4NIQ

Crystal Structure of Vps4 MIT-Vfa1 MIM2


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.301 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.236 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Vfa1 Binds to the N-terminal Microtubule-interacting and Trafficking (MIT) Domain of Vps4 and Stimulates Its ATPase Activity.

Vild, C.J.Xu, Z.

(2014) J.Biol.Chem. 289: 10378-10386

  • DOI: 10.1074/jbc.M113.532960

  • PubMed Abstract: 
  • The endosomal sorting complexes required for transport (ESCRT) are responsible for multivesicular body biogenesis, membrane abscission during cytokinesis, and retroviral budding. They function as transiently assembled molecular complexes on the membr ...

    The endosomal sorting complexes required for transport (ESCRT) are responsible for multivesicular body biogenesis, membrane abscission during cytokinesis, and retroviral budding. They function as transiently assembled molecular complexes on the membrane, and their disassembly requires the action of the AAA-ATPase Vps4. Vps4 is regulated by a multitude of ESCRT and ESCRT-related proteins. Binding of these proteins to Vps4 is often mediated via the microtubule-interacting and trafficking (MIT) domain of Vps4. Recently, a new Vps4-binding protein Vfa1 was identified in a yeast genetic screen, where overexpression of Vfa1 caused defects in vacuolar morphology. However, the function of Vfa1 and its role in vacuolar biology were largely unknown. Here, we provide the first detailed biochemical and biophysical study of Vps4-Vfa1 interaction. The MIT domain of Vps4 binds to the C-terminal 17 residues of Vfa1. This interaction is of high affinity and greatly stimulates the ATPase activity of Vps4. The crystal structure of the Vps4-Vfa1 complex shows that Vfa1 adopts a canonical MIT-interacting motif 2 structure that has been observed previously in other Vps4-ESCRT interactions. These findings suggest that Vfa1 is a novel positive regulator of Vps4 function.


    Organizational Affiliation

    From the Life Sciences Institute and Department of Biological Chemistry, Medical School, University of Michigan, Ann Arbor, Michigan 48109.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Vacuolar protein sorting-associated protein 4
A, B
83Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
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
VPS4-associated protein 1
C, D
23Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: VFA1
Find proteins for P40080 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P40080
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.301 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.236 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 38.476α = 90.00
b = 56.711β = 90.00
c = 84.233γ = 90.00
Software Package:
Software NamePurpose
HKL-3000data collection
DENZOdata reduction
SCALEPACKdata scaling
PDB_EXTRACTdata extraction
PHENIXrefinement
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2013-11-06 
  • Released Date: 2014-03-05 
  • Deposition Author(s): Vild, C.J., Xu, Z.

Revision History 

  • Version 1.0: 2014-03-05
    Type: Initial release
  • Version 1.1: 2014-04-30
    Type: Database references
  • Version 1.2: 2017-11-22
    Type: Refinement description