6cch - Revision history

OCA at 10:39, 14 June 2023

2023-06-14T10:39:38Z

←Older revision		Revision as of 10:39, 14 June 2023
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	==NMR data-driven model of GTPase KRas-GMPPNP tethered to a nanodisc (E3 state)==		==NMR data-driven model of GTPase KRas-GMPPNP tethered to a nanodisc (E3 state)==
-	<StructureSection load='6cch' size='340' side='right'caption='[[6cch~~]], [[NMR_Ensembles_of_Models \| 7 NMR models~~]]' scene=''>	+	<StructureSection load='6cch' size='340' side='right'caption='[[6cch]]' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6cch]] is a 3 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Human Human~~]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6CCH OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=6CCH FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6cch]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6CCH OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6CCH FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=17F:O-[(S)-({(2R)-2,3-BIS[(9Z)-OCTADEC-9-ENOYLOXY]PROPYL}OXY)(HYDROXY)PHOSPHORYL]-L-SERINE'>17F</scene>, <scene name='pdbligand=GNP:PHOSPHOAMINOPHOSPHONIC+ACID-GUANYLATE+ESTER'>GNP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PCW:1,2-DIOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE'>PCW</scene>~~</td></tr>~~	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=17F:O-[(S)-({(2R)-2,3-BIS[(9Z)-OCTADEC-9-ENOYLOXY]PROPYL}OXY)(HYDROXY)PHOSPHORYL]-L-SERINE'>17F</scene>, <scene name='pdbligand=GNP:PHOSPHOAMINOPHOSPHONIC+ACID-GUANYLATE+ESTER'>GNP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PCW:1,2-DIOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE'>PCW</scene></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">APOA1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN]), KRAS, KRAS2, RASK2 ([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'>[https://proteopedia.org/fgij/fg.htm?mol=6cch FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6cch OCA], [https://pdbe.org/6cch PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6cch RCSB], [https://www.ebi.ac.uk/pdbsum/6cch PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6cch 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=6cch FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6cch OCA], [~~http~~://pdbe.org/6cch PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6cch RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6cch PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6cch ProSAT]</span></td></tr>	+
	</table>		</table>
	== Disease ==		== Disease ==
-	[[http://www.uniprot.org/uniprot/APOA1_HUMAN APOA1_HUMAN]] Defects in APOA1 are a cause of high density lipoprotein deficiency type 2 (HDLD2) [MIM:[http://omim.org/entry/604091 604091]]; also known as familial hypoalphalipoproteinemia (FHA). Inheritance is autosomal dominant.<ref>PMID:8240372</ref> <ref>PMID:8282791</ref> Defects in APOA1 are a cause of the low HDL levels observed in high density lipoprotein deficiency type 1 (HDLD1) [MIM:[http://omim.org/entry/205400 205400]]; also known as analphalipoproteinemia or Tangier disease (TGD). HDLD1 is a recessive disorder characterized by the absence of plasma HDL, accumulation of cholesteryl esters, premature coronary artery disease, hepatosplenomegaly, recurrent peripheral neuropathy and progressive muscle wasting and weakness. In HDLD1 patients, ApoA-I fails to associate with HDL probably because of the faulty conversion of pro-ApoA-I molecules into mature chains, either due to a defect in the converting enzyme activity or a specific structural defect in Tangier ApoA-I.