5UIE | pdb_00005uie

Vps4-Vta1 complex


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 5.70 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

Validation slider image for 5UIE

This is version 1.5 of the entry. See complete history

Literature

Structural basis of protein translocation by the Vps4-Vta1 AAA ATPase.

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

(2017) Elife 6

  • DOI: https://doi.org/10.7554/eLife.24487
  • Primary Citation Related Structures: 
    5UIE

  • PubMed Abstract: 

    Many important cellular membrane fission reactions are driven by ESCRT pathways, which culminate in disassembly of ESCRT-III polymers by the AAA ATPase Vps4. We report a 4.3 Å resolution cryo-EM structure of the active Vps4 hexamer with its cofactor Vta1, ADP·BeF x , and an ESCRT-III substrate peptide. Four Vps4 subunits form a helix whose interfaces are consistent with ATP binding, is stabilized by Vta1, and binds the substrate peptide. The fifth subunit approximately continues this helix but appears to be dissociating. The final Vps4 subunit completes a notched-washer configuration as if transitioning between the ends of the helix. We propose that ATP binding propagates growth at one end of the helix while hydrolysis promotes disassembly at the other end, so that Vps4 'walks' along ESCRT-III until it encounters the ordered N-terminal domain to destabilize the ESCRT-III lattice. This model may be generally applicable to other protein-translocating AAA ATPases.


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

Macromolecule Content 

  • Total Structure Weight: 740.85 kDa 
  • Atom Count: 18,682 
  • Modeled Residue Count: 2,387 
  • Deposited Residue Count: 6,591 
  • Unique protein chains: 3

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Vacuolar protein sorting-associated protein 4
A, B, C, D, E
A, B, C, D, E, F
437Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: VPS4CSC1DID6END13GRD13VPL4VPT10YPR173CP9705.10
UniProt
Find proteins for P52917 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P52917 
Go to UniProtKB:  P52917
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP52917
Sequence Annotations
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Reference Sequence
Find similar proteins by:  Sequence   |   3D Structure  
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
DOA4-independent degradation protein 49Saccharomyces cerevisiaeMutation(s): 0 
Find similar proteins by:|  3D Structure
Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
Vacuolar protein sorting-associated protein VTA1
H, I, J, K, L
H, I, J, K, L, M, N, O, P, Q, R, S
330Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: VTA1YLR181C
UniProt
Find proteins for Q06263 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore Q06263 
Go to UniProtKB:  Q06263
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ06263
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ADP

Query on ADP



Download:Ideal Coordinates CCD File
CA [auth D],
DA [auth E],
T [auth A],
W [auth B],
Z [auth C]
ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
BEF

Query on BEF



Download:Ideal Coordinates CCD File
AA [auth C],
U [auth A],
Y [auth C]
BERYLLIUM TRIFLUORIDE ION
Be F3
OGIAHMCCNXDTIE-UHFFFAOYSA-K
MG

Query on MG



Download:Ideal Coordinates CCD File
BA [auth C],
V [auth A],
X [auth B]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 5.70 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION1.4

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesP50 GM082545

Revision History  (Full details and data files)

  • Version 1.0: 2017-04-12
    Type: Initial release
  • Version 1.1: 2017-09-13
    Changes: Author supporting evidence, Data collection
  • Version 1.2: 2018-07-18
    Changes: Data collection, Experimental preparation
  • Version 1.3: 2018-10-24
    Changes: Data collection, Database references, Structure summary
  • Version 1.4: 2020-01-01
    Changes: Author supporting evidence, Derived calculations
  • Version 1.5: 2024-11-20
    Changes: Data collection, Database references, Derived calculations, Structure summary