5o74 - Revision history

OCA at 19:10, 29 November 2023

OCA — Wed, 29 Nov 2023 19:10:11 GMT

←Older revision		Revision as of 19:10, 29 November 2023
Line 1:		Line 1:

	==Crystal structure of human Rab1b covalently bound to the GEF domain of DrrA/SidM from Legionella pneumophila in the presence of GDP==		==Crystal structure of human Rab1b covalently bound to the GEF domain of DrrA/SidM from Legionella pneumophila in the presence of GDP==
-	<StructureSection load='5o74' size='340' side='right' caption='[[5o74]], [[Resolution\|resolution]] 2.50Å' scene=''>	+	<StructureSection load='5o74' size='340' side='right'caption='[[5o74]], [[Resolution\|resolution]] 2.50Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5o74]] is a 12 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Atcc_33152 Atcc 33152~~] and [~~http~~://en.wikipedia.org/wiki/~~Human Human~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5O74 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5O74 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5o74]] is a 12 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens] and [https://en.wikipedia.org/wiki/Legionella_pneumophila Legionella pneumophila]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5O74 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5O74 FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat">~~<scene name='pdbligand=GDP:GUANOSINE~~-5~~-DIPHOSPHATE'>GDP</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]] 2.5Å</td></tr>
-	<tr id='~~NonStdRes~~'><td class="sblockLbl"><b>[[~~Non-Standard_Residue~~\|~~NonStd Res~~:]]</b></td><td class="sblockDat"><scene name='pdbligand=9MN:'>9MN</scene><~~/td></tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=9MN:(2~{S})-2-azanyl-6-(6-bromanylhexanoylamino)hexanoic+acid'>9MN</scene>, <scene name='pdbligand=GDP:GUANOSINE-5-DIPHOSPHATE'>GDP</scene></td></tr>
-	~~<tr id~~='~~gene'><td class~~=~~"sblockLbl"><b>[[Gene\|Gene~~:~~]]</b~~></td><td class="sblockDat">drrA, sidM ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=446 ATCC 33152]), RAB1B ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN]), RAB1B ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=446 ATCC 33152])</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=5o74 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5o74 OCA], [https://pdbe.org/5o74 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5o74 RCSB], [https://www.ebi.ac.uk/pdbsum/5o74 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5o74 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=5o74 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5o74 OCA], [~~http~~://pdbe.org/5o74 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5o74 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5o74 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5o74 ProSAT]</span></td></tr>	+
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/DRRA_LEGPN DRRA_LEGPN]] Virulence effector that plays a key role in hijacking the host vesicular trafficking by recruiting the small guanosine triphosphatase (GTPase) Rab1 to the cytosolic face of the Legionella-containing vacuole (LCVs). Acts as a GDP-GTP exchange factor (GEF) for the small GTPase Rab1 (RAB1A, RAB1B or RAB1C), thereby converting Rab1 to an active GTP-bound state, leading to the incorporation of Rab1 into LCVs. Also shows RabGDI displacement factor (GDF) activity; however, this probably represents a passive activity following the GEF activity. Also acts as an adenylyltransferase by mediating the addition of adenosine 5'-monophosphate (AMP) to 'Tyr-77' of host RAB1B, thereby rendering RAB1B constitutively active. Also has adenylyltransferase activity towards Rab6 and Rab35. Also displays guanylyltransferase activity by mediating the addition of guanosine 5'-monophosphate (GMP) to host RAB1B in vitro; however such activity remains uncertain in vivo. Specifically binds phosphatidylinositol 4-phosphate (PtdIns(4)P) lipids on the cytosolic surface of the phagosomal membrane shortly after infection.<ref>PMID:16906144</ref> <ref>PMID:17952054</ref> <ref>PMID:20651120</ref> ~~[[http://www.uniprot.org/uniprot/RAB1B_HUMAN RAB1B_HUMAN]] Protein transport. Regulates vesicular transport between the endoplasmic reticulum and successive Golgi compartments.<ref>PMID:9437002</ref>~~	+	[https://www.uniprot.org/uniprot/DRRA_LEGPN DRRA_LEGPN] Virulence effector that plays a key role in hijacking the host vesicular trafficking by recruiting the small guanosine triphosphatase (GTPase) Rab1 to the cytosolic face of the Legionella-containing vacuole (LCVs). Acts as a GDP-GTP exchange factor (GEF) for the small GTPase Rab1 (RAB1A, RAB1B or RAB1C), thereby converting Rab1 to an active GTP-bound state, leading to the incorporation of Rab1 into LCVs. Also shows RabGDI displacement factor (GDF) activity; however, this probably represents a passive activity following the GEF activity. Also acts as an adenylyltransferase by mediating the addition of adenosine 5'-monophosphate (AMP) to 'Tyr-77' of host RAB1B, thereby rendering RAB1B constitutively active. Also has adenylyltransferase activity towards Rab6 and Rab35. Also displays guanylyltransferase activity by mediating the addition of guanosine 5'-monophosphate (GMP) to host RAB1B in vitro; however such activity remains uncertain in vivo. Specifically binds phosphatidylinositol 4-phosphate (PtdIns(4)P) lipids on the cytosolic surface of the phagosomal membrane shortly after infection.<ref>PMID:16906144</ref> <ref>PMID:17952054</ref> <ref>PMID:20651120</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 5o74" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 5o74" 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: ~~Atcc 33152~~]]	+	[[Category: Homo sapiens]]
-	[[Category: ~~Human]]~~	+	[[Category: Large Structures]]
-	~~[[Category: Cigler, M]]~~	+
-	~~[[Category: Fottner, M]]~~	+
-	~~[[Category: Goody, R S]]~~	+
-	~~[[Category: Horn-Ghetko, D]]~~	+
-	~~[[Category: Itzen, A]]~~	+
-	~~[[Category: Lang, K]]~~	+
-	~~[[Category: Mueller, M P]]~~	+
-	~~[[Category: Mueller, T]]~~	+
-	~~[[Category: Wrisberg, M K.von]]~~	+
-	~~[[Category: Drra]]~~	+
-	~~[[Category: Exchange factor]]~~	+
-	~~[[Category: Hydrolase~~]]	+
	[[Category: Legionella pneumophila]]		[[Category: Legionella pneumophila]]
-	[[Category: ~~Rab1b~~]]	+	[[Category: Cigler M]]
		+	[[Category: Fottner M]]
		+	[[Category: Goody RS]]
		+	[[Category: Horn-Ghetko D]]
		+	[[Category: Itzen A]]
		+	[[Category: Lang K]]
		+	[[Category: Mueller MP]]
		+	[[Category: Mueller T]]
		+	[[Category: Von Wrisberg MK]]