<ref>PMID:8240372</ref> <ref>PMID:8282791</ref> Note=A mutation in APOA1 is the cause of amyloid polyneuropathy-nephropathy Iowa type (AMYLIOWA); also known as amyloidosis van Allen type or familial amyloid polyneuropathy type III. AMYLIOWA is a hereditary generalized amyloidosis due to deposition of amyloid mainly constituted by apolipoprotein A1. The clinical picture is dominated by neuropathy in the early stages of the disease and nephropathy late in the course. Death is due in most cases to renal amyloidosis. Severe peptic ulcer disease can occurr in some and hearing loss is frequent. Cataracts is present in several, but vitreous opacities are not observed.<ref>PMID:8240372</ref> <ref>PMID:8282791</ref> <ref>PMID:3142462</ref> <ref>PMID:2123470</ref> Defects in APOA1 are a cause of amyloidosis type 8 (AMYL8) [MIM:[http://omim.org/entry/105200 105200]]; also known as systemic non-neuropathic amyloidosis or Ostertag-type amyloidosis. AMYL8 is a hereditary generalized amyloidosis due to deposition of apolipoprotein A1, fibrinogen and lysozyme amyloids. Viscera are particularly affected. There is no involvement of the nervous system. Clinical features include renal amyloidosis resulting in nephrotic syndrome, arterial hypertension, hepatosplenomegaly, cholestasis, petechial skin rash.<ref>PMID:8240372</ref> <ref>PMID:8282791</ref> <ref>PMID:1502149</ref> [[http://www.uniprot.org/uniprot/RASK_HUMAN RASK_HUMAN]] Defects in KRAS are a cause of acute myelogenous leukemia (AML) [MIM:[~~http~~://omim.org/entry/601626 601626]]. AML is a malignant disease in which hematopoietic precursors are arrested in an early stage of development.<ref>PMID:8955068</ref> Defects in KRAS are a cause of juvenile myelomonocytic leukemia (JMML) [MIM:[~~http~~://omim.org/entry/607785 607785]]. JMML is a pediatric myelodysplastic syndrome that constitutes approximately 30% of childhood cases of myelodysplastic syndrome (MDS) and 2% of leukemia. It is characterized by leukocytosis with tissue infiltration and in vitro hypersensitivity of myeloid progenitors to granulocyte-macrophage colony stimulating factor. Defects in KRAS are the cause of Noonan syndrome type 3 (NS3) [MIM:[~~http~~://omim.org/entry/609942 609942]]. Noonan syndrome (NS) [MIM:[~~http~~://omim.org/entry/163950 163950]] is a disorder characterized by dysmorphic facial features, short stature, hypertelorism, cardiac anomalies, deafness, motor delay, and a bleeding diathesis. It is a genetically heterogeneous and relatively common syndrome, with an estimated incidence of 1 in 1000-2500 live births. Rarely, NS is associated with juvenile myelomonocytic leukemia (JMML). NS3 inheritance is autosomal dominant.<ref>PMID:16773572</ref> <ref>PMID:16474405</ref> <ref>PMID:17468812</ref> <ref>PMID:17056636</ref> <ref>PMID:19396835</ref> <ref>PMID:20949621</ref> Defects in KRAS are a cause of gastric cancer (GASC) [MIM:[~~http~~://omim.org/entry/613659 613659]]; also called gastric cancer intestinal or stomach cancer. Gastric cancer is a malignant disease which starts in the stomach, can spread to the esophagus or the small intestine, and can extend through the stomach wall to nearby lymph nodes and organs. It also can metastasize to other parts of the body. The term gastric cancer or gastric carcinoma refers to adenocarcinoma of the stomach that accounts for most of all gastric malignant tumors. Two main histologic types are recognized, diffuse type and intestinal type carcinomas. Diffuse tumors are poorly differentiated infiltrating lesions, resulting in thickening of the stomach. In contrast, intestinal tumors are usually exophytic, often ulcerating, and associated with intestinal metaplasia of the stomach, most often observed in sporadic disease.