9CKX | pdb_00009ckx

Crystal structure of Dsk2 Sti1 domain bound to a transmembrane domain


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.98 Å
  • R-Value Free: 
    0.232 (Depositor), 0.244 (DCC) 
  • R-Value Work: 
    0.220 (Depositor) 
  • R-Value Observed: 
    0.221 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 9CKX

This is version 1.1 of the entry. See complete history

Literature

ALS mutations disrupt self-association between the Ubiquilin Sti1 hydrophobic groove and internal placeholder sequences.

Onwunma, J.Binsabaan, S.Allen, S.P.Sankaran, B.Wohlever, M.L.

(2025) bioRxiv 

  • DOI: https://doi.org/10.1101/2024.07.10.602902
  • Primary Citation Related Structures: 
    9CKX

  • PubMed Abstract: 

    Ubiquilins are molecular chaperones that play multifaceted roles in proteostasis, with point mutations in UBQLN2 leading to altered phase separation properties and Amyotrophic Lateral Sclerosis (ALS). Our mechanistic understanding of this essential process has been hindered by a lack of structural information on the Sti1 domain, which is essential for Ubiquilin chaperone activity and phase separation. Here, we present the first crystal structure of a Ubiquilin family Sti1 domain bound to a transmembrane domain (TMD) and show that ALS mutations disrupt the Sti1-TMD interaction. We then demonstrate that Ubiquilins contain multiple conserved, internal sequences that bind to the Sti1 domain, including the PXX region which is a hotspot for ALS mutations. We propose that these placeholder sequences prevent solvent exposure of the Sti1 hydrophobic groove and contribute to the multivalency that drives Ubiquilin phase separation. Together, this work provides a new paradigm for understanding how Sti1 domains modulate Ubiquilin chaperone activity and phase separation and offer insights into the molecular basis of ALS pathogenesis.


  • Organizational Affiliation
    • Previously at University of Toledo, Department of Chemistry & Biochemistry.

Macromolecule Content 

  • Total Structure Weight: 48.84 kDa 
  • Atom Count: 3,516 
  • Modeled Residue Count: 444 
  • Deposited Residue Count: 444 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Ubiquitin-domain-containing protein,Response regulator FrzS,Vesicle-associated membrane protein 2
A, B
222Metschnikowia bicuspidataMyxococcus xanthusHomo sapiens
This entity is chimeric
Mutation(s): 6 
Gene Names: METBIDRAFT_39938N3T43_21095VAMP2SYB2
UniProt & NIH Common Fund Data Resources
Find proteins for P63027 (Homo sapiens)
Explore P63027 
Go to UniProtKB:  P63027
PHAROS:  P63027
GTEx:  ENSG00000220205 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP63027
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.98 Å
  • R-Value Free:  0.232 (Depositor), 0.244 (DCC) 
  • R-Value Work:  0.220 (Depositor) 
  • R-Value Observed: 0.221 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 67.41α = 90
b = 63.92β = 98.83
c = 67.43γ = 90
Software Package:
Software NamePurpose
MOSFLMdata reduction
PHENIXrefinement
PHENIXphasing
Cootmodel building
MolProbitymodel building
SCALAdata scaling

Structure Validation

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Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Science Foundation (NSF, United States)United StatesCAREER 2343131
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR35 GM137904
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesP30 GM124169-01

Revision History  (Full details and data files)

  • Version 1.0: 2025-03-12
    Type: Initial release
  • Version 1.1: 2025-07-23
    Changes: Database references