8FDS

Ankyrin domain of SKD3 isoform 2

  • Classification: CHAPERONE, HYDROLASE
  • Organism(s): Homo sapiens
  • Expression System: Escherichia coli
  • Mutation(s): No 

  • Deposited: 2022-12-04 Released: 2023-04-19 
  • Deposition Author(s): Lee, S., Tsai, F.T.F., Chang, C.
  • Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK), Robert A. Welch Foundation, Cancer Prevention and Research Institute of Texas (CPRIT), National Institutes of Health/Office of the Director

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.65 Å
  • R-Value Free: 0.221 
  • R-Value Work: 0.199 
  • R-Value Observed: 0.200 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structural basis of impaired disaggregase function in the oxidation-sensitive SKD3 mutant causing 3-methylglutaconic aciduria.

Lee, S.Lee, S.B.Sung, N.Xu, W.W.Chang, C.Kim, H.E.Catic, A.Tsai, F.T.F.

(2023) Nat Commun 14: 2028-2028

  • DOI: https://doi.org/10.1038/s41467-023-37657-9
  • Primary Citation of Related Structures:  
    8DEH, 8FDS

  • PubMed Abstract: 

    Mitochondria are critical to cellular and organismal health. To prevent damage, mitochondria have evolved protein quality control machines to survey and maintain the mitochondrial proteome. SKD3, also known as CLPB, is a ring-forming, ATP-fueled protein disaggregase essential for preserving mitochondrial integrity and structure. SKD3 deficiency causes 3-methylglutaconic aciduria type VII (MGCA7) and early death in infants, while mutations in the ATPase domain impair protein disaggregation with the observed loss-of-function correlating with disease severity. How mutations in the non-catalytic N-domain cause disease is unknown. Here, we show that the disease-associated N-domain mutation, Y272C, forms an intramolecular disulfide bond with Cys267 and severely impairs SKD3 Y272C function under oxidizing conditions and in living cells. While Cys267 and Tyr272 are found in all SKD3 isoforms, isoform-1 features an additional α-helix that may compete with substrate-binding as suggested by crystal structure analyses and in silico modeling, underscoring the importance of the N-domain to SKD3 function.


  • Organizational Affiliation

    Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX, 77030, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Caseinolytic peptidase B protein homolog182Homo sapiensMutation(s): 0 
Gene Names: CLPBHSP78SKD3
EC: 3.6.1
UniProt & NIH Common Fund Data Resources
Find proteins for Q9H078 (Homo sapiens)
Explore Q9H078 
Go to UniProtKB:  Q9H078
PHAROS:  Q9H078
GTEx:  ENSG00000162129 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9H078
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.65 Å
  • R-Value Free: 0.221 
  • R-Value Work: 0.199 
  • R-Value Observed: 0.200 
  • Space Group: P 65 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 60.44α = 90
b = 60.44β = 90
c = 180.313γ = 120
Software Package:
Software NamePurpose
SBC-Collectdata collection
DIALSdata reduction
DIALSdata scaling
PHASERphasing
PHENIXrefinement

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM142143
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)United StatesDK115454
Robert A. Welch FoundationUnited StatesQ-1530-20190330
Cancer Prevention and Research Institute of Texas (CPRIT)United StatesRR140038
National Institutes of Health/Office of the DirectorUnited StatesOD030246

Revision History  (Full details and data files)

  • Version 1.0: 2023-04-19
    Type: Initial release
  • Version 1.1: 2023-10-25
    Changes: Data collection, Refinement description
  • Version 1.2: 2024-05-01
    Changes: Database references