4NTO

Crystal structure of D60A mutant of Arabidopsis ACD11 (accelerated-cell-death 11) complexed with C2 ceramide-1-phosphate (d18:1/2:0) at 2.15 Angstrom resolution


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free: 0.240 
  • R-Value Work: 0.196 
  • R-Value Observed: 0.198 

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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Arabidopsis Accelerated Cell Death 11, ACD11, Is a Ceramide-1-Phosphate Transfer Protein and Intermediary Regulator of Phytoceramide Levels.

Simanshu, D.K.Zhai, X.Munch, D.Hofius, D.Markham, J.E.Bielawski, J.Bielawska, A.Malinina, L.Molotkovsky, J.G.Mundy, J.W.Patel, D.J.Brown, R.E.

(2014) Cell Rep 6: 388-399

  • DOI: https://doi.org/10.1016/j.celrep.2013.12.023
  • Primary Citation of Related Structures:  
    4NT1, 4NT2, 4NTG, 4NTI, 4NTO

  • PubMed Abstract: 

    The accelerated cell death 11 (acd11) mutant of Arabidopsis provides a genetic model for studying immune response activation and localized cellular suicide that halt pathogen spread during infection in plants. Here, we elucidate ACD11 structure and function and show that acd11 disruption dramatically alters the in vivo balance of sphingolipid mediators that regulate eukaryotic-programmed cell death. In acd11 mutants, normally low ceramide-1-phosphate (C1P) levels become elevated, but the relatively abundant cell death inducer phytoceramide rises acutely. ACD11 exhibits selective intermembrane transfer of C1P and phyto-C1P. Crystal structures establish C1P binding via a surface-localized, phosphate headgroup recognition center connected to an interior hydrophobic pocket that adaptively ensheaths lipid chains via a cleft-like gating mechanism. Point mutation mapping confirms functional involvement of binding site residues. A π helix (π bulge) near the lipid binding cleft distinguishes apo-ACD11 from other GLTP folds. The global two-layer, α-helically dominated, "sandwich" topology displaying C1P-selective binding identifies ACD11 as the plant prototype of a GLTP fold subfamily.


  • Organizational Affiliation

    Structural Biology Program, Memorial Sloan-Kettering Cancer Center, New York, NY 10065, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
accelerated-cell-death 11
A, B, C
207Arabidopsis thalianaMutation(s): 1 
Gene Names: ACD11AT2G34690
UniProt
Find proteins for O64587 (Arabidopsis thaliana)
Explore O64587 
Go to UniProtKB:  O64587
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO64587
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free: 0.240 
  • R-Value Work: 0.196 
  • R-Value Observed: 0.198 
  • Space Group: I 2 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 91.82α = 90
b = 103.574β = 90
c = 165.289γ = 90
Software Package:
Software NamePurpose
SCALEPACKdata scaling
MOLREPphasing
PHENIXrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-02-05
    Type: Initial release
  • Version 1.1: 2014-02-19
    Changes: Database references
  • Version 1.2: 2023-09-20
    Changes: Data collection, Database references, Derived calculations, Refinement description