6oge - Revision history

OCA at 03:58, 11 April 2020

OCA — Sat, 11 Apr 2020 03:58:05 GMT

←Older revision		Revision as of 03:58, 11 April 2020
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	<SX load='6oge' size='340' side='right' viewer='molstar' caption='[[6oge]], [[Resolution\|resolution]] 4.36Å' scene=''>		<SX load='6oge' size='340' side='right' viewer='molstar' caption='[[6oge]], [[Resolution\|resolution]] 4.36Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6oge]] is a 5 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=6OGE OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=6OGE FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6oge]] is a 5 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=6OGE OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6OGE FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BMA:BETA-D-MANNOSE'>BMA</scene>, <scene name='pdbligand=MAN:ALPHA-D-MANNOSE'>MAN</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BMA:BETA-D-MANNOSE'>BMA</scene>, <scene name='pdbligand=MAN:ALPHA-D-MANNOSE'>MAN</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene></td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">ERBB2, HER2, MLN19, NEU, NGL ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN]), IGKC ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN]), IGH@ ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">ERBB2, HER2, MLN19, NEU, NGL ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN]), IGKC ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN]), IGH@ ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Receptor_protein-tyrosine_kinase Receptor protein-tyrosine kinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.10.1 2.7.10.1] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Receptor_protein-tyrosine_kinase Receptor protein-tyrosine kinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.10.1 2.7.10.1] </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=6oge FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6oge OCA], [http://pdbe.org/6oge PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6oge RCSB], [http://www.ebi.ac.uk/pdbsum/6oge PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6oge ProSAT]</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=6oge FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6oge OCA], [http://pdbe.org/6oge PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6oge RCSB], [http://www.ebi.ac.uk/pdbsum/6oge PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6oge ProSAT]</span></td></tr>
	</table>		</table>
	== Disease ==		== Disease ==

OCA at 23:12, 6 March 2020

OCA — Fri, 06 Mar 2020 23:12:00 GMT

←Older revision		Revision as of 23:12, 6 March 2020
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	==Cryo-EM structure of Her2 extracellular domain-Trastuzumab Fab-Pertuzumab Fab complex==		==Cryo-EM structure of Her2 extracellular domain-Trastuzumab Fab-Pertuzumab Fab complex==
-	<~~StructureSection~~ load='6oge' size='340' side='right'caption='[[6oge]], [[Resolution\|resolution]] 4.36Å' scene=''>	+	<SX load='6oge' size='340' side='right' viewer='molstar' caption='[[6oge]], [[Resolution\|resolution]] 4.36Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[6oge]] is a 5 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=6OGE OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6OGE FirstGlance]. <br>		<table><tr><td colspan='2'>[[6oge]] is a 5 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=6OGE OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6OGE FirstGlance]. <br>
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	<references/>		<references/>
	__TOC__		__TOC__
-	</~~StructureSection~~>	+	</SX>
	[[Category: Human]]		[[Category: Human]]
	[[Category: Large Structures]]		[[Category: Large Structures]]

OCA at 07:35, 21 May 2019

OCA — Tue, 21 May 2019 07:35:43 GMT

←Older revision		Revision as of 07:35, 21 May 2019
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-	'''Unreleased structure'''

