3GGY | pdb_00003ggy

Crystal Structure of S.cerevisiae Ist1 N-terminal domain

• PDB DOI: https://doi.org/10.2210/pdb3GGY/pdb

• Classification: PROTEIN TRANSPORT, ENDOCYTOSIS
• Organism(s): Saccharomyces cerevisiae
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2009-03-02 Released: 2009-09-08 
• Deposition Author(s): Xiao, J., Xu, Z.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 
  0.249 (Depositor), 0.236 (DCC) 
• R-Value Work: 
  0.226 (Depositor), 0.226 (DCC) 

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

• PubMed: 19477918 
• DOI: https://doi.org/10.1091/mbc.e09-05-0403
• Primary Citation 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.

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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.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 44.76 kDa 
• Atom Count: 3,492 
• Modeled Residue Count: 372 
• Deposited Residue Count: 386 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Increased sodium tolerance protein 1	A, B	193	Saccharomyces cerevisiae	Mutation(s): 0  Gene Names: IST1, N0809, YNL265C
UniProt
Find proteins for P53843 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P53843  Go to UniProtKB:  P53843

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free:  0.249 (Depositor), 0.236 (DCC) 
• R-Value Work:  0.226 (Depositor), 0.226 (DCC) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 144.845	α = 90
b = 44.172	β = 110.48
c = 66.952	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
CNS	refinement
PDB_EXTRACT	data extraction
SHARP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-09-08 
Deposition Author(s): Xiao, J., Xu, Z.

Revision History  

• 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