5NXB

Mouse galactocerebrosidase in complex with saposin A


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.60 Å
  • R-Value Free: 0.231 
  • R-Value Work: 0.217 
  • R-Value Observed: 0.218 

wwPDB Validation   3D Report Full Report



Literature

The mechanism of glycosphingolipid degradation revealed by a GALC-SapA complex structure.

Hill, C.H.Cook, G.M.Spratley, S.J.Fawke, S.Graham, S.C.Deane, J.E.

(2018) Nat Commun 9: 151-151

  • DOI: 10.1038/s41467-017-02361-y
  • Primary Citation of Related Structures:  
    5NXB

  • PubMed Abstract: 
  • Sphingolipids are essential components of cellular membranes and defects in their synthesis or degradation cause severe human diseases. The efficient degradation of sphingolipids in the lysosome requires lipid-binding saposin proteins and hydrolytic ...

    Sphingolipids are essential components of cellular membranes and defects in their synthesis or degradation cause severe human diseases. The efficient degradation of sphingolipids in the lysosome requires lipid-binding saposin proteins and hydrolytic enzymes. The glycosphingolipid galactocerebroside is the primary lipid component of the myelin sheath and is degraded by the hydrolase β-galactocerebrosidase (GALC). This enzyme requires the saposin SapA for lipid processing and defects in either of these proteins causes a severe neurodegenerative disorder, Krabbe disease. Here we present the structure of a glycosphingolipid-processing complex, revealing how SapA and GALC form a heterotetramer with an open channel connecting the enzyme active site to the SapA hydrophobic cavity. This structure defines how a soluble hydrolase can cleave the polar glycosyl headgroups of these essential lipids from their hydrophobic ceramide tails. Furthermore, the molecular details of this interaction provide an illustration for how specificity of saposin binding to hydrolases is encoded.


    Organizational Affiliation

    Cambridge Institute for Medical Research, Department of Pathology, University of Cambridge, Cambridge Biomedical Campus, Hills Road, Cambridge, CB2 0XY, UK. jed55@cam.ac.uk.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
GalactocerebrosidaseAB654Mus musculusMutation(s): 0 
Gene Names: Galc
EC: 3.2.1.46
Find proteins for P54818 (Mus musculus)
Explore P54818 
Go to UniProtKB:  P54818
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
ProsaposinCD87Mus musculusMutation(s): 0 
Gene Names: PsapSgp1
Find proteins for Q61207 (Mus musculus)
Explore Q61207 
Go to UniProtKB:  Q61207
Protein Feature View
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  • Reference Sequence
Oligosaccharides

Help

Entity ID: 3
MoleculeChainsChain Length2D Diagram Glycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
E, F, H, I
2 N-Glycosylation Oligosaccharides Interaction
Entity ID: 4
MoleculeChainsChain Length2D Diagram Glycosylation3D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
G, J
3 N-Glycosylation Oligosaccharides Interaction
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG

Download Ideal Coordinates CCD File 
A, B
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
CA
Query on CA

Download Ideal Coordinates CCD File 
A, B
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.60 Å
  • R-Value Free: 0.231 
  • R-Value Work: 0.217 
  • R-Value Observed: 0.218 
  • Space Group: P 62 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 187.183α = 90
b = 187.183β = 90
c = 360.24γ = 120
Software Package:
Software NamePurpose
BUSTERrefinement
DIALSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2017-05-24
    Type: Initial release
  • Version 1.1: 2018-01-24
    Changes: Database references
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Derived calculations, Structure summary