6BMF

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


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.2 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

The AAA ATPase Vps4 binds ESCRT-III substrates through a repeating array of dipeptide-binding pockets.

Han, H.Monroe, N.Sundquist, W.I.Shen, P.S.Hill, C.P.

(2017) Elife 6: --

  • DOI: 10.7554/eLife.31324
  • Primary Citation of Related Structures:  6AP1

  • PubMed Abstract: 
  • 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, Han et al. 2017), we now report a 3.2 Å structure of Vps4 bound to an ESC ...

    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, Han 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 b-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.


    Organizational Affiliation

    Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, United States.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Vacuolar protein sorting-associated protein 4
A, B, C, D, E
337Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Gene Names: VPS4 (CSC1,DID6,END13,GRD13,VPL4,VPT10) 
Find proteins for P52917 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P52917
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Vps2p
G
10N/AN/A
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ADP
Query on ADP

Download SDF File 
Download CCD File 
A, B, C, D, E
ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
 Ligand Interaction
MG
Query on MG

Download SDF File 
Download CCD File 
A, B, C, D
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
BEF
Query on BEF

Download SDF File 
Download CCD File 
A, B, C
BERYLLIUM TRIFLUORIDE ION
Be F3
OGIAHMCCNXDTIE-UHFFFAOYSA-K
 Ligand Interaction
Modified Residues 2 Unique
IDChainsTypeFormula2D DiagramParent
NH2
Query on NH2
G
NON-POLYMERH2 N

--

ACE
Query on ACE
G
NON-POLYMERC2 H4 O

--

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.2 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
Software Package:
Software NamePurpose
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2017-12-06
    Type: Initial release