3GGZ

Crystal Structure of S.cerevisiae Ist1 N-terminal domain in complex with Did2 MIM motif


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.80 Å
  • R-Value Free: 0.307 
  • R-Value Work: 0.289 
  • R-Value Observed: 0.289 

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, C, D
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
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Vacuolar protein-sorting-associated protein 46
E, F, G, H
29Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: CHM1DID2FTI1VPS46YKR035W-A
UniProt
Find proteins for P69771 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P69771 
Go to UniProtKB:  P69771
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP69771
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.80 Å
  • R-Value Free: 0.307 
  • R-Value Work: 0.289 
  • R-Value Observed: 0.289 
  • Space Group: P 42 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 165.916α = 90
b = 165.916β = 90
c = 121.559γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
CNSrefinement
PDB_EXTRACTdata extraction

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, Refinement description