5klr - Revision history

OCA at 10:03, 27 September 2023

OCA — Wed, 27 Sep 2023 10:03:25 GMT

←Older revision		Revision as of 10:03, 27 September 2023
Line 1:		Line 1:

	==Prototypical P4[R]cNLS==		==Prototypical P4[R]cNLS==
-	<StructureSection load='5klr' size='340' side='right' caption='[[5klr]], [[Resolution\|resolution]] 2.20Å' scene=''>	+	<StructureSection load='5klr' size='340' side='right'caption='[[5klr]], [[Resolution\|resolution]] 2.20Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5klr]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Lk3_transgenic_mice Lk3 transgenic mice~~] and [~~http~~://en.wikipedia.org/wiki/~~Synthetic_construct_sequences~~ Synthetic construct ~~sequences~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5KLR OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5KLR FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5klr]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Mus_musculus Mus musculus] and [https://en.wikipedia.org/wiki/Synthetic_construct Synthetic construct]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5KLR OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5KLR FirstGlance]. <br>
-	</td></tr><tr id='~~related~~'><td class="sblockLbl"><b>[[~~Related_structure~~\|~~Related~~:]]</b></td><td class="sblockDat"~~>[[5klt\|5klt]]</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~~='gene'><td class~~="~~sblockLbl~~">~~<b>~~[[~~Gene~~\|~~Gene:~~]]~~</b></td><td class="sblockDat">Kpna2, Rch1 ([http://www~~.~~ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info~~&~~srchmode=5&id=10090 LK3 transgenic mice])~~</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=5klr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5klr OCA], [https://pdbe.org/5klr PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5klr RCSB], [https://www.ebi.ac.uk/pdbsum/5klr PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5klr 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=5klr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5klr OCA], [~~http~~://pdbe.org/5klr PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5klr RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5klr PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5klr ProSAT]</span></td></tr>	+
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/IMA1_MOUSE IMA1_MOUSE]] Functions in nuclear protein import as an adapter protein for nuclear receptor KPNB1. Binds specifically and directly to substrates containing either a simple or bipartite NLS motif. Docking of the importin/substrate complex to the nuclear pore complex (NPC) is mediated by KPNB1 through binding to nucleoporin FxFG repeats and the complex is subsequently translocated through the pore by an energy requiring, Ran-dependent mechanism. At the nucleoplasmic side of the NPC, Ran binds to importin-beta and the three components separate and importin-alpha and -beta are re-exported from the nucleus to the cytoplasm where GTP hydrolysis releases Ran from importin. The directionality of nuclear import is thought to be conferred by an asymmetric distribution of the GTP- and GDP-bound forms of Ran between the cytoplasm and nucleus.	+	[https://www.uniprot.org/uniprot/IMA1_MOUSE IMA1_MOUSE] Functions in nuclear protein import as an adapter protein for nuclear receptor KPNB1. Binds specifically and directly to substrates containing either a simple or bipartite NLS motif. Docking of the importin/substrate complex to the nuclear pore complex (NPC) is mediated by KPNB1 through binding to nucleoporin FxFG repeats and the complex is subsequently translocated through the pore by an energy requiring, Ran-dependent mechanism. At the nucleoplasmic side of the NPC, Ran binds to importin-beta and the three components separate and importin-alpha and -beta are re-exported from the nucleus to the cytoplasm where GTP hydrolysis releases Ran from importin. The directionality of nuclear import is thought to be conferred by an asymmetric distribution of the GTP- and GDP-bound forms of Ran between the cytoplasm and nucleus.
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 21:		Line 20:

	==See Also==		==See Also==
-	*[[Importin\|Importin]]	+	*[[Importin 3D structures\|Importin 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Lk3 transgenic mice~~]]	+	[[Category: Large Structures]]
-	[[Category: ~~Synthetic construct sequences~~]]	+	[[Category: Mus musculus]]
-	[[Category: ~~Forwood, J K~~]]	+	[[Category: Synthetic construct]]
-	[[Category: ~~Smith, K M~~]]	+	[[Category: Forwood JK]]
-	[[Category: ~~Complex]]~~	+	[[Category: Smith KM]]
-	~~[[Category: Importin alpha]]~~	+
-	~~[[Category: Nuclear localisation signal]]~~	+
-	~~[[Category: Protein transport-viral protein complex~~]]	+

