4NT2

Crystal structure of Arabidopsis ACD11 (accelerated-cell-death 11) complexed with lyso-sphingomyelin (d18:1) at 2.4 Angstrom resolution


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.223 
  • R-Value Work: 0.191 
  • R-Value Observed: 0.192 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.3 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 11207Arabidopsis thalianaMutation(s): 0 
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
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
SPU
Query on SPU

Download Ideal Coordinates CCD File 
B [auth A],
C [auth A]
2-{[(R)-{[(2S,3R,4E)-2-amino-3-hydroxyoctadec-4-en-1-yl]oxy}(hydroxy)phosphoryl]oxy}-N,N,N-trimethylethanaminium
C23 H50 N2 O5 P
JLVSPVFPBBFMBE-HXSWCURESA-O
SO4
Query on SO4

Download Ideal Coordinates CCD File 
D [auth A],
E [auth A],
F [auth A],
G [auth A],
H [auth A]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
EDO
Query on EDO

Download Ideal Coordinates CCD File 
I [auth A],
J [auth A]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.223 
  • R-Value Work: 0.191 
  • R-Value Observed: 0.192 
  • Space Group: P 63 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 108.827α = 90
b = 108.827β = 90
c = 105.007γ = 120
Software Package:
Software NamePurpose
MOLREPphasing
PHENIXrefinement
PDB_EXTRACTdata extraction
DENZOdata reduction
SCALEPACKdata scaling
HKL-2000data scaling

Structure Validation

View Full Validation Report



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: 2017-11-22
    Changes: Refinement description
  • Version 1.3: 2023-09-20
    Changes: Data collection, Database references, Derived calculations, Refinement description