OCA at 07:43, 6 December 2017

OCA — Wed, 06 Dec 2017 07:43:58 GMT

←Older revision		Revision as of 07:43, 6 December 2017
Line 3:		Line 3:
	<StructureSection load='5o74' size='340' side='right' caption='[[5o74]], [[Resolution\|resolution]] 2.50Å' scene=''>		<StructureSection load='5o74' size='340' side='right' caption='[[5o74]], [[Resolution\|resolution]] 2.50Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5o74]] is a 12 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5O74 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5O74 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5o74]] is a 12 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_33152 Atcc 33152] and [http://en.wikipedia.org/wiki/Human Human]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5O74 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5O74 FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GDP:GUANOSINE-5-DIPHOSPHATE'>GDP</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GDP:GUANOSINE-5-DIPHOSPHATE'>GDP</scene></td></tr>
	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=9MN:'>9MN</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=9MN:'>9MN</scene></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">drrA, sidM ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=446 ATCC 33152]), RAB1B ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN]), RAB1B ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=446 ATCC 33152])</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=5o74 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5o74 OCA], [http://pdbe.org/5o74 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5o74 RCSB], [http://www.ebi.ac.uk/pdbsum/5o74 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5o74 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=5o74 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5o74 OCA], [http://pdbe.org/5o74 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5o74 RCSB], [http://www.ebi.ac.uk/pdbsum/5o74 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5o74 ProSAT]</span></td></tr>
	</table>		</table>
Line 23:		Line 24:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Atcc 33152]]
		+	[[Category: Human]]
	[[Category: Cigler, M]]		[[Category: Cigler, M]]
	[[Category: Fottner, M]]		[[Category: Fottner, M]]

