3cue: Difference between revisions

Latest revision as of 05:44, 17 October 2024

Crystal structure of a TRAPP subassembly activating the Rab Ypt1p

Structural highlights

3cue is a 24 chain structure with sequence from Saccharomyces cerevisiae. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 3.7Å
Ligands:	PLM
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

TRS23_YEAST Component of the TRAPP I, TRAPP II and TRAPP III complexes which act as guanine nucleotide exchange factors (GEF) for YPT1. TRAPP I plays a key role in the late stages of endoplasmic reticulum to Golgi traffic. TRAPP II plays a role in intra-Golgi transport. TRAPP III plays a role in autophagosome formation.^[1] ^[2] ^[3]

Evolutionary Conservation

Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.

Publication Abstract from PubMed

The multimeric membrane-tethering complexes TRAPPI and TRAPPII share seven subunits, of which four (Bet3p, Bet5p, Trs23p, and Trs31p) are minimally needed to activate the Rab GTPase Ypt1p in an event preceding membrane fusion. Here, we present the structure of a heteropentameric TRAPPI assembly complexed with Ypt1p. We propose that TRAPPI facilitates nucleotide exchange primarily by stabilizing the nucleotide-binding pocket of Ypt1p in an open, solvent-accessible form. Bet3p, Bet5p, and Trs23p interact directly with Ypt1p to stabilize this form, while the C terminus of Bet3p invades the pocket to participate in its remodeling. The Trs31p subunit does not interact directly with the GTPase but allosterically regulates the TRAPPI interface with Ypt1p. Our findings imply that TRAPPII activates Ypt1p by an identical mechanism. This view of a multimeric membrane-tethering assembly complexed with a Rab provides a framework for understanding events preceding membrane fusion at the molecular level.

The structural basis for activation of the Rab Ypt1p by the TRAPP membrane-tethering complexes.,Cai Y, Chin HF, Lazarova D, Menon S, Fu C, Cai H, Sclafani A, Rodgers DW, De La Cruz EM, Ferro-Novick S, Reinisch KM Cell. 2008 Jun 27;133(7):1202-13. PMID:18585354^[4]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

↑ Sacher M, Barrowman J, Wang W, Horecka J, Zhang Y, Pypaert M, Ferro-Novick S. TRAPP I implicated in the specificity of tethering in ER-to-Golgi transport. Mol Cell. 2001 Feb;7(2):433-42. PMID:11239471
↑ Yip CK, Berscheminski J, Walz T. Molecular architecture of the TRAPPII complex and implications for vesicle tethering. Nat Struct Mol Biol. 2010 Nov;17(11):1298-304. doi: 10.1038/nsmb.1914. Epub 2010 , Oct 24. PMID:20972447 doi:https://dx.doi.org/10.1038/nsmb.1914
↑ Lynch-Day MA, Bhandari D, Menon S, Huang J, Cai H, Bartholomew CR, Brumell JH, Ferro-Novick S, Klionsky DJ. Trs85 directs a Ypt1 GEF, TRAPPIII, to the phagophore to promote autophagy. Proc Natl Acad Sci U S A. 2010 Apr 27;107(17):7811-6. doi:, 10.1073/pnas.1000063107. Epub 2010 Apr 7. PMID:20375281 doi:https://dx.doi.org/10.1073/pnas.1000063107
↑ Cai Y, Chin HF, Lazarova D, Menon S, Fu C, Cai H, Sclafani A, Rodgers DW, De La Cruz EM, Ferro-Novick S, Reinisch KM. The structural basis for activation of the Rab Ypt1p by the TRAPP membrane-tethering complexes. Cell. 2008 Jun 27;133(7):1202-13. PMID:18585354 doi:10.1016/j.cell.2008.04.049

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OCA

[1] Sacher M, Barrowman J, Wang W, Horecka J, Zhang Y, Pypaert M, Ferro-Novick S. TRAPP I implicated in the specificity of tethering in ER-to-Golgi transport. Mol Cell. 2001 Feb;7(2):433-42. PMID:11239471

[2] Yip CK, Berscheminski J, Walz T. Molecular architecture of the TRAPPII complex and implications for vesicle tethering. Nat Struct Mol Biol. 2010 Nov;17(11):1298-304. doi: 10.1038/nsmb.1914. Epub 2010 , Oct 24. PMID:20972447 doi:https://dx.doi.org/10.1038/nsmb.1914

[3] Lynch-Day MA, Bhandari D, Menon S, Huang J, Cai H, Bartholomew CR, Brumell JH, Ferro-Novick S, Klionsky DJ. Trs85 directs a Ypt1 GEF, TRAPPIII, to the phagophore to promote autophagy. Proc Natl Acad Sci U S A. 2010 Apr 27;107(17):7811-6. doi:, 10.1073/pnas.1000063107. Epub 2010 Apr 7. PMID:20375281 doi:https://dx.doi.org/10.1073/pnas.1000063107

[4] Cai Y, Chin HF, Lazarova D, Menon S, Fu C, Cai H, Sclafani A, Rodgers DW, De La Cruz EM, Ferro-Novick S, Reinisch KM. The structural basis for activation of the Rab Ypt1p by the TRAPP membrane-tethering complexes. Cell. 2008 Jun 27;133(7):1202-13. PMID:18585354 doi:10.1016/j.cell.2008.04.049

[1]

[2]

[3]

[4]

