Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction | Predict Membrane 

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 51.07 kDa 
• Atom Count: 4019 
• Modelled Residue Count: 412 
• Deposited Residue Count: 427 
• Unique protein chains: 1

5KAR

Murine acid sphingomyelinase-like phosphodiesterase 3b (SMPDL3B)

• PDB DOI: 10.2210/pdb5KAR/pdb

• Classification: HYDROLASE
• Organism(s): Mus musculus
• Expression System: Spodoptera frugiperda
• Mutation(s): No 
• Membrane Protein: Yes  OPM


• Deposited: 2016-06-02 Released: 2016-10-05 
• Deposition Author(s): Gorelik, A., Illes, K., Heinz, L.X., Superti-Furga, G., Nagar, B.
• Funding Organization(s): Canadian Institutes of Health Research (CIHR)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.14 Å
• R-Value Free: 0.152 
• R-Value Work: 0.135 
• R-Value Observed: 0.136 

Literature

Crystal Structure of the Acid Sphingomyelinase-like Phosphodiesterase SMPDL3B Provides Insights into Determinants of Substrate Specificity.

Gorelik, A., Heinz, L.X., Illes, K., Superti-Furga, G., Nagar, B.

(2016) J Biol Chem 291: 24054-24064

• PubMed: 27687724 
• DOI: 10.1074/jbc.M116.755801
• Primary Citation of Related Structures:  
  5KAR, 5KAS


• PubMed Abstract: 
  

The enzyme acid sphingomyelinase-like phosphodiesterase 3B (SMPDL3B) was shown to act as a negative regulator of innate immune signaling, affecting cellular lipid composition and membrane fluidity. Furthermore, several reports identified this enzyme as an off target of the therapeutic antibody rituximab, with implications in kidney disorders. However, structural information for this protein is lacking. Here we present the high resolution crystal structure of murine SMPDL3B, which reveals a substrate binding site strikingly different from its paralogs. The active site is located in a narrow boot-shaped cavity. We identify a unique loop near the active site that appears to impose size constraints on incoming substrates. A structure in complex with phosphocholine indicates that the protein recognizes this head group via an aromatic box, a typical choline-binding motif. Although a potential substrate for SMPDL3B is sphingomyelin, we identify other possible substrates such as CDP-choline, ATP, and ADP. Functional experiments employing structure-guided mutagenesis in macrophages highlight amino acid residues potentially involved in recognition of endogenous substrates. Our study is an important step toward elucidating the specific function of this poorly characterized enzyme.

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Organizational Affiliation: 

From the Department of Biochemistry and Groupe de Recherche Axé sur la Structure des Protéines, McGill University, Montreal, Quebec H3G 0B1, Canada, [e-mail].

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Acid sphingomyelinase-like phosphodiesterase 3b	A	427	Mus musculus	Mutation(s): 0  Gene Names: Smpdl3b, Asml3b EC: 3.1.4 Membrane Entity: Yes
UniProt
Find proteins for P58242 (Mus musculus) Explore P58242  Go to UniProtKB:  P58242

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Chain Length	2D Diagram	Glycosylation
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	B	2		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT GlyCosmos:  G42666HT GlyGen:  G42666HT

Entity ID: 3
Molecule	Chains	Chain Length	2D Diagram	Glycosylation
alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	C	5		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G22768VO GlyCosmos:  G22768VO GlyGen:  G22768VO

Entity ID: 4
Molecule	Chains	Chain Length	2D Diagram	Glycosylation
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose	D	3		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G21290RB GlyCosmos:  G21290RB GlyGen:  G21290RB

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	I [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
ZN	E [auth A], F [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
NO3	G [auth A], H [auth A]	NITRATE ION N O3 NHNBFGGVMKEFGY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.14 Å
• R-Value Free: 0.152 
• R-Value Work: 0.135 
• R-Value Observed: 0.136 
• Space Group: P 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 50.892	α = 90
b = 47.031	β = 98.07
c = 93.861	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHENIX	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Deposited Date: 2016-06-02 
• Released Date: 2016-10-05 
Deposition Author(s): Gorelik, A., Illes, K., Heinz, L.X., Superti-Furga, G., Nagar, B.

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Funding Organization	Location	Grant Number
Canadian Institutes of Health Research (CIHR)	Canada	MOP-133535

Revision History  

• Version 1.0: 2016-10-05
  Type: Initial release
  
• Version 1.1: 2016-10-12
  Changes: Database references
• Version 1.2: 2016-11-23
  Changes: Database references
• Version 1.3: 2020-01-08
  Changes: Author supporting evidence, Data collection, Database references
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Derived calculations, Structure summary