OCA at 07:05, 31 October 2018

OCA — Wed, 31 Oct 2018 07:05:53 GMT

←Older revision		Revision as of 07:05, 31 October 2018
Line 3:		Line 3:
	<StructureSection load='5klr' size='340' side='right' caption='[[5klr]], [[Resolution\|resolution]] 2.20Å' scene=''>		<StructureSection load='5klr' size='340' side='right' caption='[[5klr]], [[Resolution\|resolution]] 2.20Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5klr]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5KLR OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5KLR FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5klr]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Lk3_transgenic_mice Lk3 transgenic mice] and [http://en.wikipedia.org/wiki/Synthetic_construct_sequences Synthetic construct sequences]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5KLR OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5KLR FirstGlance]. <br>
	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5klt\|5klt]]</td></tr>		</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5klt\|5klt]]</td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">Kpna2, Rch1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10090 LK3 transgenic mice])</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=5klr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5klr OCA], [http://pdbe.org/5klr PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5klr RCSB], [http://www.ebi.ac.uk/pdbsum/5klr PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5klr 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=5klr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5klr OCA], [http://pdbe.org/5klr PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5klr RCSB], [http://www.ebi.ac.uk/pdbsum/5klr PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5klr ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
	[[http://www.uniprot.org/uniprot/IMA1_MOUSE IMA1_MOUSE]] Functions in nuclear protein import as an adapter protein for nuclear receptor KPNB1. Binds specifically and directly to substrates containing either a simple or bipartite NLS motif. Docking of the importin/substrate complex to the nuclear pore complex (NPC) is mediated by KPNB1 through binding to nucleoporin FxFG repeats and the complex is subsequently translocated through the pore by an energy requiring, Ran-dependent mechanism. At the nucleoplasmic side of the NPC, Ran binds to importin-beta and the three components separate and importin-alpha and -beta are re-exported from the nucleus to the cytoplasm where GTP hydrolysis releases Ran from importin. The directionality of nuclear import is thought to be conferred by an asymmetric distribution of the GTP- and GDP-bound forms of Ran between the cytoplasm and nucleus.		[[http://www.uniprot.org/uniprot/IMA1_MOUSE IMA1_MOUSE]] Functions in nuclear protein import as an adapter protein for nuclear receptor KPNB1. Binds specifically and directly to substrates containing either a simple or bipartite NLS motif. Docking of the importin/substrate complex to the nuclear pore complex (NPC) is mediated by KPNB1 through binding to nucleoporin FxFG repeats and the complex is subsequently translocated through the pore by an energy requiring, Ran-dependent mechanism. At the nucleoplasmic side of the NPC, Ran binds to importin-beta and the three components separate and importin-alpha and -beta are re-exported from the nucleus to the cytoplasm where GTP hydrolysis releases Ran from importin. The directionality of nuclear import is thought to be conferred by an asymmetric distribution of the GTP- and GDP-bound forms of Ran between the cytoplasm and nucleus.
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Nuclear import involves the recognition by importin (IMP) superfamily members of nuclear localization signals (NLSs) within protein cargoes destined for the nucleus, the best understood being recognition of classical NLSs (cNLSs) by the IMPalpha/beta1 heterodimer. Although the cNLS consensus [K-(K/R)-X-(K/R) for positions P2-P5] is generally accepted, recent studies indicated that the contribution made by different residues at the P4 position can vary. Here, we apply a combination of microscopy, molecular dynamics, crystallography, in vitro binding, and bioinformatics approaches to show that the nature of residues at P4 indeed modulates cNLS function in the context of a prototypical Simian Virus 40 large tumor antigen-derived cNLS (KKRK, P2-5). Indeed, all hydrophobic substitutions in place of R impaired binding to IMPalpha and nuclear targeting, with the largest effect exerted by a G residue at P4. Substitution of R with neutral hydrophobic residues caused the loss of electrostatic and van der Waals interactions between the P4 residue side chains and IMPalpha. Detailed bioinformatics analysis confirmed the importance of the P4 residue for cNLS function across the human proteome, with specific residues such as G being associated with low activity. Furthermore, we validate our findings for two additional cNLSs from human cytomegalovirus (HCMV) DNA polymerase catalytic subunit UL54 and processivity factor UL44, where a G residue at P4 results in a 2-3-fold decrease in NLS activity. Our results thus showed that the P4 residue makes a hitherto poorly appreciated contribution to nuclear import efficiency, which is essential to determining the precise nuclear levels of cargoes.
		+
		+	Contribution of the residue at position 4 within classical nuclear localization signals to modulating interaction with importins and nuclear targeting.,Smith KM, Di Antonio V, Bellucci L, Thomas DR, Caporuscio F, Ciccarese F, Ghassabian H, Wagstaff KM, Forwood JK, Jans DA, Palu G, Alvisi G Biochim Biophys Acta Mol Cell Res. 2018 Aug;1865(8):1114-1129. doi:, 10.1016/j.bbamcr.2018.05.006. Epub 2018 May 8. PMID:29750988<ref>PMID:29750988</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 5klr" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Importin\|Importin]]
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Lk3 transgenic mice]]
		+	[[Category: Synthetic construct sequences]]
	[[Category: Forwood, J K]]		[[Category: Forwood, J K]]
	[[Category: Smith, K M]]		[[Category: Smith, K M]]

