4Y9J

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

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.186 
  • R-Value Work: 0.145 
  • R-Value Observed: 0.147 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

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

  • 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 ...

    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.


    Related Citations: 
    • Purification, crystallization and preliminary crystallographic analysis of very-long-chain acyl-CoA dehydrogenase from Caenorhabditis elegans
      Li, Z., Zhai, Y., Fang, J., Zhou, Q., Geng, Y., Sun, F.
      (2010) Acta Crystallogr Sect F Struct Biol Cryst Commun 66: 426

    Organizational Affiliation

    Department of Biology, Howard Hughes Medical Institute, McGovern Institute for Brain Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA. Electronic address: horvitz@mit.edu.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Protein ACDH-11, isoform bA, B593Caenorhabditis elegansMutation(s): 0 
Gene Names: acdh-11CELE_Y45F3A.3Y45F3A.3
EC: 1.3.8.9 (PDB Primary Data), 1.3.99 (UniProt)
Find proteins for Q9XWZ2 (Caenorhabditis elegans)
Explore Q9XWZ2 
Go to UniProtKB:  Q9XWZ2
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
UCC
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
IZWCGXGZGYKDHR-GRBGHKMPSA-N
 Ligand Interaction
FAD
Query on FAD

Download Ideal Coordinates CCD File 
C [auth A], E [auth B]FLAVIN-ADENINE DINUCLEOTIDE
C27 H33 N9 O15 P2
VWWQXMAJTJZDQX-UYBVJOGSSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • 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
REFMACrefinement
PDB_EXTRACTdata extraction
PHASERphasing
Cootmodel building

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data

  • Deposited Date: 2015-02-17 
  • Released Date: 2015-06-03 
  • Deposition Author(s): Li, Z.J., Sun, F.

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