<ref>PMID:3034404</ref> <ref>PMID:7773929</ref> <ref>PMID:14534542</ref> Note=Defects in KRAS are a cause of pylocytic astrocytoma (PA). Pylocytic astrocytomas are neoplasms of the brain and spinal cord derived from glial cells which vary from histologically benign forms to highly anaplastic and malignant tumors.<ref>PMID:8439212</ref> Defects in KRAS are a cause of cardiofaciocutaneous syndrome (CFC syndrome) [MIM:[~~http~~://omim.org/entry/115150 115150]]; also known as cardio-facio-cutaneous syndrome. CFC syndrome is characterized by a distinctive facial appearance, heart defects and mental retardation. Heart defects include pulmonic stenosis, atrial septal defects and hypertrophic cardiomyopathy. Some affected individuals present with ectodermal abnormalities such as sparse, friable hair, hyperkeratotic skin lesions and a generalized ichthyosis-like condition. Typical facial features are similar to Noonan syndrome. They include high forehead with bitemporal constriction, hypoplastic supraorbital ridges, downslanting palpebral fissures, a depressed nasal bridge, and posteriorly angulated ears with prominent helices. The inheritance of CFC syndrome is autosomal dominant. Note=KRAS mutations are involved in cancer development.	+	[https://www.uniprot.org/uniprot/RASK_HUMAN RASK_HUMAN] Defects in KRAS are a cause of acute myelogenous leukemia (AML) [MIM:[https://omim.org/entry/601626 601626]. AML is a malignant disease in which hematopoietic precursors are arrested in an early stage of development.<ref>PMID:8955068</ref> Defects in KRAS are a cause of juvenile myelomonocytic leukemia (JMML) [MIM:[https://omim.org/entry/607785 607785]. JMML is a pediatric myelodysplastic syndrome that constitutes approximately 30% of childhood cases of myelodysplastic syndrome (MDS) and 2% of leukemia. It is characterized by leukocytosis with tissue infiltration and in vitro hypersensitivity of myeloid progenitors to granulocyte-macrophage colony stimulating factor. Defects in KRAS are the cause of Noonan syndrome type 3 (NS3) [MIM:[https://omim.org/entry/609942 609942]. Noonan syndrome (NS) [MIM:[https://omim.org/entry/163950 163950] is a disorder characterized by dysmorphic facial features, short stature, hypertelorism, cardiac anomalies, deafness, motor delay, and a bleeding diathesis. It is a genetically heterogeneous and relatively common syndrome, with an estimated incidence of 1 in 1000-2500 live births. Rarely, NS is associated with juvenile myelomonocytic leukemia (JMML). NS3 inheritance is autosomal dominant.