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), 0.234 (DCC) 
  • R-Value Work: 
    0.220 (Depositor), 0.222 (DCC) 
  • R-Value Observed: 
    0.221 (Depositor) 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


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 of Related Structures:  
    9CKX

  • PubMed Abstract: 

    Ubiquilins are a family of cytosolic proteins that ferry ubiquitinated substrates to the proteasome for degradation. Recent work has demonstrated that Ubiquilins can also act as molecular chaperones, utilizing internal Sti1 domains to directly bind to hydrophobic sequences. Ubiquilins are associated with several neurodegenerative diseases with point mutations in UBQLN2 causing dominant, X-linked Amyotrophic Lateral Sclerosis (ALS). The molecular basis of Ubiquilin chaperone activity and how ALS mutations in the Sti1 domains affect Ubiquilin activity are poorly understood. This study presents the first crystal structure of the Sti1 domain from a fungal Ubiquilin homolog bound to a transmembrane domain (TMD). The structure reveals that two Sti1 domains form a head-to-head dimer, creating a hydrophobic cavity that accommodates two TMDs. Mapping the UBQLN2 sequence onto the structure shows that several ALS mutations are predicted to disrupt the hydrophobic groove. Using a newly developed competitive binding assay, we show that Ubiquilins preferentially bind to hydrophobic substrates with low helical propensity, motifs that are enriched in both substrates and in Ubiquilins. This study provides insights into the molecular and structural basis for Ubiquilin substrate binding, with broad implications for the role of the Sti1 domain in phase separation and ALS.


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

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  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), 0.234 (DCC) 
  • R-Value Work:  0.220 (Depositor), 0.222 (DCC) 
  • 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