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Structure paper

TitleThe AAA ATPase Vps4 binds ESCRT-III substrates through a repeating array of dipeptide-binding pockets.
Journal, issue, pagesElife, Vol. 6, Year 2017
Publish dateNov 22, 2017
AuthorsHan Han / Nicole Monroe / Wesley I Sundquist / Peter S Shen / Christopher P Hill /
PubMed AbstractThe hexameric AAA ATPase Vps4 drives membrane fission by remodeling and disassembling ESCRT-III filaments. Building upon our earlier 4.3 Å resolution cryo-EM structure (Monroe et al., 2017), we now ...The hexameric AAA ATPase Vps4 drives membrane fission by remodeling and disassembling ESCRT-III filaments. Building upon our earlier 4.3 Å resolution cryo-EM structure (Monroe et al., 2017), we now report a 3.2 Å structure of Vps4 bound to an ESCRT-III peptide substrate. The new structure reveals that the peptide approximates a β-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.
External linksElife / PubMed:29165244 / PubMed Central
MethodsEM (single particle)
Resolution3.2 - 6.2 Å
Structure data

8887

6ap1

6bmf

EMDB-8887, PDB-6ap1, PDB-6bmf:
Vps4p-Vta1p complex with peptide binding to the central pore of Vps4p
Method: EM (single particle) / Resolution: 3.2 Å

EMDB-8888:
Unsharpened Map of Vps4p-Vta1p complex with peptide binding to the central pore of Vps4p
Method: EM (single particle) / Resolution: 4.1 Å

EMDB-8889:
Focused classification map for high position subunit F of Vps4p-Vta1p complex with peptide binding to the central pore of Vps4p
Method: EM (single particle) / Resolution: 3.7 Å

EMDB-8890:
Focused classification map for low position subunit F of Vps4p-Vta1p complex with peptide binding to the central pore of Vps4p
Method: EM (single particle) / Resolution: 3.6 Å

EMDB-8891:
Focused classification map for VSL dimer bridging Subunit A and B of Vps4p-Vta1p complex with peptide binding to the central pore of Vps4p
Method: EM (single particle) / Resolution: 4.9 Å

EMDB-8892:
Focused classification map for VSL dimer bridging Subunit B and C of Vps4p-Vta1p complex with peptide binding to the central pore of Vps4p
Method: EM (single particle) / Resolution: 4.8 Å

EMDB-8893:
Focused classification map for VSL dimer bridging Subunit C and D of Vps4p-Vta1p complex with peptide binding to the central pore of Vps4p
Method: EM (single particle) / Resolution: 4.5 Å

EMDB-8894:
Focused classification map for VSL dimer bridging Subunit D and E of Vps4p-Vta1p complex with peptide binding to the central pore of Vps4p
Method: EM (single particle) / Resolution: 4.6 Å

EMDB-8895:
Focused classification map for VSL dimer bridging Subunit E and F of Vps4p-Vta1p complex with peptide binding to the central pore of Vps4p
Method: EM (single particle) / Resolution: 6.2 Å

EMDB-8896:
Focused classification map for VSL dimer bridging Subunit F and A of Vps4p-Vta1p complex with peptide binding to the central pore of Vps4p
Method: EM (single particle) / Resolution: 5.2 Å

Chemicals

ChemComp-ADP:
ADENOSINE-5'-DIPHOSPHATE / ADP, energy-carrying molecule*YM

ChemComp-BEF:
BERYLLIUM TRIFLUORIDE ION

ChemComp-MG:
Unknown entry

Source
  • saccharomyces cerevisiae (brewer's yeast)
  • pseudomonas aeruginosa (strain atcc 15692 / dsm 22644 / cip 104116 / jcm 14847 / lmg 12228 / 1c / prs 101 / pao1) (bacteria)
  • saccharomyces cerevisiae (strain atcc 204508 / s288c) (yeast)
KeywordsTRANSPORT PROTEIN / Vps4 / ESCRT / Vta1 / AAA ATPase

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