OCA at 15:47, 27 July 2016

OCA — Wed, 27 Jul 2016 15:47:48 GMT

←Older revision		Revision as of 15:47, 27 July 2016
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5klr is ~~ON HOLD~~	+	==Prototypical P4[R]cNLS==
-		+	<StructureSection load='5klr' size='340' side='right' caption='[[5klr]], [[Resolution\|resolution]] 2.20Å' scene=''>
-	~~Authors~~: ~~Smith~~, K.M., ~~Forwood~~, J.K.	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[5klr]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5KLR OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5KLR FirstGlance]. <br>
-	~~Description~~: ~~Prototypical P4~~[R]~~cNLS~~	+	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5klt\|5klt]]</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=5klr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5klr OCA], [http://pdbe.org/5klr PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5klr RCSB], [http://www.ebi.ac.uk/pdbsum/5klr PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5klr ProSAT]</span></td></tr>
-	[[Category: Forwood, J.K]]	+	</table>
-	[[Category: Smith, K.M]]	+	== Function ==
		+	[[http://www.uniprot.org/uniprot/IMA1_MOUSE IMA1_MOUSE]] Functions in nuclear protein import as an adapter protein for nuclear receptor KPNB1. Binds specifically and directly to substrates containing either a simple or bipartite NLS motif. Docking of the importin/substrate complex to the nuclear pore complex (NPC) is mediated by KPNB1 through binding to nucleoporin FxFG repeats and the complex is subsequently translocated through the pore by an energy requiring, Ran-dependent mechanism. At the nucleoplasmic side of the NPC, Ran binds to importin-beta and the three components separate and importin-alpha and -beta are re-exported from the nucleus to the cytoplasm where GTP hydrolysis releases Ran from importin. The directionality of nuclear import is thought to be conferred by an asymmetric distribution of the GTP- and GDP-bound forms of Ran between the cytoplasm and nucleus.
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Forwood, J K]]
		+	[[Category: Smith, K M]]
		+	[[Category: Complex]]
		+	[[Category: Importin alpha]]
		+	[[Category: Nuclear localisation signal]]
		+	[[Category: Protein transport-viral protein complex]]

OCA: Protected "5klr" [edit=sysop:move=sysop]

OCA — Wed, 13 Jul 2016 00:32:20 GMT

Protected "5klr" [edit=sysop:move=sysop]

←Older revision

Revision as of 00:32, 13 July 2016

OCA: New page: '''Unreleased structure''' The entry 5klr is ON HOLD Authors: Smith, K.M., Forwood, J.K. Description: Prototypical P4[R]cNLS Category: Unreleased Structures [[Category: Forwood, J....

OCA — Wed, 13 Jul 2016 00:32:19 GMT

New page: '''Unreleased structure''' The entry 5klr is ON HOLD Authors: Smith, K.M., Forwood, J.K. Description: Prototypical P4[R]cNLS Category: Unreleased Structures [[Category: Forwood, J....

New page

'''Unreleased structure'''

The entry 5klr is ON HOLD

Authors: Smith, K.M., Forwood, J.K.

Description: Prototypical P4[R]cNLS
[[Category: Unreleased Structures]]
[[Category: Forwood, J.K]]
[[Category: Smith, K.M]]