<ref>PMID:16773572</ref> <ref>PMID:16474405</ref> <ref>PMID:17468812</ref> <ref>PMID:17056636</ref> <ref>PMID:19396835</ref> <ref>PMID:20949621</ref> Defects in KRAS are a cause of gastric cancer (GASC) [MIM:[https://omim.org/entry/613659 613659]; also called gastric cancer intestinal or stomach cancer. Gastric cancer is a malignant disease which starts in the stomach, can spread to the esophagus or the small intestine, and can extend through the stomach wall to nearby lymph nodes and organs. It also can metastasize to other parts of the body. The term gastric cancer or gastric carcinoma refers to adenocarcinoma of the stomach that accounts for most of all gastric malignant tumors. Two main histologic types are recognized, diffuse type and intestinal type carcinomas. Diffuse tumors are poorly differentiated infiltrating lesions, resulting in thickening of the stomach. In contrast, intestinal tumors are usually exophytic, often ulcerating, and associated with intestinal metaplasia of the stomach, most often observed in sporadic disease.<ref>PMID:3034404</ref> <ref>PMID:7773929</ref> <ref>PMID:14534542</ref> Note=Defects in KRAS are a cause of pylocytic astrocytoma (PA). Pylocytic astrocytomas are neoplasms of the brain and spinal cord derived from glial cells which vary from histologically benign forms to highly anaplastic and malignant tumors.<ref>PMID:8439212</ref> Defects in KRAS are a cause of cardiofaciocutaneous syndrome (CFC syndrome) [MIM:[https://omim.org/entry/115150 115150]; also known as cardio-facio-cutaneous syndrome. CFC syndrome is characterized by a distinctive facial appearance, heart defects and mental retardation. Heart defects include pulmonic stenosis, atrial septal defects and hypertrophic cardiomyopathy. Some affected individuals present with ectodermal abnormalities such as sparse, friable hair, hyperkeratotic skin lesions and a generalized ichthyosis-like condition. Typical facial features are similar to Noonan syndrome. They include high forehead with bitemporal constriction, hypoplastic supraorbital ridges, downslanting palpebral fissures, a depressed nasal bridge, and posteriorly angulated ears with prominent helices. The inheritance of CFC syndrome is autosomal dominant. Note=KRAS mutations are involved in cancer development.
	== Function ==		== Function ==
-	[[http://www.uniprot.org/uniprot/APOA1_HUMAN APOA1_HUMAN]] Participates in the reverse transport of cholesterol from tissues to the liver for excretion by promoting cholesterol efflux from tissues and by acting as a cofactor for the lecithin cholesterol acyltransferase (LCAT). As part of the SPAP complex, activates spermatozoa motility.<ref>PMID:1909888</ref> [[http://www.uniprot.org/uniprot/RASK_HUMAN RASK_HUMAN]] Ras proteins bind GDP/GTP and possess intrinsic GTPase activity.	+	[https://www.uniprot.org/uniprot/RASK_HUMAN RASK_HUMAN] Ras proteins bind GDP/GTP and possess intrinsic GTPase activity.
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 21:		Line 20:
	</div>		</div>
	<div class="pdbe-citations 6cch" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 6cch" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[GTPase KRas 3D structures\|GTPase KRas 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Human~~]]	+	[[Category: Homo sapiens]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Fang, Z]]	+	[[Category: Fang Z]]
-	[[Category: Gossert~~, A D~~]]	+	[[Category: Gossert AD]]
-	[[Category: Ikura, M]]	+	[[Category: Ikura M]]
-	[[Category: Jahnke, W]]	+	[[Category: Jahnke W]]
-	[[Category: Jansen~~, J M~~]]	+	[[Category: Jansen JM]]
-	[[Category: Marshall~~, C B~~]]	+	[[Category: Marshall CB]]
-	[[Category: Nishikawa, T]]	+	[[Category: Nishikawa T]]
-	~~[[Category: Membrane protein-oncoprotein complex]]~~	+
-	~~[[Category: Protein-bilayer-compound complex~~]]	+

