6G7O

Crystal structure of human alkaline ceramidase 3 (ACER3) at 2.7 Angstrom resolution


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.270 
  • R-Value Work: 0.248 
  • R-Value Observed: 0.249 

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Literature

Structure of a human intramembrane ceramidase explains enzymatic dysfunction found in leukodystrophy.

Vasiliauskaite-Brooks, I.Healey, R.D.Rochaix, P.Saint-Paul, J.Sounier, R.Grison, C.Waltrich-Augusto, T.Fortier, M.Hoh, F.Saied, E.M.Arenz, C.Basu, S.Leyrat, C.Granier, S.

(2018) Nat Commun 9: 5437-5437

  • DOI: https://doi.org/10.1038/s41467-018-07864-w
  • Primary Citation of Related Structures:  
    6G7O

  • PubMed Abstract: 

    Alkaline ceramidases (ACERs) are a class of poorly understood transmembrane enzymes controlling the homeostasis of ceramides. They are implicated in human pathophysiology, including progressive leukodystrophy, colon cancer as well as acute myeloid leukemia. We report here the crystal structure of the human ACER type 3 (ACER3). Together with computational studies, the structure reveals that ACER3 is an intramembrane enzyme with a seven transmembrane domain architecture and a catalytic Zn 2+ binding site in its core, similar to adiponectin receptors. Interestingly, we uncover a Ca 2+ binding site physically and functionally connected to the Zn 2+ providing a structural explanation for the known regulatory role of Ca 2+ on ACER3 enzymatic activity and for the loss of function in E33G-ACER3 mutant found in leukodystrophic patients.


  • Organizational Affiliation

    IGF, University of Montpellier, CNRS, INSERM, Montpellier, 34094, France.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Alkaline ceramidase 3,Soluble cytochrome b562350Homo sapiensEscherichia coli
This entity is chimeric
Mutation(s): 0 
Gene Names: ACER3APHCPHCAcybC
EC: 3.5.1
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for P0ABE7 (Escherichia coli)
Explore P0ABE7 
Go to UniProtKB:  P0ABE7
Find proteins for Q9NUN7 (Homo sapiens)
Explore Q9NUN7 
Go to UniProtKB:  Q9NUN7
PHAROS:  Q9NUN7
GTEx:  ENSG00000078124 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupsP0ABE7Q9NUN7
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 6 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
OLB
Query on OLB

Download Ideal Coordinates CCD File 
L [auth A](2S)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate
C21 H40 O4
RZRNAYUHWVFMIP-QJRAZLAKSA-N
SO4
Query on SO4

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

Download Ideal Coordinates CCD File 
B [auth A]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
CA
Query on CA

Download Ideal Coordinates CCD File 
M [auth A]CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
MG
Query on MG

Download Ideal Coordinates CCD File 
N [auth A],
O [auth A]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
NA
Query on NA

Download Ideal Coordinates CCD File 
I [auth A],
J [auth A],
K [auth A]
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.270 
  • R-Value Work: 0.248 
  • R-Value Observed: 0.249 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 60.88α = 90
b = 68.83β = 90
c = 257.52γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
PDB_EXTRACTdata extraction

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
European CommissionFrance647687

Revision History  (Full details and data files)

  • Version 1.0: 2019-01-02
    Type: Initial release
  • Version 1.1: 2024-01-17
    Changes: Advisory, Data collection, Database references, Derived calculations, Refinement description