4NTI

Crystal structure of D60N mutant of Arabidopsis ACD11 (accelerated-cell-death 11) complexed with C12 ceramide-1-phosphate (d18:1/12:0) at 2.9 Angstrom resolution


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.899 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.195 

wwPDB Validation 3D Report Full Report


This is version 1.1 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: 10.1016/j.celrep.2013.12.023
  • Primary Citation of Related Structures:  

  • 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 f ...

    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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
accelerated-cell-death 11
A, B
207Arabidopsis thalianaMutation(s): 1 
Gene Names: ACD11
Find proteins for O64587 (Arabidopsis thaliana)
Go to UniProtKB:  O64587
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PEG
Query on PEG

Download SDF File 
Download CCD File 
B
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
 Ligand Interaction
1PZ
Query on 1PZ

Download SDF File 
Download CCD File 
A, B
(2S,3R,4E)-2-(dodecanoylamino)-3-hydroxyoctadec-4-en-1-yl dihydrogen phosphate
C30 H60 N O6 P
KXEMZGPJXBKYJP-VARSQMIESA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.899 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.195 
  • Space Group: P 32 2 1
Unit Cell:
Length (Å)Angle (°)
a = 118.118α = 90.00
b = 118.118β = 90.00
c = 152.378γ = 120.00
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
MOLREPphasing
SCALEPACKdata scaling
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-02-05
    Type: Initial release
  • Version 1.1: 2014-02-19
    Type: Database references