5lpn - Revision history

OCA at 18:40, 18 October 2023

OCA — Wed, 18 Oct 2023 18:40:32 GMT

←Older revision		Revision as of 18:40, 18 October 2023
Line 3:		Line 3:
	<StructureSection load='5lpn' size='340' side='right'caption='[[5lpn]], [[Resolution\|resolution]] 2.80Å' scene=''>		<StructureSection load='5lpn' size='340' side='right'caption='[[5lpn]], [[Resolution\|resolution]] 2.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5lpn]] is a 3 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=5LPN OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=5LPN FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5lpn]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5LPN OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5LPN FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=GNP:PHOSPHOAMINOPHOSPHONIC+ACID~~-~~GUANYLATE+ESTER'>GNP</scene>~~, ~~<scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>~~</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]] 2.8Å</td></tr>
-	<tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat">~~RAB10 ([http~~:/~~/www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode~~=~~Info&srchmode~~=~~5&id=9606 HUMAN]), MICAL1, MICAL, NICAL ([http~~:/~~/www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])~~</td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GNP:PHOSPHOAMINOPHOSPHONIC+ACID-GUANYLATE+ESTER'>GNP</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'>[~~http~~://proteopedia.org/fgij/fg.htm?mol=5lpn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5lpn OCA], [~~http~~://pdbe.org/5lpn PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5lpn RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5lpn PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5lpn ProSAT]</span></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=5lpn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5lpn OCA], [https://pdbe.org/5lpn PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5lpn RCSB], [https://www.ebi.ac.uk/pdbsum/5lpn PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5lpn ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/RAB10_HUMAN RAB10_HUMAN]] The small GTPases Rab are key regulators of intracellular membrane trafficking, from the formation of transport vesicles to their fusion with membranes. Rabs cycle between an inactive GDP-bound form and an active GTP-bound form that is able to recruit to membranes different set of downstream effectors directly responsible for vesicle formation, movement, tethering and fusion (By similarity). That Rab is mainly involved in the biosynthetic transport of proteins from the Golgi to the plasma membrane. Regulates, for instance, SLC2A4/GLUT4 glucose transporter-enriched vesicles delivery to the plasma membrane. In parallel, it regulates the transport of TLR4, a toll-like receptor to the plasma membrane and therefore may be important for innate immune response. Plays also a specific role in asymmetric protein transport to the plasma membrane within the polarized neuron and epithelial cells. In neurons, it is involved in axonogenesis through regulation of vesicular membrane trafficking toward the axonal plasma membrane while in epithelial cells, it regulates transport from the Golgi to the basolateral membrane. Moreover, may play a role in the basolateral recycling pathway and in phagosome maturation. According to PubMed:23263280, may play a role in endoplasmic reticulum dynamics and morphology controlling tubulation along microtubules and tubules fusion.<ref>PMID:16641372</ref> <ref>PMID:21248164</ref> <ref>PMID:23263280</ref> [[http://www.uniprot.org/uniprot/MICA1_HUMAN MICA1_HUMAN]] Monooxygenase that promotes depolymerization of F-actin by mediating oxidation of specific methionine residues on actin. Acts by modifying actin subunits through the addition of oxygen to form methionine-sulfoxide, leading to promote actin filament severing and prevent repolymerization (Probable). Acts as a cytoskeletal regulator that connects NEDD9 to intermediate filaments. Also acts as a negative regulator of apoptosis via its interaction with STK38 and STK38L; acts by antagonizing STK38 and STK38L activation by MST1/STK4.<ref>PMID:18305261</ref> <ref>PMID:21864500</ref>	+	[https://www.uniprot.org/uniprot/RAB10_HUMAN RAB10_HUMAN] The small GTPases Rab are key regulators of intracellular membrane trafficking, from the formation of transport vesicles to their fusion with membranes. Rabs cycle between an inactive GDP-bound form and an active GTP-bound form that is able to recruit to membranes different set of downstream effectors directly responsible for vesicle formation, movement, tethering and fusion (By similarity). That Rab is mainly involved in the biosynthetic transport of proteins from the Golgi to the plasma membrane. Regulates, for instance, SLC2A4/GLUT4 glucose transporter-enriched vesicles delivery to the plasma membrane. In parallel, it regulates the transport of TLR4, a toll-like receptor to the plasma membrane and therefore may be important for innate immune response. Plays also a specific role in asymmetric protein transport to the plasma membrane within the polarized neuron and epithelial cells. In neurons, it is involved in axonogenesis through regulation of vesicular membrane trafficking toward the axonal plasma membrane while in epithelial cells, it regulates transport from the Golgi to the basolateral membrane. Moreover, may play a role in the basolateral recycling pathway and in phagosome maturation. According to PubMed:23263280, may play a role in endoplasmic reticulum dynamics and morphology controlling tubulation along microtubules and tubules fusion.<ref>PMID:16641372</ref> <ref>PMID:21248164</ref> <ref>PMID:23263280</ref>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
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	</div>		</div>
	<div class="pdbe-citations 5lpn" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 5lpn" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Ras-related protein Rab 3D structures\|Ras-related protein Rab 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Human~~]]	+	[[Category: Homo sapiens]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Campos, J]]	+	[[Category: Campos J]]
-	[[Category: Friese, T]]	+	[[Category: Friese T]]
-	[[Category: Fu, Y]]	+	[[Category: Fu Y]]
-	[[Category: Gazdag~~, E M~~]]	+	[[Category: Gazdag EM]]
-	[[Category: Goody~~, R S~~]]	+	[[Category: Goody RS]]
-	[[Category: Itzen, A]]	+	[[Category: Itzen A]]
-	[[Category: Mueller~~, M P~~]]	+	[[Category: Mueller MP]]
-	[[Category: Oprisko, A]]	+	[[Category: Oprisko A]]
-	[[Category: Rai, A]]	+	[[Category: Rai A]]
-	~~[[Category: Duf3585]]~~	+
-	~~[[Category: Endocytosis]]~~	+
-	~~[[Category: Mical]]~~	+
-	~~[[Category: Mical-1]]~~	+
-	~~[[Category: Oxidoreductase]]~~	+
-	~~[[Category: Rab effector]]~~	+
-	~~[[Category: Rab10~~]]	+