OCA at 06:58, 27 March 2019

2019-03-27T06:58:51Z

←Older revision		Revision as of 06:58, 27 March 2019
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	==NMR data-driven model of GTPase KRas-GMPPNP tethered to a nanodisc (E3 state)==		==NMR data-driven model of GTPase KRas-GMPPNP tethered to a nanodisc (E3 state)==
-	<StructureSection load='6cch' size='340' side='right' caption='[[6cch]], [[NMR_Ensembles_of_Models \| 7 NMR models]]' scene=''>	+	<StructureSection load='6cch' size='340' side='right'caption='[[6cch]], [[NMR_Ensembles_of_Models \| 7 NMR models]]' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[6cch]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Human Human]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6CCH OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6CCH FirstGlance]. <br>		<table><tr><td colspan='2'>[[6cch]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Human Human]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6CCH OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6CCH FirstGlance]. <br>
Line 26:		Line 26:
	</StructureSection>		</StructureSection>
	[[Category: Human]]		[[Category: Human]]
		+	[[Category: Large Structures]]
	[[Category: Fang, Z]]		[[Category: Fang, Z]]
	[[Category: Gossert, A D]]		[[Category: Gossert, A D]]

OCA at 10:26, 5 September 2018

2018-09-05T10:26:27Z

←Older revision		Revision as of 10:26, 5 September 2018
Line 3:		Line 3:
	<StructureSection load='6cch' size='340' side='right' caption='[[6cch]], [[NMR_Ensembles_of_Models \| 7 NMR models]]' scene=''>		<StructureSection load='6cch' size='340' side='right' caption='[[6cch]], [[NMR_Ensembles_of_Models \| 7 NMR models]]' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6cch]] is a 3 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6CCH OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6CCH FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6cch]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Human Human]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6CCH OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6CCH FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=17F:O-[(S)-({(2R)-2,3-BIS[(9Z)-OCTADEC-9-ENOYLOXY]PROPYL}OXY)(HYDROXY)PHOSPHORYL]-L-SERINE'>17F</scene>, <scene name='pdbligand=GNP:PHOSPHOAMINOPHOSPHONIC+ACID-GUANYLATE+ESTER'>GNP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PCW:1,2-DIOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE'>PCW</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=17F:O-[(S)-({(2R)-2,3-BIS[(9Z)-OCTADEC-9-ENOYLOXY]PROPYL}OXY)(HYDROXY)PHOSPHORYL]-L-SERINE'>17F</scene>, <scene name='pdbligand=GNP:PHOSPHOAMINOPHOSPHONIC+ACID-GUANYLATE+ESTER'>GNP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PCW:1,2-DIOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE'>PCW</scene></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">APOA1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN]), KRAS, KRAS2, RASK2 ([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=6cch FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6cch OCA], [http://pdbe.org/6cch PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6cch RCSB], [http://www.ebi.ac.uk/pdbsum/6cch PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6cch 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=6cch FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6cch OCA], [http://pdbe.org/6cch PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6cch RCSB], [http://www.ebi.ac.uk/pdbsum/6cch PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6cch ProSAT]</span></td></tr>
	</table>		</table>
Line 11:		Line 12:
	== Function ==		== Function ==
	[[http://www.uniprot.org/uniprot/APOA1_HUMAN APOA1_HUMAN]] Participates in the reverse transport of cholesterol from tissues to the liver for excretion by promoting cholesterol efflux from tissues and by acting as a cofactor for the lecithin cholesterol acyltransferase (LCAT). As part of the SPAP complex, activates spermatozoa motility.<ref>PMID:1909888</ref> [[http://www.uniprot.org/uniprot/RASK_HUMAN RASK_HUMAN]] Ras proteins bind GDP/GTP and possess intrinsic GTPase activity.		[[http://www.uniprot.org/uniprot/APOA1_HUMAN APOA1_HUMAN]] Participates in the reverse transport of cholesterol from tissues to the liver for excretion by promoting cholesterol efflux from tissues and by acting as a cofactor for the lecithin cholesterol acyltransferase (LCAT). As part of the SPAP complex, activates spermatozoa motility.<ref>PMID:1909888</ref> [[http://www.uniprot.org/uniprot/RASK_HUMAN RASK_HUMAN]] Ras proteins bind GDP/GTP and possess intrinsic GTPase activity.
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	KRAS is frequently mutated in several of the most lethal types of cancer; however, the KRAS protein has proven a challenging drug target. K-RAS4B must be localized to the plasma membrane by prenylation to activate oncogenic signaling, thus we endeavored to target the protein-membrane interface with small-molecule compounds. While all reported lead compounds have low affinity for KRAS in solution, the potency of Cmpd2 was strongly enhanced when prenylated K-RAS4B is associated with a lipid bilayer. We have elucidated a unique mechanism of action of Cmpd2, which simultaneously engages a shallow pocket on KRAS and associates with the lipid bilayer, thereby stabilizing KRAS in an orientation in which the membrane occludes its effector-binding site, reducing RAF binding and impairing activation of RAF. Furthermore, enrichment of Cmpd2 on the bilayer enhances potency by promoting interaction with KRAS. This insight reveals a novel approach to developing inhibitors of membrane-associated proteins.
		+
		+	Inhibition of K-RAS4B by a Unique Mechanism of Action: Stabilizing Membrane-Dependent Occlusion of the Effector-Binding Site.,Fang Z, Marshall CB, Nishikawa T, Gossert AD, Jansen JM, Jahnke W, Ikura M Cell Chem Biol. 2018 Aug 14. pii: S2451-9456(18)30261-7. doi:, 10.1016/j.chembiol.2018.07.009. PMID:30122370<ref>PMID:30122370</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 6cch" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Human]]
	[[Category: Fang, Z]]		[[Category: Fang, Z]]
	[[Category: Gossert, A D]]		[[Category: Gossert, A D]]

