7Y8W

Crystal structure of DLC-1/SAO-1 complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.285 
  • R-Value Work: 0.253 
  • R-Value Observed: 0.254 

wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


Literature

Interaction between DLC-1 and SAO-1 facilitates CED-4 translocation during apoptosis in the Caenorhabditis elegans germline.

Zhang, D.Yang, H.Jiang, L.Zhao, C.Wang, M.Hu, B.Yu, C.Wei, Z.Tse, Y.C.

(2022) Cell Death Discov 8: 441-441

  • DOI: https://doi.org/10.1038/s41420-022-01233-9
  • Primary Citation of Related Structures:  
    7Y8W

  • PubMed Abstract: 

    Apoptosis is one of the major forms of programmed cell death, and it serves vital biological functions in multicellular animal and plant cells. The core mechanism of apoptosis is highly conserved in metazoans, where the translocation of CED-4/Apaf-1 from mitochondria to the nuclear membrane is required to initiate and execute apoptosis. However, the underlying molecular mechanisms of this translocation are poorly understood. In this study, we showed that SAO-1 binds DLC-1 and prevents its degradation to promote apoptosis in C. elegans germ cells. We demonstrated that SAO-1 and DLC-1 regulate CED-4/Apaf-1 nuclear membrane accumulation during apoptosis. Isothermal titration calorimetry-based assay and high-resolution crystal structure analysis further revealed that SAO-1 interacted with DLC-1 to form a 2:4 complex: each of the two β-sheets in the SAO-1 peptide interacted with two DLC-1 dimers. Point mutations at the SAO-1-DLC-1 binding interface significantly inhibited apoptotic corpse formation and CED-4 nuclear membrane accumulation within C. elegans germ cells. In conclusion, our study provides a new perspective on the regulation of CED-4-mediated apoptosis.


  • Organizational Affiliation

    School of Life Science and Technology, Harbin Institute of Technology, Harbin, 150001, China.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Dynein light chain 1, cytoplasmic
A, B, C, D, G
A, B, C, D, G, H, I, J, M, N, Q, R
95Caenorhabditis elegansMutation(s): 0 
Gene Names: dlc-1T26A5.9
UniProt
Find proteins for Q22799 (Caenorhabditis elegans)
Explore Q22799 
Go to UniProtKB:  Q22799
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ22799
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Isoform b of Suppressor of aph-1
E, F, K, L, O
E, F, K, L, O, P, S, T
30Caenorhabditis elegansMutation(s): 0 
Gene Names: sao-1R10D12.14
UniProt
Find proteins for C6KRN1 (Caenorhabditis elegans)
Explore C6KRN1 
Go to UniProtKB:  C6KRN1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupC6KRN1
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.285 
  • R-Value Work: 0.253 
  • R-Value Observed: 0.254 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 40.274α = 90
b = 163.515β = 90.46
c = 229.132γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data scaling
PHASERphasing
PDB_EXTRACTdata extraction
HKL-3000data reduction

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China31870757
National Natural Science Foundation of China (NSFC)China31971131
National Natural Science Foundation of China (NSFC)China32170697

Revision History  (Full details and data files)

  • Version 1.0: 2023-07-26
    Type: Initial release