OCA at 10:45, 12 August 2020

OCA — Wed, 12 Aug 2020 10:45:52 GMT

←Older revision		Revision as of 10:45, 12 August 2020
Line 1:		Line 1:

	==Structure of human Rab10 in complex with the bMERB domain of Mical-1==		==Structure of human Rab10 in complex with the bMERB domain of Mical-1==
-	<StructureSection load='5lpn' size='340' side='right' caption='[[5lpn]], [[Resolution\|resolution]] 2.80Å' scene=''>	+	<StructureSection load='5lpn' size='340' side='right'caption='[[5lpn]], [[Resolution\|resolution]] 2.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5lpn]] is a 3 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5LPN OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5LPN FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5lpn]] is a 3 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=5LPN OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5LPN FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GNP:PHOSPHOAMINOPHOSPHONIC+ACID-GUANYLATE+ESTER'>GNP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GNP:PHOSPHOAMINOPHOSPHONIC+ACID-GUANYLATE+ESTER'>GNP</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'>[http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5lpn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5lpn OCA], [http://pdbe.org/5lpn PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5lpn RCSB], [http://www.ebi.ac.uk/pdbsum/5lpn PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5lpn ProSAT]</span></td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">RAB10 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN]), MICAL1, MICAL, NICAL ([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://proteopedia.org/fgij/fg.htm?mol=5lpn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5lpn OCA], [http://pdbe.org/5lpn PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5lpn RCSB], [http://www.ebi.ac.uk/pdbsum/5lpn PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5lpn ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 22:		Line 23:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Human]]
		+	[[Category: Large Structures]]
	[[Category: Campos, J]]		[[Category: Campos, J]]
	[[Category: Friese, T]]		[[Category: Friese, T]]

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

OCA — Fri, 09 Sep 2016 05:14:32 GMT

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

←Older revision

Revision as of 05:14, 9 September 2016

OCA: New page: ==Structure of human Rab10 in complex with the bMERB domain of Mical-1==
OCA — Fri, 09 Sep 2016 05:14:30 GMT

New page: ==Structure of human Rab10 in complex with the bMERB domain of Mical-1== <StructureSection load='5lpn' size='340' side='right' caption='5lpn, resolution 2.80Å' sc...

