OCA at 10:11, 22 May 2024

OCA — Wed, 22 May 2024 10:11:39 GMT

←Older revision		Revision as of 10:11, 22 May 2024
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	==Cryo-EM structure of the N-terminal DC repeat (NDC) of NDC-NDC chimera (human sequence) bound to 13-protofilament GDP-microtubule==		==Cryo-EM structure of the N-terminal DC repeat (NDC) of NDC-NDC chimera (human sequence) bound to 13-protofilament GDP-microtubule==
-	<StructureSection load='6rf8' size='340' side='right'caption='[[6rf8]]' scene=''>	+	<StructureSection load='6rf8' size='340' side='right'caption='[[6rf8]], [[Resolution\|resolution]] 3.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6RF8 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=6RF8 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6rf8]] is a 5 chain structure with sequence from [https://en.wikipedia.org/wiki/Bos_taurus Bos taurus] and [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6RF8 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6RF8 FirstGlance]. <br>
-	</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=6rf8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6rf8 OCA], [~~http~~://pdbe.org/6rf8 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6rf8 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6rf8 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6rf8 ProSAT]</span></td></tr>	+	</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models\|Method:]]</b></td><td class="sblockDat" id="methodDat">Electron Microscopy, [[Resolution\|Resolution]] 3.8Å</td></tr>
		+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GDP:GUANOSINE-5-DIPHOSPHATE'>GDP</scene>, <scene name='pdbligand=GTP:GUANOSINE-5-TRIPHOSPHATE'>GTP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</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=6rf8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6rf8 OCA], [https://pdbe.org/6rf8 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6rf8 RCSB], [https://www.ebi.ac.uk/pdbsum/6rf8 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6rf8 ProSAT]</span></td></tr>
	</table>		</table>
		+	== Disease ==
		+	[https://www.uniprot.org/uniprot/DCX_HUMAN DCX_HUMAN] Defects in DCX are the cause of lissencephaly X-linked type 1 (LISX1) [MIM:[https://omim.org/entry/300067 300067]; also called X-LIS or LIS. LISX1 is a classic lissencephaly characterized by mental retardation and seizures that are more severe in male patients. Affected boys show an abnormally thick cortex with absent or severely reduced gyri. Clinical manifestations include feeding problems, abnormal muscular tone, seizures and severe to profound psychomotor retardation. Female patients display a less severe phenotype referred to as 'doublecortex'.<ref>PMID:9489699</ref> <ref>PMID:9489700</ref> <ref>PMID:9668176</ref> <ref>PMID:9817918</ref> <ref>PMID:11468322</ref> <ref>PMID:12552055</ref> Defects in DCX are the cause of subcortical band heterotopia X-linked (SBHX) [MIM:[https://omim.org/entry/300067 300067]; also known as double cortex or subcortical laminar heterotopia (SCLH). SBHX is a mild brain malformation of the lissencephaly spectrum. It is characterized by bilateral and symmetric plates or bands of gray matter found in the central white matter between the cortex and cerebral ventricles, cerebral convolutions usually appearing normal.<ref>PMID:9618162</ref> <ref>PMID:9989615</ref> <ref>PMID:10369164</ref> <ref>PMID:10441340</ref> <ref>PMID:10807542</ref> <ref>PMID:11601509</ref> <ref>PMID:11175293</ref> <ref>PMID:12390976</ref> Note=A chromosomal aberration involving DCX is found in lissencephaly. Translocation t(X;2)(q22.3;p25.1).
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/DCX_HUMAN DCX_HUMAN] Microtubule-associated protein required for initial steps of neuronal dispersion and cortex lamination during cerebral cortex development. May act by competing with the putative neuronal protein kinase DCLK1 in binding to a target protein. May in that way participate in a signaling pathway that is crucial for neuronal interaction before and during migration, possibly as part of a calcium ion-dependent signal transduction pathway. May be part with PAFAH1B1/LIS-1 of overlapping, but distinct, signaling pathways that promote neuronal migration.<ref>PMID:22359282</ref>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Microtubules are polar filaments built from alphabeta-tubulin heterodimers that exhibit a range of architectures in vitro and in vivo. Tubulin heterodimers are arranged helically in the microtubule wall but many physiologically relevant architectures exhibit a break in helical symmetry known as the seam. Noisy 2D cryo-electron microscopy projection images of pseudo-helical microtubules therefore depict distinct but highly similar views owing to the high structural similarity of alpha- and beta-tubulin. The determination of the alphabeta-tubulin register and seam location during image processing is essential for alignment accuracy that enables determination of biologically relevant structures. Here we present a pipeline designed for image processing and high-resolution reconstruction of cryo-electron microscopy microtubule datasets, based in the popular and user-friendly RELION image-processing package, Microtubule RELION-based Pipeline (MiRP). The pipeline uses a combination of supervised classification and prior knowledge about geometric lattice constraints in microtubules to accurately determine microtubule architecture and seam location. The presented method is fast and semi-automated, producing near-atomic resolution reconstructions with test datasets that contain a range of microtubule architectures and binding proteins.
		+
		+	A microtubule RELION-based pipeline for cryo-EM image processing.,Cook AD, Manka SW, Wang S, Moores CA, Atherton J J Struct Biol. 2020 Jan 1;209(1):107402. doi: 10.1016/j.jsb.2019.10.004. Epub, 2019 Oct 11. PMID:31610239<ref>PMID:31610239</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 6rf8" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Tubulin 3D Structures\|Tubulin 3D Structures]]
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Bos taurus]]
		+	[[Category: Homo sapiens]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: Manka SW]]		[[Category: Manka SW]]