OCA at 07:26, 29 August 2018

2018-08-29T07:26:03Z

←Older revision		Revision as of 07:26, 29 August 2018
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 6cch is ~~ON HOLD until Paper Publication~~	+	==NMR data-driven model of GTPase KRas-GMPPNP tethered to a nanodisc (E3 state)==
-		+	<StructureSection load='6cch' size='340' side='right' caption='[[6cch]], [[NMR_Ensembles_of_Models \| 7 NMR models]]' scene=''>
-	~~Authors~~: ~~Fang~~, Z., ~~Marshall~~, C.B., ~~Nishikawa~~, T., ~~Gossert~~, A.D., ~~Jansen~~, J.M., ~~Jahnke~~, W., ~~Ikura~~, M.	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[6cch]] is a 3 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6CCH OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6CCH FirstGlance]. <br>
-	~~Description~~: ~~NMR data-driven model~~ of ~~GTPase KRas-GMPPNP tethered~~ to a ~~nanodisc~~ (~~E3 state~~)	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=17F:O-[(S)-({(2R)-2,3-BIS[(9Z)-OCTADEC-9-ENOYLOXY]PROPYL}OXY)(HYDROXY)PHOSPHORYL]-L-SERINE'>17F</scene>, <scene name='pdbligand=GNP:PHOSPHOAMINOPHOSPHONIC+ACID-GUANYLATE+ESTER'>GNP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PCW:1,2-DIOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE'>PCW</scene></td></tr>
-	[[Category: ~~Unreleased Structures~~]]	+	<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=6cch FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6cch OCA], [http://pdbe.org/6cch PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6cch RCSB], [http://www.ebi.ac.uk/pdbsum/6cch PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6cch ProSAT]</span></td></tr>
		+	</table>
		+	== Disease ==
		+	[[http://www.uniprot.org/uniprot/APOA1_HUMAN APOA1_HUMAN]] Defects in APOA1 are a cause of high density lipoprotein deficiency type 2 (HDLD2) [MIM:[http://omim.org/entry/604091 604091]]; also known as familial hypoalphalipoproteinemia (FHA). Inheritance is autosomal dominant.<ref>PMID:8240372</ref> <ref>PMID:8282791</ref> Defects in APOA1 are a cause of the low HDL levels observed in high density lipoprotein deficiency type 1 (HDLD1) [MIM:[http://omim.org/entry/205400 205400]]; also known as analphalipoproteinemia or Tangier disease (TGD). HDLD1 is a recessive disorder characterized by the absence of plasma HDL, accumulation of cholesteryl esters, premature coronary artery disease, hepatosplenomegaly, recurrent peripheral neuropathy and progressive muscle wasting and weakness. In HDLD1 patients, ApoA-I fails to associate with HDL probably because of the faulty conversion of pro-ApoA-I molecules into mature chains, either due to a defect in the converting enzyme activity or a specific structural defect in Tangier ApoA-I.<ref>PMID:8240372</ref> <ref>PMID:8282791</ref> Note=A mutation in APOA1 is the cause of amyloid polyneuropathy-nephropathy Iowa type (AMYLIOWA); also known as amyloidosis van Allen type or familial amyloid polyneuropathy type III. AMYLIOWA is a hereditary generalized amyloidosis due to deposition of amyloid mainly constituted by apolipoprotein A1. The clinical picture is dominated by neuropathy in the early stages of the disease and nephropathy late in the course. Death is due in most cases to renal amyloidosis. Severe peptic ulcer disease can occurr in some and hearing loss is frequent. Cataracts is present in several, but vitreous opacities are not observed.<ref>PMID:8240372</ref> <ref>PMID:8282791</ref> <ref>PMID:3142462</ref> <ref>PMID:2123470</ref> Defects in APOA1 are a cause of amyloidosis type 8 (AMYL8) [MIM:[http://omim.org/entry/105200 105200]]; also known as systemic non-neuropathic amyloidosis or Ostertag-type amyloidosis. AMYL8 is a hereditary generalized amyloidosis due to deposition of apolipoprotein A1, fibrinogen and lysozyme amyloids. Viscera are particularly affected. There is no involvement of the nervous system. Clinical features include renal amyloidosis resulting in nephrotic syndrome, arterial hypertension, hepatosplenomegaly, cholestasis, petechial skin rash.<ref>PMID:8240372</ref> <ref>PMID:8282791</ref> <ref>PMID:1502149</ref> [[http://www.uniprot.org/uniprot/RASK_HUMAN RASK_HUMAN]] Defects in KRAS are a cause of acute myelogenous leukemia (AML) [MIM:[http://omim.org/entry/601626 601626]]. AML is a malignant disease in which hematopoietic precursors are arrested in an early stage of development.