@@ Line 4: / Line 4: @@
 == Structural highlights ==
 <table><tr><td colspan='2'>[[3cue]] is a 24 chain structure with sequence from [https://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3CUE OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3CUE FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=PLM:PALMITIC+ACID'>PLM</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]] 3.7&#8491;</td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">TRS23 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=4932 Saccharomyces cerevisiae]), TRS31 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=4932 Saccharomyces cerevisiae]), BET5 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=4932 Saccharomyces cerevisiae]), BET3 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=4932 Saccharomyces cerevisiae]), YPT1, YP2 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=4932 Saccharomyces cerevisiae])</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=PLM:PALMITIC+ACID'>PLM</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=3cue FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3cue OCA], [https://pdbe.org/3cue PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3cue RCSB], [https://www.ebi.ac.uk/pdbsum/3cue PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3cue ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[https://www.uniprot.org/uniprot/BET3_YEAST BET3_YEAST]] Component of the TRAPP I, TRAPP II and TRAPP III complexes which act as guanine nucleotide exchange factors (GEF) for YPT1. TRAPP I plays a key role in the late stages of endoplasmic reticulum to Golgi traffic. TRAPP II plays a role in intra-Golgi transport. TRAPP III plays a role in autophagosome formation. Required for sporulation. Has a role late in meiosis following DNA replication.<ref>PMID:8590804</ref> <ref>PMID:9564032</ref> <ref>PMID:11239471</ref> <ref>PMID:20972447</ref> <ref>PMID:20375281</ref>  [[https://www.uniprot.org/uniprot/TRS23_YEAST TRS23_YEAST]] Component of the TRAPP I, TRAPP II and TRAPP III complexes which act as guanine nucleotide exchange factors (GEF) for YPT1. TRAPP I plays a key role in the late stages of endoplasmic reticulum to Golgi traffic. TRAPP II plays a role in intra-Golgi transport. TRAPP III plays a role in autophagosome formation.<ref>PMID:11239471</ref> <ref>PMID:20972447</ref> <ref>PMID:20375281</ref>  [[https://www.uniprot.org/uniprot/BET5_YEAST BET5_YEAST]] Component of the TRAPP I, TRAPP II and TRAPP III complexes which act as guanine nucleotide exchange factors (GEF) for YPT1. TRAPP I plays a key role in the late stages of endoplasmic reticulum to Golgi traffic. TRAPP II plays a role in intra-Golgi transport. TRAPP III plays a role in autophagosome formation. Required for sporulation. Has a role late in meiosis following DNA replication.<ref>PMID:9611195</ref> <ref>PMID:11239471</ref> <ref>PMID:20972447</ref> <ref>PMID:20375281</ref>  [[https://www.uniprot.org/uniprot/TRS31_YEAST TRS31_YEAST]] Component of the TRAPP I, TRAPP II and TRAPP III complexes which act as guanine nucleotide exchange factors (GEF) for YPT1. TRAPP I plays a key role in the late stages of endoplasmic reticulum to Golgi traffic. TRAPP II plays a role in intra-Golgi transport. TRAPP III plays a role in autophagosome formation.<ref>PMID:9564032</ref> <ref>PMID:11239471</ref> <ref>PMID:20972447</ref> <ref>PMID:20375281</ref>  [[https://www.uniprot.org/uniprot/YPT1_YEAST YPT1_YEAST]] Involved in the trafficking of secretory vesicles from the endoplasmic reticulum (ER) to the Golgi. Regulates correct targeting and tethering of vesicles to target membranes by catalyzing the selective recruitment of proteins required for tethering and fusion onto membranes. Vesicular transport depends on shuttling of YPT1 between membrane and cytosol by GDI1, probably by recycling it to its membrane of origin after a vesicle fusion event. Required for sorting and transport of proteins from the ER through the Golgi compartment. Also involved in the recycling of membrane proteins.<ref>PMID:3286011</ref> [:]<ref>PMID:11879636</ref> <ref>PMID:12189143</ref> <ref>PMID:12802060</ref> <ref>PMID:15082776</ref>
+[https://www.uniprot.org/uniprot/TRS23_YEAST TRS23_YEAST] Component of the TRAPP I, TRAPP II and TRAPP III complexes which act as guanine nucleotide exchange factors (GEF) for YPT1. TRAPP I plays a key role in the late stages of endoplasmic reticulum to Golgi traffic. TRAPP II plays a role in intra-Golgi transport. TRAPP III plays a role in autophagosome formation.<ref>PMID:11239471</ref> <ref>PMID:20972447</ref> <ref>PMID:20375281</ref>
 == Evolutionary Conservation ==
 [[Image:Consurf_key_small.gif|200px|right]]
@@ Line 15: / Line 15: @@
    <jmolCheckbox>
      <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/cu/3cue_consurf.spt"</scriptWhenChecked>
-     <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
+     <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.spt</scriptWhenUnchecked>
      <text>to colour the structure by Evolutionary Conservation</text>
    </jmolCheckbox>
@@ Line 38: / Line 38: @@
 [[Category: Large Structures]]
 [[Category: Saccharomyces cerevisiae]]
-[[Category: Cai, Y]]
+[[Category: Cai Y]]
-[[Category: Reinisch, K M]]
+[[Category: Reinisch KM]]
-[[Category: Endoplasmic reticulum]]
-[[Category: Er-golgi transport]]
-[[Category: Gef]]
-[[Category: Golgi apparatus]]
-[[Category: Gtp-binding]]
-[[Category: Guanine nucleotide exchange factor]]
-[[Category: Lipoprotein]]
-[[Category: Membrane traffic]]
-[[Category: Nucleotide-binding]]
-[[Category: Palmitate]]
-[[Category: Phosphoprotein]]
-[[Category: Prenylation]]
-[[Category: Protein transport]]
-[[Category: Rab activation]]
-[[Category: Tethering complex]]
-[[Category: Transport]]

3cue: Difference between revisions

Latest revision as of 05:44, 17 October 2024

Crystal structure of a TRAPP subassembly activating the Rab Ypt1p

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

See Also

References

Contents

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