-	The entry ~~6oge~~ is ~~ON HOLD~~ ~~until Paper~~ Publication	+	==Cryo-EM structure of Her2 extracellular domain-Trastuzumab Fab-Pertuzumab Fab complex==
		+	<StructureSection load='6oge' size='340' side='right'caption='[[6oge]], [[Resolution\|resolution]] 4.36Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[6oge]] is a 5 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=6OGE OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6OGE FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BMA:BETA-D-MANNOSE'>BMA</scene>, <scene name='pdbligand=MAN:ALPHA-D-MANNOSE'>MAN</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">ERBB2, HER2, MLN19, NEU, NGL ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN]), IGKC ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN]), IGH@ ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])</td></tr>
		+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Receptor_protein-tyrosine_kinase Receptor protein-tyrosine kinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.10.1 2.7.10.1] </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=6oge FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6oge OCA], [http://pdbe.org/6oge PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6oge RCSB], [http://www.ebi.ac.uk/pdbsum/6oge PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6oge ProSAT]</span></td></tr>
		+	</table>
		+	== Disease ==
		+	[[http://www.uniprot.org/uniprot/ERBB2_HUMAN ERBB2_HUMAN]] Defects in ERBB2 are a cause of hereditary diffuse gastric cancer (HDGC) [MIM:[http://omim.org/entry/137215 137215]]. A cancer predisposition syndrome with increased susceptibility to diffuse gastric cancer. Diffuse gastric cancer is a malignant disease characterized by poorly differentiated infiltrating lesions resulting in thickening of the stomach. Malignant tumors start 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. Defects in ERBB2 are involved in the development of glioma (GLM) [MIM:[http://omim.org/entry/137800 137800]]. Gliomas are central nervous system neoplasms derived from glial cells and comprise astrocytomas, glioblastoma multiforme, oligodendrogliomas, and ependymomas. Defects in ERBB2 are a cause of susceptibility to ovarian cancer (OC) [MIM:[http://omim.org/entry/167000 167000]]. Ovarian cancer common malignancy originating from ovarian tissue. Although many histologic types of ovarian neoplasms have been described, epithelial ovarian carcinoma is the most common form. Ovarian cancers are often asymptomatic and the recognized signs and symptoms, even of late-stage disease, are vague. Consequently, most patients are diagnosed with advanced disease. Defects in ERBB2 may be a cause of lung cancer (LNCR) [MIM:[http://omim.org/entry/211980 211980]]. LNCR is a common malignancy affecting tissues of the lung. The most common form of lung cancer is non-small cell lung cancer (NSCLC) that can be divided into 3 major histologic subtypes: squamous cell carcinoma, adenocarcinoma, and large cell lung cancer. NSCLC is often diagnosed at an advanced stage and has a poor prognosis. Defects in ERBB2 are a cause of gastric cancer (GASC) [MIM:[http://omim.org/entry/613659 613659]]. 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. Note=Chromosomal aberrations involving ERBB2 may be a cause gastric cancer. Deletions within 17q12 region producing fusion transcripts with CDK12, leading to CDK12-ERBB2 fusion leading to truncated CDK12 protein not in-frame with ERBB2.
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/ERBB2_HUMAN ERBB2_HUMAN]] Protein tyrosine kinase that is part of several cell surface receptor complexes, but that apparently needs a coreceptor for ligand binding. Essential component of a neuregulin-receptor complex, although neuregulins do not interact with it alone. GP30 is a potential ligand for this receptor. Regulates outgrowth and stabilization of peripheral microtubules (MTs). Upon ERBB2 activation, the MEMO1-RHOA-DIAPH1 signaling pathway elicits the phosphorylation and thus the inhibition of GSK3B at cell membrane. This prevents the phosphorylation of APC and CLASP2, allowing its association with the cell membrane. In turn, membrane-bound APC allows the localization of MACF1 to the cell membrane, which is required for microtubule capture and stabilization.<ref>PMID:10358079</ref> <ref>PMID:15380516</ref> <ref>PMID:16794579</ref> <ref>PMID:19372587</ref> <ref>PMID:20937854</ref> <ref>PMID:21555369</ref> In the nucleus is involved in transcriptional regulation. Associates with the 5'-TCAAATTC-3' sequence in the PTGS2/COX-2 promoter and activates its transcription. Implicated in transcriptional activation of CDKN1A; the function involves STAT3 and SRC. Involved in the transcription of rRNA genes by RNA Pol I and enhances protein synthesis and cell growth.<ref>PMID:10358079</ref> <ref>PMID:15380516</ref> <ref>PMID:16794579</ref> <ref>PMID:19372587</ref> <ref>PMID:20937854</ref> <ref>PMID:21555369</ref>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Trastuzumab and pertuzumab are monoclonal antibodies that bind to distinct subdomains of the extracellular domain of human epidermal growth factor receptor 2 (HER2). Adding these monoclonal antibodies to the treatment regimen of HER2-positive breast cancer has changed the paradigm for treatment in that form of cancer. Synergistic activity has been observed with the combination of these two antibodies leading to hypotheses regarding the mechanism(s) and to the development of bispecific antibodies to maximize the clinical effect further. Although the individual crystal structures of HER2-trastuzumab and HER2-pertuzumab revealed the distinct binding sites and provided the structural basis for their anti-tumor activities, detailed structural information on the HER2-trastuzumab-pertuzumab complex has been elusive. Here we present the cryo-EM structure of HER2-trastuzumab-pertuzumab at 4.36 A resolution. Comparison with the binary complexes reveals no cooperative interaction between trastuzumab and pertuzumab, and provides key insights into the design of novel, high-avidity bispecific molecules with potentially greater clinical efficacy.

