6oo2: Difference between revisions

Revision as of 07:07, 11 April 2020

Vps4 with Cyclic Peptide Bound in the Central PoreVps4 with Cyclic Peptide Bound in the Central Pore

6oo2, resolution 4.40Å

Structural highlights

6oo2 is a 19 chain structure with sequence from Atcc 18824. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:
Gene:	VPS4, CSC1, DID6, END13, GRD13, VPL4, VPT10, YPR173C, P9705.10 (ATCC 18824), VTA1, YLR181C (ATCC 18824)
Experimental data:	Check
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

[VPS4_YEAST] Involved in the transport of biosynthetic membrane proteins from the prevacuolar/endosomal compartment to the vacuole. Required for multivesicular body (MVB) protein sorting. Catalyzes the ATP-dependent dissociation of class E VPS proteins from endosomal membranes, such as the disassembly of the ESCRT-III complex.^[1] ^[2] ^[3] [VTA1_YEAST] Has a role in the formation of the multivesicular body (MVB). Required for the sorting of lipids to form intralumenal vesicles and for fluid-phase transport to the vacuole. Required for sorting the plasma membrane proteins STE2 and STE3 into the MVB. Acts a cofactor of VSP4, promotes the oligomerization of VPS4 and stimulates its ATPase activity by 6- to 8-fold.^[4] ^[5] ^[6] ^[7]

Publication Abstract from PubMed

Many AAA+ ATPases form hexamers that unfold protein substrates by translocating them through their central pore. Multiple structures have shown how a helical assembly of subunits binds a single strand of substrate, and indicate that translocation results from the ATP-driven movement of subunits from one end of the helical assembly to the other end. To understand how more complex substrates are bound and translocated, we demonstrated that linear and cyclic versions of peptides bind to the S. cerevisiae AAA+ ATPase Vps4 with similar affinities, and determined cryo-EM structures of cyclic peptide complexes. The peptides bind in a hairpin conformation, with one primary strand equivalent to the single chain peptide ligands, while the second strand returns through the translocation pore without making intimate contacts with Vps4. These observations indicate a general mechanism by which AAA+ ATPases may translocate a variety of substrates that include extended chains, hairpins, and crosslinked polypeptide chains.

Structure of Vps4 with circular peptides and implications for translocation of two polypeptide chains by AAA+ ATPases.,Han H, Fulcher JM, Dandey VP, Iwasa JH, Sundquist WI, Kay MS, Shen PS, Hill CP Elife. 2019 Jun 11;8. pii: 44071. doi: 10.7554/eLife.44071. PMID:31184588^[8]

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

References

↑ Zahn R, Stevenson BJ, Schroder-Kohne S, Zanolari B, Riezman H, Munn AL. End13p/Vps4p is required for efficient transport from early to late endosomes in Saccharomyces cerevisiae. J Cell Sci. 2001 May;114(Pt 10):1935-47. PMID:11329380
↑ Babst M, Sato TK, Banta LM, Emr SD. Endosomal transport function in yeast requires a novel AAA-type ATPase, Vps4p. EMBO J. 1997 Apr 15;16(8):1820-31. PMID:9155008 doi:10.1093/emboj/16.8.1820
↑ Babst M, Wendland B, Estepa EJ, Emr SD. The Vps4p AAA ATPase regulates membrane association of a Vps protein complex required for normal endosome function. EMBO J. 1998 Jun 1;17(11):2982-93. PMID:9606181 doi:10.1093/emboj/17.11.2982
↑ Yeo SC, Xu L, Ren J, Boulton VJ, Wagle MD, Liu C, Ren G, Wong P, Zahn R, Sasajala P, Yang H, Piper RC, Munn AL. Vps20p and Vta1p interact with Vps4p and function in multivesicular body sorting and endosomal transport in Saccharomyces cerevisiae. J Cell Sci. 2003 Oct 1;116(Pt 19):3957-70. PMID:12953057 doi:http://dx.doi.org/10.1242/jcs.00751
↑ Shiflett SL, Ward DM, Huynh D, Vaughn MB, Simmons JC, Kaplan J. Characterization of Vta1p, a class E Vps protein in Saccharomyces cerevisiae. J Biol Chem. 2004 Mar 19;279(12):10982-90. Epub 2003 Dec 29. PMID:14701806 doi:10.1074/jbc.M312669200
↑ Azmi I, Davies B, Dimaano C, Payne J, Eckert D, Babst M, Katzmann DJ. Recycling of ESCRTs by the AAA-ATPase Vps4 is regulated by a conserved VSL region in Vta1. J Cell Biol. 2006 Feb 27;172(5):705-17. PMID:16505166 doi:jcb.200508166
↑ Lottridge JM, Flannery AR, Vincelli JL, Stevens TH. Vta1p and Vps46p regulate the membrane association and ATPase activity of Vps4p at the yeast multivesicular body. Proc Natl Acad Sci U S A. 2006 Apr 18;103(16):6202-7. Epub 2006 Apr 6. PMID:16601096 doi:0601712103
↑ Han H, Fulcher JM, Dandey VP, Iwasa JH, Sundquist WI, Kay MS, Shen PS, Hill CP. Structure of Vps4 with circular peptides and implications for translocation of two polypeptide chains by AAA+ ATPases. Elife. 2019 Jun 11;8. pii: 44071. doi: 10.7554/eLife.44071. PMID:31184588 doi:http://dx.doi.org/10.7554/eLife.44071