New page

==Structure of human Rab10 in complex with the bMERB domain of Mical-1==
<StructureSection load='5lpn' size='340' side='right' caption='[[5lpn]], [[Resolution|resolution]] 2.80Å' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[5lpn]] is a 3 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5LPN OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5LPN FirstGlance]. <br>
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GNP:PHOSPHOAMINOPHOSPHONIC+ACID-GUANYLATE+ESTER'>GNP</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'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5lpn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5lpn OCA], [http://pdbe.org/5lpn PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5lpn RCSB], [http://www.ebi.ac.uk/pdbsum/5lpn PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5lpn ProSAT]</span></td></tr>
</table>
== Function ==
[[http://www.uniprot.org/uniprot/RAB10_HUMAN RAB10_HUMAN]] The small GTPases Rab are key regulators of intracellular membrane trafficking, from the formation of transport vesicles to their fusion with membranes. Rabs cycle between an inactive GDP-bound form and an active GTP-bound form that is able to recruit to membranes different set of downstream effectors directly responsible for vesicle formation, movement, tethering and fusion (By similarity). That Rab is mainly involved in the biosynthetic transport of proteins from the Golgi to the plasma membrane. Regulates, for instance, SLC2A4/GLUT4 glucose transporter-enriched vesicles delivery to the plasma membrane. In parallel, it regulates the transport of TLR4, a toll-like receptor to the plasma membrane and therefore may be important for innate immune response. Plays also a specific role in asymmetric protein transport to the plasma membrane within the polarized neuron and epithelial cells. In neurons, it is involved in axonogenesis through regulation of vesicular membrane trafficking toward the axonal plasma membrane while in epithelial cells, it regulates transport from the Golgi to the basolateral membrane. Moreover, may play a role in the basolateral recycling pathway and in phagosome maturation. According to PubMed:23263280, may play a role in endoplasmic reticulum dynamics and morphology controlling tubulation along microtubules and tubules fusion.<ref>PMID:16641372</ref> <ref>PMID:21248164</ref> <ref>PMID:23263280</ref> [[http://www.uniprot.org/uniprot/MICA1_HUMAN MICA1_HUMAN]] Monooxygenase that promotes depolymerization of F-actin by mediating oxidation of specific methionine residues on actin. Acts by modifying actin subunits through the addition of oxygen to form methionine-sulfoxide, leading to promote actin filament severing and prevent repolymerization (Probable). Acts as a cytoskeletal regulator that connects NEDD9 to intermediate filaments. Also acts as a negative regulator of apoptosis via its interaction with STK38 and STK38L; acts by antagonizing STK38 and STK38L activation by MST1/STK4.<ref>PMID:18305261</ref> <ref>PMID:21864500</ref>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
In their active GTP-bound form, Rab proteins interact with proteins termed effector molecules. In this study we have thoroughly characterised a Rab effector domain that is present in proteins of the Mical and EHBP families, both known to act in endosomal trafficking. Within our study, we show that these effectors display a preference for Rab8 family proteins (Rab8, 10, 13 and 15) and that some of the effector domains can bind two Rab proteins via separate binding sites. Structural analysis allowed us to explain the specificity towards Rab8 family members and the presence of two similar Rab binding sites that must have evolved via gene duplication. This study is the first to thoroughly characterise a Rab effector protein that contains two separate Rab binding sites within a single domain, allowing Micals and EHBPs to bind two Rabs simultaneously, thus suggesting previously unknown functions of these effector molecules in endosomal trafficking.

bMERB domains are bivalent Rab8 family effectors evolved by gene duplication.,Rai A, Oprisko A, Campos J, Fu Y, Friese T, Itzen A, Goody RS, Gazdag EM, Muller MP Elife. 2016 Aug 23;5. pii: e18675. doi: 10.7554/eLife.18675. PMID:27552051<ref>PMID:27552051</ref>

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 5lpn" style="background-color:#fffaf0;"></div>
== References ==
<references/>
TOC
</StructureSection>
[[Category: Campos, J]]
[[Category: Friese, T]]
[[Category: Fu, Y]]
[[Category: Gazdag, E M]]
[[Category: Goody, R S]]
[[Category: Itzen, A]]
[[Category: Mueller, M P]]
[[Category: Oprisko, A]]
[[Category: Rai, A]]
[[Category: Duf3585]]
[[Category: Endocytosis]]
[[Category: Mical]]
[[Category: Mical-1]]
[[Category: Oxidoreductase]]
[[Category: Rab effector]]
[[Category: Rab10]]