5FD7

X-ray Crystal Structure of ESCRT-III Snf7 core domain (conformation A)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.263 
  • R-Value Work: 0.259 
  • R-Value Observed: 0.259 

wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

Structural basis for activation, assembly and membrane binding of ESCRT-III Snf7 filaments.

Tang, S.Henne, W.M.Borbat, P.P.Buchkovich, N.J.Freed, J.H.Mao, Y.Fromme, J.C.Emr, S.D.

(2015) Elife 4

  • DOI: https://doi.org/10.7554/eLife.12548
  • Primary Citation of Related Structures:  
    5FD7, 5FD9

  • PubMed Abstract: 

    The endosomal sorting complexes required for transport (ESCRTs) constitute hetero-oligomeric machines that catalyze multiple topologically similar membrane-remodeling processes. Although ESCRT-III subunits polymerize into spirals, how individual ESCRT-III subunits are activated and assembled together into a membrane-deforming filament remains unknown. Here, we determine X-ray crystal structures of the most abundant ESCRT-III subunit Snf7 in its active conformation. Using pulsed dipolar electron spin resonance spectroscopy (PDS), we show that Snf7 activation requires a prominent conformational rearrangement to expose protein-membrane and protein-protein interfaces. This promotes the assembly of Snf7 arrays with ~30 Å periodicity into a membrane-sculpting filament. Using a combination of biochemical and genetic approaches, both in vitro and in vivo, we demonstrate that mutations on these protein interfaces halt Snf7 assembly and block ESCRT function. The architecture of the activated and membrane-bound Snf7 polymer provides crucial insights into the spatially unique ESCRT-III-mediated membrane remodeling.


  • Organizational Affiliation

    Weill Institute of Cell and Molecular Biology, Cornell University, Ithaca, United States.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Vacuolar-sorting protein SNF7140Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: SNF7DID1VPS32YLR025W
Membrane Entity: Yes 
UniProt
Find proteins for P39929 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P39929 
Go to UniProtKB:  P39929
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP39929
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

Unit Cell:
Length ( Å )Angle ( ˚ )
a = 29.451α = 90
b = 52.196β = 97.52
c = 54.486γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RESOLVEmodel building
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Cornell UniversityUnited StatesCU3704
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR01GM098621
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR01GM094347
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesT32GM007273

Revision History  (Full details and data files)

  • Version 1.0: 2015-12-30
    Type: Initial release
  • Version 1.1: 2017-08-23
    Changes: Data collection, Derived calculations, Refinement description
  • Version 1.2: 2017-09-20
    Changes: Author supporting evidence
  • Version 1.3: 2019-12-25
    Changes: Author supporting evidence
  • Version 1.4: 2023-09-27
    Changes: Data collection, Database references, Refinement description