13GJ | pdb_000013gj

IST1 bound to PI(4,5)P2 containing membrane


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.00 Å
  • Aggregation State: HELICAL ARRAY 
  • Reconstruction Method: HELICAL 

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Validation slider image for 13GJ

This is version 1.1 of the entry. See complete history

Literature

Phosphatidylinositol diphosphate binding by ESCRT-III filaments.

Alian, A.McCullough, J.Moss 3rd, F.R.Talledge, N.Mohammed, A.Gerstner, C.D.Dalluge, J.A.Paine, E.L.Davulcu, O.Chang, C.L.Frost, A.Sundquist, W.I.

(2026) Proc Natl Acad Sci U S A 123

  • DOI: https://doi.org/10.1073/pnas.2616668123
  • Primary Citation Related Structures: 
    13GH, 13GJ, 13GM

  • PubMed Abstract: 

    Different inositol phospholipids (PIPs) distribute to distinct subcellular organelles, creating an addressing system that dictates the sites of action of PIP-binding proteins, including components of the Endosomal Sorting Complexes Required for Transport (ESCRT). The ESCRT machinery is recruited to remodel many different cellular membranes through combinatorial binding interactions made by the early-acting ESCRT-I and ESCRT-II complexes with PIPs, ubiquitin modifications, and membrane-specific adaptors. Membrane remodeling, constriction, and fission are then mediated by membrane-associated filaments formed by subunits of the late-acting ESCRT-III complexes, together with their associated VPS4 AAA ATPases. Here, we describe two different classes of helical ESCRT-III filaments that can surround and tubulate membranes containing PIP 2 lipids. Cryo-EM reconstructions revealed that protofilaments comprising closed IST1 subunits formed 8-stranded nanotubes that encase membrane monolayers. The nanotube coordinates exposed PI(4,5)P 2 or PI(3,5)P 2 headgroups within a basic pocket formed at the junction of three IST1 subunits, and our structures reveal how the pocket can accommodate either PIP 2 isomer with minimal adjustment. In contrast, protofilaments comprising open CHMP1A subunits formed one start helices that encase membrane bilayers and bind exposed PI(4,5)P 2 headgroups across a basic surface that spans adjacent subunits of the CHMP1A protofilament. These two different structures extend the known plasticity of ESCRT-III polymers, reveal how PIP 2 lipids can promote ESCRT-III filament assembly and membrane remodeling, and define the molecular contacts that underlie specific ESCRT-III/PIP 2 interactions.


  • Organizational Affiliation
    • Department of Biochemistry, University of Utah Spencer Fox Eccles School of Medicine, Salt Lake City, UT 84112.

Macromolecule Content 

  • Total Structure Weight: 40.54 kDa 
  • Atom Count: 1,583 
  • Modeled Residue Count: 183 
  • Deposited Residue Count: 364 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
IST1 homolog364Homo sapiensMutation(s): 0 
Gene Names: IST1
UniProt & NIH Common Fund Data Resources
Find proteins for P53990 (Homo sapiens)
Explore P53990 
Go to UniProtKB:  P53990
PHAROS:  P53990
GTEx:  ENSG00000182149 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP53990
Sequence Annotations
Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PIO
(Subject of Investigation/LOI)

Query on PIO



Download:Ideal Coordinates CCD File
B [auth A][(2R)-2-octanoyloxy-3-[oxidanyl-[(1R,2R,3S,4R,5R,6S)-2,3,6-tris(oxidanyl)-4,5-diphosphonooxy-cyclohexyl]oxy-phosphoryl]oxy-propyl] octanoate
C25 H49 O19 P3
XLNCEHRXXWQMPK-MJUMVPIBSA-N

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.00 Å
  • Aggregation State: HELICAL ARRAY 
  • Reconstruction Method: HELICAL 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONcryoSPARC4.7.1
MODEL REFINEMENTPHENIX2.0-5936

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesR37 AI051174

Revision History  (Full details and data files)

  • Version 1.0: 2026-07-08
    Type: Initial release
  • Version 1.1: 2026-07-15
    Changes: Data collection, Database references