<ref>PMID:8955068</ref> Defects in KRAS are a cause of juvenile myelomonocytic leukemia (JMML) [MIM:[http://omim.org/entry/607785 607785]]. JMML is a pediatric myelodysplastic syndrome that constitutes approximately 30% of childhood cases of myelodysplastic syndrome (MDS) and 2% of leukemia. It is characterized by leukocytosis with tissue infiltration and in vitro hypersensitivity of myeloid progenitors to granulocyte-macrophage colony stimulating factor. Defects in KRAS are the cause of Noonan syndrome type 3 (NS3) [MIM:[http://omim.org/entry/609942 609942]]. Noonan syndrome (NS) [MIM:[http://omim.org/entry/163950 163950]] is a disorder characterized by dysmorphic facial features, short stature, hypertelorism, cardiac anomalies, deafness, motor delay, and a bleeding diathesis. It is a genetically heterogeneous and relatively common syndrome, with an estimated incidence of 1 in 1000-2500 live births. Rarely, NS is associated with juvenile myelomonocytic leukemia (JMML). NS3 inheritance is autosomal dominant.<ref>PMID:16773572</ref> <ref>PMID:16474405</ref> <ref>PMID:17468812</ref> <ref>PMID:17056636</ref> <ref>PMID:19396835</ref> <ref>PMID:20949621</ref> Defects in KRAS are a cause of gastric cancer (GASC) [MIM:[http://omim.org/entry/613659 613659]]; also called gastric cancer intestinal or stomach cancer. Gastric cancer is a malignant disease which starts in the stomach, can spread to the esophagus or the small intestine, and can extend through the stomach wall to nearby lymph nodes and organs. It also can metastasize to other parts of the body. The term gastric cancer or gastric carcinoma refers to adenocarcinoma of the stomach that accounts for most of all gastric malignant tumors. Two main histologic types are recognized, diffuse type and intestinal type carcinomas. Diffuse tumors are poorly differentiated infiltrating lesions, resulting in thickening of the stomach. In contrast, intestinal tumors are usually exophytic, often ulcerating, and associated with intestinal metaplasia of the stomach, most often observed in sporadic disease.<ref>PMID:3034404</ref> <ref>PMID:7773929</ref> <ref>PMID:14534542</ref> Note=Defects in KRAS are a cause of pylocytic astrocytoma (PA). Pylocytic astrocytomas are neoplasms of the brain and spinal cord derived from glial cells which vary from histologically benign forms to highly anaplastic and malignant tumors.<ref>PMID:8439212</ref> Defects in KRAS are a cause of cardiofaciocutaneous syndrome (CFC syndrome) [MIM:[http://omim.org/entry/115150 115150]]; also known as cardio-facio-cutaneous syndrome. CFC syndrome is characterized by a distinctive facial appearance, heart defects and mental retardation. Heart defects include pulmonic stenosis, atrial septal defects and hypertrophic cardiomyopathy. Some affected individuals present with ectodermal abnormalities such as sparse, friable hair, hyperkeratotic skin lesions and a generalized ichthyosis-like condition. Typical facial features are similar to Noonan syndrome. They include high forehead with bitemporal constriction, hypoplastic supraorbital ridges, downslanting palpebral fissures, a depressed nasal bridge, and posteriorly angulated ears with prominent helices. The inheritance of CFC syndrome is autosomal dominant. Note=KRAS mutations are involved in cancer development.
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/APOA1_HUMAN APOA1_HUMAN]] Participates in the reverse transport of cholesterol from tissues to the liver for excretion by promoting cholesterol efflux from tissues and by acting as a cofactor for the lecithin cholesterol acyltransferase (LCAT). As part of the SPAP complex, activates spermatozoa motility.<ref>PMID:1909888</ref> [[http://www.uniprot.org/uniprot/RASK_HUMAN RASK_HUMAN]] Ras proteins bind GDP/GTP and possess intrinsic GTPase activity.
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Fang, Z]]
		+	[[Category: Gossert, A D]]
	[[Category: Ikura, M]]		[[Category: Ikura, M]]
-	[[Category: ~~Fang~~, Z]]	+	[[Category: Jahnke, W]]
		+	[[Category: Jansen, J M]]
		+	[[Category: Marshall, C B]]
	[[Category: Nishikawa, T]]		[[Category: Nishikawa, T]]
-	[[Category: ~~Jahnke, W~~]]	+	[[Category: Membrane protein-oncoprotein complex]]
-	[[Category: ~~Jansen, J.M]]~~	+	[[Category: Protein-bilayer-compound complex]]
-	~~[[Category: Marshall, C.B]]~~	+
-	~~[[Category: Gossert, A.D~~]]	+

