>PMID:9829912</ref> [:]<ref>PMID:10533030</ref> <ref>PMID:10408776</ref> <ref>PMID:16502427</ref> Defects in VHL are the cause of familial erythrocytosis type 2 (ECYT2) [MIM:[https://omim.org/entry/263400 263400]; also called VHL-dependent polycythemia or Chuvash type polycythemia. ECYT2 is an autosomal recessive disorder characterized by an increase in serum red blood cell mass, hypersensitivity of erythroid progenitors to erythropoietin, increased erythropoietin serum levels, and normal oxygen affinity. Patients with ECYT2 carry a high risk for peripheral thrombosis and cerebrovascular events.<ref>PMID:12844285</ref> <ref>PMID:12393546</ref> Defects in VHL are a cause of renal cell carcinoma (RCC) [MIM:[https://omim.org/entry/144700 144700]. Renal cell carcinoma is a heterogeneous group of sporadic or hereditary carcinoma derived from cells of the proximal renal tubular epithelium. It is subclassified into clear cell renal carcinoma (non-papillary carcinoma), papillary renal cell carcinoma, chromophobe renal cell carcinoma, collecting duct carcinoma with medullary carcinoma of the kidney, and unclassified renal cell carcinoma.<ref>PMID:11986208</ref>
-	[[Category: Kraemer, A]]	+	== Function ==
		+	[https://www.uniprot.org/uniprot/VHL_HUMAN VHL_HUMAN] Involved in the ubiquitination and subsequent proteasomal degradation via the von Hippel-Lindau ubiquitination complex. Seems to act as target recruitment subunit in the E3 ubiquitin ligase complex and recruits hydroxylated hypoxia-inducible factor (HIF) under normoxic conditions. Involved in transcriptional repression through interaction with HIF1A, HIF1AN and histone deacetylases. Ubiquitinates, in an oxygen-responsive manner, ADRB2.<ref>PMID:9751722</ref> <ref>PMID:10944113</ref> <ref>PMID:19584355</ref>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Homo sapiens]]
		+	[[Category: Large Structures]]
		+	[[Category: Doelle A]]
		+	[[Category: Knapp S]]
		+	[[Category: Kraemer A]]

OCA at 03:50, 26 October 2022

2022-10-26T03:50:06Z

←Older revision		Revision as of 03:50, 26 October 2022
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 8bb5 is ON HOLD ~~until sometime in the future~~	+	The entry 8bb5 is ON HOLD

	Authors: Kraemer, A., Doelle, A., Knapp, S., Structural Genomics Consortium (SGC)		Authors: Kraemer, A., Doelle, A., Knapp, S., Structural Genomics Consortium (SGC)

OCA: Protected "8bb5" [edit=sysop:move=sysop]

2022-10-19T17:03:34Z

Protected "8bb5" [edit=sysop:move=sysop]

←Older revision

Revision as of 17:03, 19 October 2022

OCA: New page: '''Unreleased structure''' The entry 8bb5 is ON HOLD until sometime in the future Authors: Kraemer, A., Doelle, A., Knapp, S., Structural Genomics Consortium (SGC) Description: Structu...

2022-10-19T17:03:33Z

New page: '''Unreleased structure''' The entry 8bb5 is ON HOLD until sometime in the future Authors: Kraemer, A., Doelle, A., Knapp, S., Structural Genomics Consortium (SGC) Description: Structu...

New page

'''Unreleased structure'''

The entry 8bb5 is ON HOLD until sometime in the future

Authors: Kraemer, A., Doelle, A., Knapp, S., Structural Genomics Consortium (SGC)

Description: Structure of human WDR5 and pVHL:ElonginC:ElonginB bound to PROTAC with Aryl linker
[[Category: Unreleased Structures]]
[[Category: Knapp, S]]
[[Category: Structural Genomics Consortium (Sgc)]]
[[Category: Doelle, A]]
[[Category: Kraemer, A]]