OCA at 06:51, 11 October 2017

OCA — Wed, 11 Oct 2017 06:51:52 GMT

←Older revision		Revision as of 06:51, 11 October 2017
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5o74 is ~~ON HOLD~~ ~~until Paper~~ Publication	+	==Crystal structure of human Rab1b covalently bound to the GEF domain of DrrA/SidM from Legionella pneumophila in the presence of GDP==
		+	<StructureSection load='5o74' size='340' side='right' caption='[[5o74]], [[Resolution\|resolution]] 2.50Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[5o74]] is a 12 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5O74 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5O74 FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GDP:GUANOSINE-5-DIPHOSPHATE'>GDP</scene></td></tr>
		+	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=9MN:'>9MN</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=5o74 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5o74 OCA], [http://pdbe.org/5o74 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5o74 RCSB], [http://www.ebi.ac.uk/pdbsum/5o74 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5o74 ProSAT]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/DRRA_LEGPN DRRA_LEGPN]] Virulence effector that plays a key role in hijacking the host vesicular trafficking by recruiting the small guanosine triphosphatase (GTPase) Rab1 to the cytosolic face of the Legionella-containing vacuole (LCVs). Acts as a GDP-GTP exchange factor (GEF) for the small GTPase Rab1 (RAB1A, RAB1B or RAB1C), thereby converting Rab1 to an active GTP-bound state, leading to the incorporation of Rab1 into LCVs. Also shows RabGDI displacement factor (GDF) activity; however, this probably represents a passive activity following the GEF activity. Also acts as an adenylyltransferase by mediating the addition of adenosine 5'-monophosphate (AMP) to 'Tyr-77' of host RAB1B, thereby rendering RAB1B constitutively active. Also has adenylyltransferase activity towards Rab6 and Rab35. Also displays guanylyltransferase activity by mediating the addition of guanosine 5'-monophosphate (GMP) to host RAB1B in vitro; however such activity remains uncertain in vivo. Specifically binds phosphatidylinositol 4-phosphate (PtdIns(4)P) lipids on the cytosolic surface of the phagosomal membrane shortly after infection.<ref>PMID:16906144</ref> <ref>PMID:17952054</ref> <ref>PMID:20651120</ref> [[http://www.uniprot.org/uniprot/RAB1B_HUMAN RAB1B_HUMAN]] Protein transport. Regulates vesicular transport between the endoplasmic reticulum and successive Golgi compartments.<ref>PMID:9437002</ref>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The characterization of low-affinity protein complexes is challenging due to their dynamic nature. Here we present a method to stabilize transient protein complexes in vivo by generating a covalent and conformationally flexible bridge between the interaction partners. A highly active pyrrolysyl tRNA synthetase mutant directs the incorporation of unnatural amino acids bearing bromoalkyl moieties (BrCnK) into proteins. We demonstrate for the first time that low-affinity protein complexes between BrCnK-containing proteins and their binding partners can be stabilized in vivo in bacterial and mammalian cells. Using this approach we determined the crystal structure of a transient GDP-bound complex between a small G-protein and its nucleotide exchange factor. We envision that this approach will prove valuable as a general tool for validating and characterizing protein-protein interactions in vitro and in vivo.

