Crystal Structure of Caenorhabditis elegans ACDH-11 in complex with C11-CoA

  • Classification: OXIDOREDUCTASE
  • Organism(s): Caenorhabditis elegans
  • Expression System: Escherichia coli
  • Mutation(s): No 

  • Deposited: 2015-02-17 Released: 2015-06-03 
  • Deposition Author(s): Li, Z.J., Sun, F.
  • Funding Organization(s): the 973 program of the Chinese Ministry of Science and Technology, the National Natural Science Foundation of China

Experimental Data Snapshot

  • Resolution: 1.80 Å
  • R-Value Free: 0.186 
  • R-Value Work: 0.145 
  • R-Value Observed: 0.147 

Starting Model: experimental
View more details

wwPDB Validation   3D Report Full Report

Ligand Structure Quality Assessment 

This is version 1.3 of the entry. See complete history


Acyl-CoA Dehydrogenase Drives Heat Adaptation by Sequestering Fatty Acids

Ma, D.K.Li, Z.Lu, A.Y.Sun, F.Chen, S.Rothe, M.Menzel, R.Sun, F.Horvitz, H.R.

(2015) Cell 161: 1152-1163

  • DOI: https://doi.org/10.1016/j.cell.2015.04.026
  • Primary Citation of Related Structures:  
    4Y9J, 4Y9L

  • PubMed Abstract: 

    Cells adapt to temperature shifts by adjusting levels of lipid desaturation and membrane fluidity. This fundamental process occurs in nearly all forms of life, but its mechanism in eukaryotes is unknown. We discovered that the evolutionarily conserved Caenorhabditis elegans gene acdh-11 (acyl-CoA dehydrogenase [ACDH]) facilitates heat adaptation by regulating the lipid desaturase FAT-7. Human ACDH deficiency causes the most common inherited disorders of fatty acid oxidation, with syndromes that are exacerbated by hyperthermia. Heat upregulates acdh-11 expression to decrease fat-7 expression. We solved the high-resolution crystal structure of ACDH-11 and established the molecular basis of its selective and high-affinity binding to C11/C12-chain fatty acids. ACDH-11 sequesters C11/C12-chain fatty acids and prevents these fatty acids from activating nuclear hormone receptors and driving fat-7 expression. Thus, the ACDH-11 pathway drives heat adaptation by linking temperature shifts to regulation of lipid desaturase levels and membrane fluidity via an unprecedented mode of fatty acid signaling.

  • Organizational Affiliation

    Department of Biology, Howard Hughes Medical Institute, McGovern Institute for Brain Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA. Electronic address: dengke.ma@ucsf.edu.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Protein ACDH-11, isoform b
A, B
593Caenorhabditis elegansMutation(s): 0 
Gene Names: acdh-11CELE_Y45F3A.3Y45F3A.3
Find proteins for Q9XWZ2 (Caenorhabditis elegans)
Explore Q9XWZ2 
Go to UniProtKB:  Q9XWZ2
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9XWZ2
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on UCC

Download Ideal Coordinates CCD File 
D [auth A],
F [auth B]
S-{(3S,5R,9R)-1-[(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-4-hydroxy-3-(phosphonooxy)tetrahydrofuran-2-yl]-3,5,9-trihydroxy-8,8-dimethyl-3,5-dioxido-10,14-dioxo-2,4,6-trioxa-11,15-diaza-3lambda~5~,5lambda~5~-diphosphaheptadecan-17-yl} undecanethioate
C32 H56 N7 O17 P3 S
Query on FAD

Download Ideal Coordinates CCD File 
C [auth A],
E [auth B]
C27 H33 N9 O15 P2
Experimental Data & Validation

Experimental Data

  • Resolution: 1.80 Å
  • R-Value Free: 0.186 
  • R-Value Work: 0.145 
  • R-Value Observed: 0.147 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 138.561α = 90
b = 116.676β = 124.02
c = 115.289γ = 90
Software Package:
Software NamePurpose
HKL-2000data scaling
PDB_EXTRACTdata extraction
Cootmodel building

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment 

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
the 973 program of the Chinese Ministry of Science and TechnologyChinaNos. 2006CB911001 and 2006CB806506
the National Natural Science Foundation of ChinaChinaNo. 30721003

Revision History  (Full details and data files)

  • Version 1.0: 2015-06-03
    Type: Initial release
  • Version 1.1: 2020-02-05
    Changes: Data collection, Derived calculations, Source and taxonomy
  • Version 1.2: 2024-03-20
    Changes: Data collection, Database references
  • Version 1.3: 2024-04-03
    Changes: Refinement description