OCA at 06:56, 15 April 2020

OCA — Wed, 15 Apr 2020 06:56:24 GMT

←Older revision		Revision as of 06:56, 15 April 2020
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-	'''Unreleased structure'''

-	~~The entry 6rf8 is ON HOLD~~	+	==Cryo-EM structure of the N-terminal DC repeat (NDC) of NDC-NDC chimera (human sequence) bound to 13-protofilament GDP-microtubule==
-		+	<StructureSection load='6rf8' size='340' side='right'caption='[[6rf8]]' scene=''>
-	~~Authors: Manka, S.W.~~	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6RF8 OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6RF8 FirstGlance]. <br>
-	~~Description:~~ Cryo-EM structure of the N-terminal DC repeat (NDC) of NDC-NDC chimera (human sequence) bound to 13-protofilament GDP-microtubule	+	</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=6rf8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6rf8 OCA], [http://pdbe.org/6rf8 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6rf8 RCSB], [http://www.ebi.ac.uk/pdbsum/6rf8 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6rf8 ProSAT]</span></td></tr>
-	[[Category: ~~Unreleased~~ Structures]]	+	</table>
-	[[Category: Manka~~, S.W~~]]	+	__TOC__
		+	</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Manka SW]]

OCA: Protected "6rf8" [edit=sysop:move=sysop]

OCA — Wed, 24 Apr 2019 05:14:33 GMT

Protected "6rf8" [edit=sysop:move=sysop]

←Older revision

Revision as of 05:14, 24 April 2019

OCA: New page: '''Unreleased structure''' The entry 6rf8 is ON HOLD Authors: Manka, S.W. Description: Cryo-EM structure of the N-terminal DC repeat (NDC) of NDC-NDC chimera (human sequence) bound to ...

OCA — Wed, 24 Apr 2019 05:14:32 GMT

New page: '''Unreleased structure''' The entry 6rf8 is ON HOLD Authors: Manka, S.W. Description: Cryo-EM structure of the N-terminal DC repeat (NDC) of NDC-NDC chimera (human sequence) bound to ...

New page

'''Unreleased structure'''

The entry 6rf8 is ON HOLD

Authors: Manka, S.W.

Description: Cryo-EM structure of the N-terminal DC repeat (NDC) of NDC-NDC chimera (human sequence) bound to 13-protofilament GDP-microtubule
[[Category: Unreleased Structures]]
[[Category: Manka, S.W]]

6rf8 - Revision history

OCA at 10:11, 22 May 2024

OCA at 06:56, 15 April 2020

OCA: Protected "6rf8" [edit=sysop:move=sysop]

OCA: New page: '''Unreleased structure''' The entry 6rf8 is ON HOLD Authors: Manka, S.W. Description: Cryo-EM structure of the N-terminal DC repeat (NDC) of NDC-NDC chimera (human sequence) bound to ...