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OCA

[1] Zahn R, Stevenson BJ, Schroder-Kohne S, Zanolari B, Riezman H, Munn AL. End13p/Vps4p is required for efficient transport from early to late endosomes in Saccharomyces cerevisiae. J Cell Sci. 2001 May;114(Pt 10):1935-47. PMID:11329380

[2] Babst M, Sato TK, Banta LM, Emr SD. Endosomal transport function in yeast requires a novel AAA-type ATPase, Vps4p. EMBO J. 1997 Apr 15;16(8):1820-31. PMID:9155008 doi:10.1093/emboj/16.8.1820

[3] Babst M, Wendland B, Estepa EJ, Emr SD. The Vps4p AAA ATPase regulates membrane association of a Vps protein complex required for normal endosome function. EMBO J. 1998 Jun 1;17(11):2982-93. PMID:9606181 doi:10.1093/emboj/17.11.2982

[4] Yeo SC, Xu L, Ren J, Boulton VJ, Wagle MD, Liu C, Ren G, Wong P, Zahn R, Sasajala P, Yang H, Piper RC, Munn AL. Vps20p and Vta1p interact with Vps4p and function in multivesicular body sorting and endosomal transport in Saccharomyces cerevisiae. J Cell Sci. 2003 Oct 1;116(Pt 19):3957-70. PMID:12953057 doi:http://dx.doi.org/10.1242/jcs.00751

[5] Shiflett SL, Ward DM, Huynh D, Vaughn MB, Simmons JC, Kaplan J. Characterization of Vta1p, a class E Vps protein in Saccharomyces cerevisiae. J Biol Chem. 2004 Mar 19;279(12):10982-90. Epub 2003 Dec 29. PMID:14701806 doi:10.1074/jbc.M312669200

[6] Azmi I, Davies B, Dimaano C, Payne J, Eckert D, Babst M, Katzmann DJ. Recycling of ESCRTs by the AAA-ATPase Vps4 is regulated by a conserved VSL region in Vta1. J Cell Biol. 2006 Feb 27;172(5):705-17. PMID:16505166 doi:jcb.200508166

[7] Lottridge JM, Flannery AR, Vincelli JL, Stevens TH. Vta1p and Vps46p regulate the membrane association and ATPase activity of Vps4p at the yeast multivesicular body. Proc Natl Acad Sci U S A. 2006 Apr 18;103(16):6202-7. Epub 2006 Apr 6. PMID:16601096 doi:0601712103

[8] Han H, Fulcher JM, Dandey VP, Iwasa JH, Sundquist WI, Kay MS, Shen PS, Hill CP. Structure of Vps4 with circular peptides and implications for translocation of two polypeptide chains by AAA+ ATPases. Elife. 2019 Jun 11;8. pii: 44071. doi: 10.7554/eLife.44071. PMID:31184588 doi:http://dx.doi.org/10.7554/eLife.44071

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@@ Line 3: / Line 3: @@
 <SX load='6oo2' size='340' side='right' viewer='molstar' caption='[[6oo2]], [[Resolution|resolution]] 4.40&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[6oo2]] is a 19 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_18824 Atcc 18824]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6OO2 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6OO2 FirstGlance]. <br>
+<table><tr><td colspan='2'>[[6oo2]] is a 19 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_18824 Atcc 18824]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6OO2 OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6OO2 FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ADP:ADENOSINE-5-DIPHOSPHATE'>ADP</scene>, <scene name='pdbligand=BEF:BERYLLIUM+TRIFLUORIDE+ION'>BEF</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=ADP:ADENOSINE-5-DIPHOSPHATE'>ADP</scene>, <scene name='pdbligand=BEF:BERYLLIUM+TRIFLUORIDE+ION'>BEF</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
 <tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=UNK:UNKNOWN'>UNK</scene></td></tr>
 <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">VPS4, CSC1, DID6, END13, GRD13, VPL4, VPT10, YPR173C, P9705.10 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=4932 ATCC 18824]), VTA1, YLR181C ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=4932 ATCC 18824])</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=6oo2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6oo2 OCA], [http://pdbe.org/6oo2 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6oo2 RCSB], [http://www.ebi.ac.uk/pdbsum/6oo2 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6oo2 ProSAT]</span></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=6oo2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6oo2 OCA], [http://pdbe.org/6oo2 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6oo2 RCSB], [http://www.ebi.ac.uk/pdbsum/6oo2 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6oo2 ProSAT]</span></td></tr>
 </table>
 == Function ==
@@ Line 20: / Line 20: @@
 </div>
 <div class="pdbe-citations 6oo2" style="background-color:#fffaf0;"></div>
+==See Also==
+*[[Vacuolar protein sorting-associated protein 3D structures|Vacuolar protein sorting-associated protein 3D structures]]
 == References ==
 <references/>

6oo2: Difference between revisions

Revision as of 07:07, 11 April 2020

Vps4 with Cyclic Peptide Bound in the Central PoreVps4 with Cyclic Peptide Bound in the Central Pore

Structural highlights

Function

Publication Abstract from PubMed

See Also

References

Contents

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Navigation menu

6oo2: Difference between revisions

Revision as of 07:07, 11 April 2020

Vps4 with Cyclic Peptide Bound in the Central PoreVps4 with Cyclic Peptide Bound in the Central Pore

Structural highlights

Function

Publication Abstract from PubMed

See Also

References

Proteopedia Page Contributors and Editors (what is this?)Proteopedia Page Contributors and Editors (what is this?)

Navigation menu

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