5fn4: Difference between revisions

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-'''Unreleased structure'''
+==Cryo-EM structure of gamma secretase in class 2 of the apo- state ensemble==
+<StructureSection load='5fn4' size='340' side='right' caption='[[5fn4]], [[Resolution|resolution]] 4.00&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[5fn4]] is a 5 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5FN4 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5FN4 FirstGlance]. <br>
+</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[5fn2|5fn2]], [[5fn3|5fn3]], [[5fn5|5fn5]]</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=5fn4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5fn4 OCA], [http://pdbe.org/5fn4 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5fn4 RCSB], [http://www.ebi.ac.uk/pdbsum/5fn4 PDBsum]</span></td></tr>
+</table>
+== Disease ==
+[[http://www.uniprot.org/uniprot/PEN2_HUMAN PEN2_HUMAN]] Hidradenitis suppurativa. The disease is caused by mutations affecting the gene represented in this entry. [[http://www.uniprot.org/uniprot/NICA_HUMAN NICA_HUMAN]] Hidradenitis suppurativa. The disease is caused by mutations affecting the gene represented in this entry. [[http://www.uniprot.org/uniprot/PSN1_HUMAN PSN1_HUMAN]] Defects in PSEN1 are a cause of Alzheimer disease type 3 (AD3) [MIM:[http://omim.org/entry/607822 607822]]. AD3 is a familial early-onset form of Alzheimer disease. Alzheimer disease is a neurodegenerative disorder characterized by progressive dementia, loss of cognitive abilities, and deposition of fibrillar amyloid proteins as intraneuronal neurofibrillary tangles, extracellular amyloid plaques and vascular amyloid deposits. The major constituent of these plaques is the neurotoxic amyloid-beta-APP 40-42 peptide (s), derived proteolytically from the transmembrane precursor protein APP by sequential secretase processing. The cytotoxic C-terminal fragments (CTFs) and the caspase-cleaved products such as C31 derived from APP, are also implicated in neuronal death.<ref>PMID:12058025</ref> <ref>PMID:7596406</ref> <ref>PMID:8634711</ref> <ref>PMID:8634712</ref> <ref>PMID:7651536</ref> <ref>PMID:7550356</ref> <ref>PMID:8733303</ref> <ref>PMID:9225696</ref> <ref>PMID:9298817</ref> <ref>PMID:9172170</ref> <ref>PMID:9833068</ref> <ref>PMID:9384602</ref> <ref>PMID:9521423</ref> <ref>PMID:10200054</ref> <ref>PMID:9719376</ref> <ref>PMID:9507958</ref> <ref>PMID:9831473</ref> <ref>PMID:10441572</ref> <ref>PMID:10090481</ref> <ref>PMID:10447269</ref> <ref>PMID:10533070</ref> <ref>PMID:10025789</ref> <ref>PMID:10208579</ref> <ref>PMID:10439444</ref> <ref>PMID:10631141</ref> <ref>PMID:10644793</ref> <ref>PMID:11027672</ref> [:]<ref>PMID:11710891</ref> <ref>PMID:11920851</ref> <ref>PMID:12048239</ref> <ref>PMID:12484344</ref> <ref>PMID:12493737</ref>   Defects in PSEN1 are a cause of frontotemporal dementia (FTD) [MIM:[http://omim.org/entry/600274 600274]].  Defects in PSEN1 are the cause of cardiomyopathy dilated type 1U (CMD1U) [MIM:[http://omim.org/entry/613694 613694]]. It is a disorder characterized by ventricular dilation and impaired systolic function, resulting in congestive heart failure and arrhythmia. Patients are at risk of premature death.<ref>PMID:17186461</ref>   Defects in PSEN1 are the cause of familial acne inversa type 3 (ACNINV3) [MIM:[http://omim.org/entry/613737 613737]]. A chronic relapsing inflammatory disease of the hair follicles characterized by recurrent draining sinuses, painful skin abscesses, and disfiguring scars. Manifestations typically appear after puberty.<ref>PMID:20929727</ref>
+== Function ==