-	~~Authors: Hao~~, Y., Yu, X., Bai, Y., ~~Huang~~, X.	+	Cryo-EM Structure of HER2-trastuzumab-pertuzumab complex.,Hao Y, Yu X, Bai Y, McBride HJ, Huang X PLoS One. 2019 May 1;14(5):e0216095. doi: 10.1371/journal.pone.0216095., eCollection 2019. PMID:31042744<ref>PMID:31042744</ref>

-	~~Description: Cryo-EM structure~~ of ~~Her2 extracellular domain~~-~~Trastuzumab Fab~~-~~Pertuzumab Fab complex~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased~~ Structures]]	+	</div>
-	[[Category: ~~Yu, X~~]]	+	<div class="pdbe-citations 6oge" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Human]]
		+	[[Category: Large Structures]]
		+	[[Category: Receptor protein-tyrosine kinase]]
	[[Category: Bai, Y]]		[[Category: Bai, Y]]
	[[Category: Hao, Y]]		[[Category: Hao, Y]]
	[[Category: Huang, X]]		[[Category: Huang, X]]
		+	[[Category: Yu, X]]
		+	[[Category: Her2 extracellular domain]]
		+	[[Category: Pertuzumab]]
		+	[[Category: Transferase-immune system complex]]
		+	[[Category: Trastuzumab]]

OCA at 07:06, 1 May 2019

OCA — Wed, 01 May 2019 07:06:13 GMT

←Older revision		Revision as of 07:06, 1 May 2019
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	'''Unreleased structure'''		'''Unreleased structure'''

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

	Authors: Hao, Y., Yu, X., Bai, Y., Huang, X.		Authors: Hao, Y., Yu, X., Bai, Y., Huang, X.
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	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
	[[Category: Yu, X]]		[[Category: Yu, X]]
-	[[Category: Huang, X]]
	[[Category: Bai, Y]]		[[Category: Bai, Y]]
	[[Category: Hao, Y]]		[[Category: Hao, Y]]
		+	[[Category: Huang, X]]

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

OCA — Wed, 10 Apr 2019 05:34:24 GMT

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

←Older revision

Revision as of 05:34, 10 April 2019

OCA: New page: '''Unreleased structure''' The entry 6oge is ON HOLD Authors: Hao, Y., Yu, X., Bai, Y., Huang, X. Description: Cryo-EM structure of Her2 extracellular domain-Trastuzumab Fab-Pertuzumab...

OCA — Wed, 10 Apr 2019 05:34:22 GMT

New page: '''Unreleased structure''' The entry 6oge is ON HOLD Authors: Hao, Y., Yu, X., Bai, Y., Huang, X. Description: Cryo-EM structure of Her2 extracellular domain-Trastuzumab Fab-Pertuzumab...

New page

'''Unreleased structure'''

The entry 6oge is ON HOLD

Authors: Hao, Y., Yu, X., Bai, Y., Huang, X.

Description: Cryo-EM structure of Her2 extracellular domain-Trastuzumab Fab-Pertuzumab Fab complex
[[Category: Unreleased Structures]]
[[Category: Yu, X]]
[[Category: Huang, X]]
[[Category: Bai, Y]]
[[Category: Hao, Y]]