3GGY | pdb_00003ggy

Crystal Structure of S.cerevisiae Ist1 N-terminal domain


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 
    0.249 (Depositor), 0.240 (DCC) 
  • R-Value Work: 
    0.226 (Depositor), 0.230 (DCC) 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Structural basis of Ist1 function and Ist1-Did2 interaction in the multivesicular body pathway and cytokinesis.

Xiao, J.Chen, X.W.Davies, B.A.Saltiel, A.R.Katzmann, D.J.Xu, Z.

(2009) Mol Biol Cell 20: 3514-3524

  • DOI: https://doi.org/10.1091/mbc.e09-05-0403
  • Primary Citation of Related Structures:  
    3GGY, 3GGZ

  • PubMed Abstract: 

    The ESCRT machinery functions in several important eukaryotic cellular processes. The AAA-ATPase Vps4 catalyzes disassembly of the ESCRT-III complex and may regulate membrane deformation and vesicle scission as well. Ist1 was proposed to be a regulator of Vps4, but its mechanism of action was unclear. The crystal structure of the N-terminal domain of Ist1 (Ist1NTD) reveals an ESCRT-III subunit-like fold, implicating Ist1 as a divergent ESCRT-III family member. Ist1NTD specifically binds to the ESCRT-III subunit Did2, and cocrystallization of Ist1NTD with a Did2 fragment shows that Ist1 interacts with the Did2 C-terminal MIM1 (MIT-interacting motif 1) via a novel MIM-binding structural motif. This arrangement indicates a mechanism for intermolecular ESCRT-III subunit association and may also suggest one form of ESCRT-III subunit autoinhibition via intramolecular interaction.


  • Organizational Affiliation
    • Life Sciences Institute and Department of Biological Chemistry, Department of Molecular and Integrative Physiology, Medical School, University of Michigan, Ann Arbor, MI 48109, USA.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Increased sodium tolerance protein 1
A, B
193Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: IST1N0809YNL265C
UniProt
Find proteins for P53843 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P53843 
Go to UniProtKB:  P53843
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP53843
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free:  0.249 (Depositor), 0.240 (DCC) 
  • R-Value Work:  0.226 (Depositor), 0.230 (DCC) 
Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 144.845α = 90
b = 44.172β = 110.48
c = 66.952γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
PDB_EXTRACTdata extraction
SHARPphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2009-09-08
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2017-11-01
    Changes: Refinement description
  • Version 1.3: 2024-02-21
    Changes: Data collection, Database references