+[[http://www.uniprot.org/uniprot/PEN2_HUMAN PEN2_HUMAN]] Essential subunit of the gamma-secretase complex, an endoprotease complex that catalyzes the intramembrane cleavage of integral membrane proteins such as Notch receptors and APP (beta-amyloid precursor protein). Probably represents the last step of maturation of gamma-secretase, facilitating endoproteolysis of presenilin and conferring gamma-secretase activity.<ref>PMID:12522139</ref> <ref>PMID:12763021</ref>  [[http://www.uniprot.org/uniprot/NICA_HUMAN NICA_HUMAN]] Essential subunit of the gamma-secretase complex, an endoprotease complex that catalyzes the intramembrane cleavage of integral membrane proteins such as Notch receptors and APP (beta-amyloid precursor protein). It probably represents a stabilizing cofactor required for the assembly of the gamma-secretase complex. [[http://www.uniprot.org/uniprot/APH1A_HUMAN APH1A_HUMAN]] Essential subunit of the gamma-secretase complex, an endoprotease complex that catalyzes the intramembrane cleavage of integral proteins such as Notch receptors and APP (beta-amyloid precursor protein). It probably represents a stabilizing cofactor for the presenilin homodimer that promotes the formation of a stable complex.<ref>PMID:12297508</ref> <ref>PMID:12522139</ref> <ref>PMID:12763021</ref>  [[http://www.uniprot.org/uniprot/PSN1_HUMAN PSN1_HUMAN]] Probable catalytic subunit of the gamma-secretase complex, an endoprotease complex that catalyzes the intramembrane cleavage of integral membrane proteins such as Notch receptors and APP (beta-amyloid precursor protein). Requires the other members of the gamma-secretase complex to have a protease activity. May play a role in intracellular signaling and gene expression or in linking chromatin to the nuclear membrane. Stimulates cell-cell adhesion though its association with the E-cadherin/catenin complex. Under conditions of apoptosis or calcium influx, cleaves E-cadherin promoting the disassembly of the E-cadherin/catenin complex and increasing the pool of cytoplasmic beta-catenin, thus negatively regulating Wnt signaling. May also play a role in hematopoiesis.<ref>PMID:10545183</ref> <ref>PMID:10593990</ref> <ref>PMID:10206644</ref> <ref>PMID:10899933</ref> <ref>PMID:10811883</ref> <ref>PMID:11226248</ref> <ref>PMID:15341515</ref> <ref>PMID:16305624</ref>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Human gamma-Secretase is an intra-membrane protease that cleaves many substrates. Aberrant cleavage of Notch is implicated in cancer, while abnormalities in cutting amyloid precursor protein lead to Alzheimer's disease. Our previous cryo-EM structure of gamma-secretase revealed considerable disorder in its catalytic subunit presenilin. Here, we describe an image classification procedure that characterizes molecular plasticity at the secondary structure level, and apply this method to identify three distinct conformations in our previous sample. In one of these conformations, an additional transmembrane helix is visible that cannot be attributed to known components of gamma-secretase. In addition, we present a gamma-secretase structure in complex with the dipeptidic inhibitor N-[N-(3,5-difluorophenacetyl)-L-alanyl]-S-phenylglycine t-butyl ester (DAPT). Our results reveal how conformational mobility in the second and sixth transmembrane helices of presenilin is greatly reduced upon binding of DAPT or the additional helix, and form the basis for a new model of how substrate enters the transmembrane domain.
-The entry 5fn4 is ON HOLD  until Paper Publication
+Sampling the conformational space of the catalytic subunit of human gamma-secretase.,Bai XC, Rajendra E, Yang G, Shi Y, Scheres SH Elife. 2015 Dec 1;4. pii: e11182. doi: 10.7554/eLife.11182. PMID:26623517<ref>PMID:26623517</ref>
-Authors: Bai, X.C., Rajendra, E., Yang, G.H., Shi, Y.G., Scheres, S.H.W.
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
-Description: Cryo-EM structure of gamma secretase in class 2 of the apo-state ensemble
+<div class="pdbe-citations 5fn4" style="background-color:#fffaf0;"></div>
-[[Category: Unreleased Structures]]
+== References ==
-[[Category: Yang, G.H]]
+<references/>
+__TOC__
+</StructureSection>
+[[Category: Bai, X C]]
 [[Category: Rajendra, E]]
-[[Category: Bai, X.C]]
+[[Category: Scheres, S H.W]]
-[[Category: Shi, Y.G]]
+[[Category: Shi, Y G]]
-[[Category: Scheres, S.H.W]]
+[[Category: Yang, G H]]
+[[Category: Hydrolase]]