6ap1: Difference between revisions

Latest revision as of 08:03, 21 November 2024

Vps4p-Vta1p complex with peptide binding to the central pore of Vps4pVps4p-Vta1p complex with peptide binding to the central pore of Vps4p

6ap1, resolution 3.20Å

Structural highlights

6ap1 is a 19 chain structure with sequence from Pseudomonas aeruginosa PAO1, Saccharomyces cerevisiae and Saccharomyces cerevisiae S288C. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	Electron Microscopy, Resolution 3.2Å
Ligands:
Experimental data:	Check
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

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.^[1] ^[2] ^[3] ^[4]

Publication Abstract from PubMed

The hexameric AAA ATPase Vps4 drives membrane fission by remodeling and disassembling ESCRT-III filaments. Building upon our earlier 4.3 A resolution cryo-EM structure (Monroe et al., 2017), we now report a 3.2 A structure of Vps4 bound to an ESCRT-III peptide substrate. The new structure reveals that the peptide approximates a beta-strand conformation whose helical symmetry matches that of the five Vps4 subunits it contacts directly. Adjacent Vps4 subunits make equivalent interactions with successive substrate dipeptides through two distinct classes of side chain binding pockets formed primarily by Vps4 pore loop 1. These pockets accommodate a wide range of residues, while main chain hydrogen bonds may help dictate substrate-binding orientation. The structure supports a 'conveyor belt' model of translocation in which ATP binding allows a Vps4 subunit to join the growing end of the helix and engage the substrate, while hydrolysis and release promotes helix disassembly and substrate release at the lagging end.

The AAA ATPase Vps4 binds ESCRT-III substrates through a repeating array of dipeptide-binding pockets.,Han H, Monroe N, Sundquist WI, Shen PS, Hill CP Elife. 2017 Nov 22;6. doi: 10.7554/eLife.31324. PMID:29165244^[5]

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

References

↑ 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, Monroe N, Sundquist WI, Shen PS, Hill CP. The AAA ATPase Vps4 binds ESCRT-III substrates through a repeating array of dipeptide-binding pockets. Elife. 2017 Nov 22;6. doi: 10.7554/eLife.31324. PMID:29165244 doi:http://dx.doi.org/10.7554/eLife.31324

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

OCA

[1] 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

[2] 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

[3] 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

[4] 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

[5] Han H, Monroe N, Sundquist WI, Shen PS, Hill CP. The AAA ATPase Vps4 binds ESCRT-III substrates through a repeating array of dipeptide-binding pockets. Elife. 2017 Nov 22;6. doi: 10.7554/eLife.31324. PMID:29165244 doi:http://dx.doi.org/10.7554/eLife.31324

[1]

[2]

[3]

[4]

[5]

@@ Line 1: / Line 1: @@
 ==Vps4p-Vta1p complex with peptide binding to the central pore of Vps4p==
-<StructureSection load='6ap1' size='340' side='right' caption='[[6ap1]], [[Resolution|resolution]] 3.20&Aring;' scene=''>
+<SX load='6ap1' size='340' side='right' viewer='molstar' caption='[[6ap1]], [[Resolution|resolution]] 3.20&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[6ap1]] is a 19 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6AP1 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6AP1 FirstGlance]. <br>
+<table><tr><td colspan='2'>[[6ap1]] is a 19 chain structure with sequence from [https://en.wikipedia.org/wiki/Pseudomonas_aeruginosa_PAO1 Pseudomonas aeruginosa PAO1], [https://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae] and [https://en.wikipedia.org/wiki/Saccharomyces_cerevisiae_S288C Saccharomyces cerevisiae S288C]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6AP1 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6AP1 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='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">Electron Microscopy, [[Resolution|Resolution]] 3.2&#8491;</td></tr>
-<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACE:ACETYL+GROUP'>ACE</scene>, <scene name='pdbligand=NH2:AMINO+GROUP'>NH2</scene></td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACE:ACETYL+GROUP'>ACE</scene>, <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>, <scene name='pdbligand=NH2:AMINO+GROUP'>NH2</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=6ap1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6ap1 OCA], [http://pdbe.org/6ap1 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6ap1 RCSB], [http://www.ebi.ac.uk/pdbsum/6ap1 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6ap1 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=6ap1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6ap1 OCA], [https://pdbe.org/6ap1 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6ap1 RCSB], [https://www.ebi.ac.uk/pdbsum/6ap1 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6ap1 ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/VPS4_YEAST 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.<ref>PMID:11329380</ref> <ref>PMID:9155008</ref> <ref>PMID:9606181</ref>  [[http://www.uniprot.org/uniprot/VTA1_YEAST 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.<ref>PMID:12953057</ref> <ref>PMID:14701806</ref> <ref>PMID:16505166</ref> <ref>PMID:16601096</ref>
+[https://www.uniprot.org/uniprot/VTA1_YEAST 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.<ref>PMID:12953057</ref> <ref>PMID:14701806</ref> <ref>PMID:16505166</ref> <ref>PMID:16601096</ref>
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==
@@ Line 19: / Line 19: @@
 </div>
 <div class="pdbe-citations 6ap1" style="background-color:#fffaf0;"></div>
+==See Also==
+*[[Vacuolar protein sorting-associated protein 3D structures|Vacuolar protein sorting-associated protein 3D structures]]
 == References ==
 <references/>
 __TOC__
-</StructureSection>
+</SX>
-[[Category: Han, H]]
+[[Category: Large Structures]]
-[[Category: Hill, C P]]
+[[Category: Pseudomonas aeruginosa PAO1]]
-[[Category: Monroe, N]]
+[[Category: Saccharomyces cerevisiae]]
-[[Category: Shen, P]]
+[[Category: Saccharomyces cerevisiae S288C]]
-[[Category: Sundquist, W I]]
+[[Category: Han H]]
-[[Category: Aaa atpase]]
+[[Category: Hill CP]]
-[[Category: Escrt]]
+[[Category: Monroe N]]
-[[Category: Transport protein]]
+[[Category: Shen P]]
-[[Category: Vps4]]
+[[Category: Sundquist WI]]
-[[Category: Vta1]]

6ap1: Difference between revisions

Latest revision as of 08:03, 21 November 2024

Vps4p-Vta1p complex with peptide binding to the central pore of Vps4pVps4p-Vta1p complex with peptide binding to the central pore of Vps4p

Structural highlights

Function

Publication Abstract from PubMed

See Also

References

Contents

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

Navigation menu

6ap1: Difference between revisions

Latest revision as of 08:03, 21 November 2024

Vps4p-Vta1p complex with peptide binding to the central pore of Vps4pVps4p-Vta1p complex with peptide binding to the central pore of Vps4p

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

Search