OCA at 03:57, 16 May 2018

2018-05-16T03:57:37Z

←Older revision		Revision as of 03:57, 16 May 2018
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	'''Unreleased structure'''		'''Unreleased structure'''

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

	Authors: Fang, Z., Marshall, C.B., Nishikawa, T., Gossert, A.D., Jansen, J.M., Jahnke, W., Ikura, M.		Authors: Fang, Z., Marshall, C.B., Nishikawa, T., Gossert, A.D., Jansen, J.M., Jahnke, W., Ikura, M.

OCA at 05:00, 28 February 2018

2018-02-28T05:00:31Z

←Older revision		Revision as of 05:00, 28 February 2018
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	Authors: Fang, Z., Marshall, C.B., Nishikawa, T., Gossert, A.D., Jansen, J.M., Jahnke, W., Ikura, M.		Authors: Fang, Z., Marshall, C.B., Nishikawa, T., Gossert, A.D., Jansen, J.M., Jahnke, W., Ikura, M.

-	Description: NMR data-driven model of GTPase KRas-GMPPNP~~:Cmpd2 complex~~ tethered to a nanodisc	+	Description: NMR data-driven model of GTPase KRas-GMPPNP tethered to a nanodisc (E3 state)
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
	[[Category: Ikura, M]]		[[Category: Ikura, M]]
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	[[Category: Nishikawa, T]]		[[Category: Nishikawa, T]]
	[[Category: Jahnke, W]]		[[Category: Jahnke, W]]
-	[[Category: Marshall, C.B]]
	[[Category: Jansen, J.M]]		[[Category: Jansen, J.M]]
		+	[[Category: Marshall, C.B]]
	[[Category: Gossert, A.D]]		[[Category: Gossert, A.D]]

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

2018-02-15T05:22:50Z

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

←Older revision

Revision as of 05:22, 15 February 2018

OCA: New page: '''Unreleased structure''' The entry 6cch is ON HOLD Authors: Fang, Z., Marshall, C.B., Nishikawa, T., Gossert, A.D., Jansen, J.M., Jahnke, W., Ikura, M. Description: NMR data-driven m...

2018-02-15T05:22:49Z

New page: '''Unreleased structure''' The entry 6cch is ON HOLD Authors: Fang, Z., Marshall, C.B., Nishikawa, T., Gossert, A.D., Jansen, J.M., Jahnke, W., Ikura, M. Description: NMR data-driven m...

New page

'''Unreleased structure'''

The entry 6cch is ON HOLD

Authors: Fang, Z., Marshall, C.B., Nishikawa, T., Gossert, A.D., Jansen, J.M., Jahnke, W., Ikura, M.

Description: NMR data-driven model of GTPase KRas-GMPPNP:Cmpd2 complex tethered to a nanodisc
[[Category: Unreleased Structures]]
[[Category: Ikura, M]]
[[Category: Fang, Z]]
[[Category: Nishikawa, T]]
[[Category: Jahnke, W]]
[[Category: Marshall, C.B]]
[[Category: Jansen, J.M]]
[[Category: Gossert, A.D]]