-	~~Authors:~~ Cigler, M., ~~Mueller, T.~~, Horn-Ghetko, D., von Wrisberg~~, M.K.~~, Fottner, M., Goody~~, R.S.~~, Itzen, A., ~~Mueller, M.P.~~, Lang, K.	+	Proximity-triggered covalent stabilization of low-affinity protein complexes in vitro and in vivo.,Cigler M, Muller TG, Horn-Ghetko D, von Wrisberg MK, Fottner M, Goody RS, Itzen A, Muller MP, Lang K Angew Chem Int Ed Engl. 2017 Sep 28. doi: 10.1002/anie.201706927. PMID:28960788<ref>PMID:28960788</ref>

-	~~Description: Crystal structure~~ of ~~human Rab1b covalently bound to~~ the ~~GEF domain~~ of ~~DrrA~~/~~SidM from Legionella pneumophila in the presence of GDP~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	~~[[Category~~: ~~Unreleased Structures]]~~	+	</div>
-	~~[[Category: Mueller, M.P]]~~	+	<div class="pdbe-citations 5o74" style="background-color:#fffaf0;"></div>
-	~~[[Category: Mueller, T]]~~	+	== References ==
-	[[Category: ~~Von Wrisberg~~, M~~.K]]~~	+	<references/>
-	~~[[Category: Goody, R.S~~]]	+	__TOC__
		+	</StructureSection>
		+	[[Category: Cigler, M]]
	[[Category: Fottner, M]]		[[Category: Fottner, M]]
-	[[Category: ~~Itzen~~, A]]	+	[[Category: Goody, R S]]
	[[Category: Horn-Ghetko, D]]		[[Category: Horn-Ghetko, D]]
		+	[[Category: Itzen, A]]
	[[Category: Lang, K]]		[[Category: Lang, K]]
-	[[Category: ~~Cigler~~, M]]	+	[[Category: Mueller, M P]]
		+	[[Category: Mueller, T]]
		+	[[Category: Wrisberg, M K.von]]
		+	[[Category: Drra]]
		+	[[Category: Exchange factor]]
		+	[[Category: Hydrolase]]
		+	[[Category: Legionella pneumophila]]
		+	[[Category: Rab1b]]

OCA: Protected "5o74" [edit=sysop:move=sysop]

OCA — Wed, 27 Sep 2017 12:05:59 GMT

Protected "5o74" [edit=sysop:move=sysop]

←Older revision

Revision as of 12:05, 27 September 2017

OCA: New page: '''Unreleased structure''' The entry 5o74 is ON HOLD until Paper Publication Authors: Cigler, M., Mueller, T., Horn-Ghetko, D., von Wrisberg, M.K., Fottner, M., Goody, R.S., Itzen, A., ...

OCA — Wed, 27 Sep 2017 12:05:58 GMT

New page: '''Unreleased structure''' The entry 5o74 is ON HOLD until Paper Publication Authors: Cigler, M., Mueller, T., Horn-Ghetko, D., von Wrisberg, M.K., Fottner, M., Goody, R.S., Itzen, A., ...

New page

'''Unreleased structure'''

The entry 5o74 is ON HOLD until Paper Publication

Authors: Cigler, M., Mueller, T., Horn-Ghetko, D., von Wrisberg, M.K., Fottner, M., Goody, R.S., Itzen, A., Mueller, M.P., Lang, K.

Description: Crystal structure of human Rab1b covalently bound to the GEF domain of DrrA/SidM from Legionella pneumophila in the presence of GDP
[[Category: Unreleased Structures]]
[[Category: Mueller, M.P]]
[[Category: Mueller, T]]
[[Category: Von Wrisberg, M.K]]
[[Category: Goody, R.S]]
[[Category: Fottner, M]]
[[Category: Itzen, A]]
[[Category: Horn-Ghetko, D]]
[[Category: Lang, K]]
[[Category: Cigler, M]]