4NTG | pdb_00004ntg

Crystal structure of D60A mutant of Arabidopsis ACD11 (accelerated-cell-death 11) complexed with C12 ceramide-1-phosphate (d18:1/12:0) at 2.55 Angstrom resolution

• PDB DOI: https://doi.org/10.2210/pdb4NTG/pdb

• Classification: TRANSPORT PROTEIN
• Organism(s): Arabidopsis thaliana
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2013-12-02 Released: 2014-02-05 
• Deposition Author(s): Simanshu, D.K., Brown, R.E., Patel, D.J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.55 Å
• R-Value Free: 
  0.236 (Depositor), 0.238 (DCC) 
• R-Value Work: 
  0.181 (Depositor), 0.185 (DCC) 
• R-Value Observed: 
  0.187 (Depositor) 

Starting Model: experimental

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

• PubMed: 24412362 
• DOI: https://doi.org/10.1016/j.celrep.2013.12.023
• Primary Citation 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.

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Organizational Affiliation: 
• Structural Biology Program, Memorial Sloan-Kettering Cancer Center, New York, NY 10065, USA.
Hormel Institute, University of Minnesota, Austin, MN 55912, USA.
Department of Biology, BioCenter, University of Copenhagen, 2200 Copenhagen N, Denmark.
Department of Biochemistry, University of Nebraska, N146 Beadle Center, Lincoln, NE 68588, USA.
Department of Biochemistry and Molecular Biology, Lipidomics Shared Resource Mass Spectrometry Lab, Medical University of South Carolina, Charleston, SC 29425, USA.
Structural Biology Unit, CIC bioGUNE, Technology Park of Bizkaia, 48160 Derio-Bilbao, Spain.
Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia.
Department of Biology, BioCenter, University of Copenhagen, 2200 Copenhagen N, Denmark. Electronic address: [e-mail].
Structural Biology Program, Memorial Sloan-Kettering Cancer Center, New York, NY 10065, USA. Electronic address: [e-mail].
Hormel Institute, University of Minnesota, Austin, MN 55912, USA. Electronic address: [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 46.63 kDa 
• Atom Count: 3,222 
• Modeled Residue Count: 400 
• Deposited Residue Count: 414 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
accelerated-cell-death 11	A, B	207	Arabidopsis thaliana	Mutation(s): 1  Gene Names: ACD11, AT2G34690
UniProt
Find proteins for O64587 (Arabidopsis thaliana) Explore O64587  Go to UniProtKB:  O64587

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
1PZ	C [auth A], D [auth B]	(2S,3R,4E)-2-(dodecanoylamino)-3-hydroxyoctadec-4-en-1-yl dihydrogen phosphate C30 H60 N O6 P KXEMZGPJXBKYJP-VARSQMIESA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.55 Å
• R-Value Free:  0.236 (Depositor), 0.238 (DCC) 
• R-Value Work:  0.181 (Depositor), 0.185 (DCC) 
• R-Value Observed: 0.187 (Depositor) 

Space Group: H 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 101.507	α = 90
b = 101.507	β = 90
c = 280.732	γ = 120

Software Package:

Software Name	Purpose
SCALEPACK	data scaling
MOLREP	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-02-05 
Deposition Author(s): Simanshu, D.K., Brown, R.E., Patel, D.J.

Revision History  

• 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